Luminous Organisms Research Articles

Evolution of bioluminescence in Anthozoa with emphasis on Octocorallia.

Bioluminescence is a widespread phenomenon that has evolved multiple times across the tree of life, converging among diverse fauna and habitat types. The ubiquity of bioluminescence, particularly in marine environments where it is commonly used for communication and defense, highlights the adaptive value of this trait, though the evolutionary origins and timing of emergence remain elusive for a majority of luminous organisms. Anthozoan cnidarians are a diverse group of animals with numerous bioluminescent species found throughout the world's oceans, from shallow waters to the light-limited deep sea where bioluminescence is particularly prominent. This study documents the presence of bioluminescent Anthozoa across depth and explores the diversity and evolutionary origins of bioluminescence among Octocorallia-a major anthozoan group of marine luminous organisms. Using a phylogenomic approach and ancestral state reconstruction, we provide evidence for a single origin of bioluminescence in Octocorallia and infer the age of occurrence to around the Cambrian era, approximately 540 Ma-setting a new record for the earliest timing of emergence of bioluminescence in the marine environment. Our results further suggest this trait was largely maintained in descendants of a deep-water ancestor and bioluminescent capabilities may have facilitated anthozoan diversification in the deep sea.

Pseudo-Luciferase Activity of the SARS-CoV-2 Spike Protein for Cypridina Luciferin.

Enzymatic reactions that involve a luminescent substrate (luciferin) and enzyme (luciferase) from luminous organisms enable a luminescence detection of target proteins and cells with high specificity, albeit that conventional assay design requires a prelabeling of target molecules with luciferase. Here, we report a luciferase-independent luminescence assay in which the target protein directly catalyzes the oxidative luminescence reaction of luciferin. The SARS-CoV-2 antigen (spike) protein catalyzes the light emission of Cypridina luciferin, whereas no such catalytic function was observed for salivary proteins. This selective luminescence reaction is due to the enzymatic recognition of the 3-(1-guanidino)propyl group in luciferin at the interfaces between the units of the spike protein, allowing a specific detection of the spike protein in human saliva without sample pretreatment. This method offers a novel platform to detect virus antigens simply and rapidly without genetic manipulation or antibodies.

Ecological role of bioluminescence of Black sea ctenophores.

Bioluminescence, which is a manifestation of the vital activity of an organism in the form of electromagnetic radiation in the visible area of the spectrum, is a highly important ecological and optical factor of the marine environment. Until recently, it was believed that microplankton - bacteria and dinoflagellates - exceptionally contribute to the formation of the bioluminescence field in the Black Sea, as well as in other regions of the World Ocean. However, the ctenophoresMnemiopsis leidyiA. Agassiz, 1865, andBeroe ovata Mayer, 1912, which invaded the Black Sea in the 1980s-1990s, are also luminous organisms whose bioluminescence intensity is millions of times greater than that of most microplankton representatives. It is known that the characteristics of bioluminescence can reveal the state of the organism and, consequently, the state of the environment. At present, there is a fairly large number of works devoted to the physiology and ecology of the Black Sea ctenophores. In recent studies, the variability of light emission parameters of ctenophores following their functional state was revealed. Intensity and duration of light emission as parameters of the ctenophore bioluminescent signal as well as the influence of various abiotic and anthropogenic environmental factors on the ctenophore luminescence have been studied. However, the significance of bioluminescence for the living activity of ctenophores remains unclear. In connection with the above, it is extremely important to assess the ecological role of the bioluminescence of the Black Sea ctenophores.

Research into bioluminescence of the Black Sea ctenophores Pleurobrachia pileus O.F. Müller, 1776.

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 0.4-0.5m s-1 . It was shown that only at a temperature not exceeding 14°C, the P. pileus remained alive for 2-3days. 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.

The Luminous Fungi of Japan

Luminous fungi have long attracted public attention in Japan, from old folklore and fiction to current tourism, children’s toys, games, and picture books. At present, 25 species of luminous fungi have been discovered in Japan, which correspond to approximately one-fourth of the globally recognized species. This species richness is arguably due to the abundant presence of mycophiles looking to find new mushroom species and a tradition of night-time activities, such as firefly watching, in Japan. Bioluminescence, a field of bioscience focused on luminous organisms, has long been studied by many Japanese researchers, including the biochemistry and chemistry of luminous fungi. A Japanese Nobel Prize winner, Osamu Shimomura (1928–2018), primarily focused on the bioluminescence system of luminous fungi in the latter part of his life, and total elucidation of the mechanism was finally accomplished by an international research team with representatives from Russia, Brazil, and Japan in 2018. In this review, we focused on multiple aspects related to luminous fungi of Japan, including myth, taxonomy, and modern sciences.

Specific Activities of Hydromedusan Ca2+ -Regulated Photoproteins.

Nowadays the recombinant Ca2+ -regulated photoproteins originating from marine luminous organisms are widely applied to monitor calcium transients in living cells due to their ability to emit light on Ca2+ binding. Here we report the specific activities of the recombinant Ca2+ -regulated photoproteins-aequorin from Aequorea victoria, obelins from Obelia longissima and Obelia geniculata, clytin from Clytia gregaria and mitrocomin from Mitrocoma cellularia. We demonstrate that along with bioluminescence spectra, kinetics of light signals and sensitivities to calcium, these photoproteins also differ in specific activities and consequently in quantum yields of bioluminescent reactions. The highest specific activities were found for obelins and mitrocomin, whereas those of aequorin and clytin were shown to be lower. To determine the factors influencing the variations in specific activities the fluorescence quantum yields for Ca2+ -discharged photoproteins were measured and found to be quite different varying in the range of 0.16-0.36. We propose that distinctions in specific activities may result from different efficiencies of singlet excited state generation and different fluorescence quantum yields of coelenteramide bound within substrate-binding cavity. This in turn may be conditioned by variations in the amino acid environment of the substrate-binding cavities and hydrogen bond distances between key residues and atoms of 2-hydroperoxycoelenterazine.

Acquisition of bioluminescent trait by non-luminous organisms from luminous organisms through various origins.

Bioluminescence is a natural light emitting phenomenon that occurs due to a chemical reaction between luciferin and luciferase. It is primarily an innate and inherited trait in most terrestrial luminous organisms. However, most luminous organisms produce light in the ocean by acquiring luminous symbionts, luciferin (substrate), and/or luciferase (enzyme) through various transmission pathways. For instance, coelenterazine, a well-known luciferin, is obtained by cnidarians, crustaceans, and deep-sea fish through multi-level dietary linkages from coelenterazine producers such as ctenophores, decapods, and copepods. In contrast, some non-luminous Vibrio bacteria became bioluminescent by obtaining lux genes from luminous Vibrio species by horizontal gene transfer. Various examples detailed in this review show how non-luminescent organisms became luminescent by acquiring symbionts, dietary luciferins and luciferases, and genes. This review highlights three modes (symbiosis, ingestion, and horizontal gene transfer) that allow organisms lacking genes for autonomous bioluminescent systems to obtain the ability to produce light. In addition to bioluminescence, this manuscript discusses the acquisition of other traits such as pigments, fluorescence, toxins, and others, to infer the potential processes of acquisition.

Leaving the Dark Side? Insights Into the Evolution of Luciferases

Bioluminescence—i.e., the emission of visible light by living organisms—is defined as a biochemical reaction involving, at least, a luciferin substrate, an oxygen derivative, and a specialised luciferase enzyme. In some cases, the enzyme and the substrate are durably associated and form a photoprotein. While this terminology is educatively useful to explain bioluminescence, it gives a false idea that all luminous organisms are using identical or homologous molecular tools to achieve light emission. As usually observed in biology, reality is more complex. To date, at least 11 different luciferins have indeed been discovered, and several non-homologous luciferases lato sensu have been identified which, all together, confirms that bioluminescence emerged independently multiple times during the evolution of living organisms. While some phylogenetically related organisms may use non-homologous luciferases (e.g., at least four convergent luciferases are found in Pancrustacea), it has also been observed that phylogenetically distant organisms may use homologous luciferases (e.g., parallel evolution observed in some cnidarians, tunicates and echinoderms that are sharing a homologous luciferase-based system). The evolution of luciferases then appears puzzling. The present review takes stock of the diversity of known “bioluminescent proteins,” their evolution and potential evolutionary origins. A total of 134 luciferase and photoprotein sequences have been investigated (from 75 species and 11 phyla), and our analyses identified 12 distinct types—defined as a group of homologous bioluminescent proteins. The literature review indicated that genes coding for luciferases and photoproteins have potentially emerged as new genes or have been co-opted from ancestral non-luciferase/photoprotein genes. In this latter case, the homologous gene’s co-options may occur independently in phylogenetically distant organisms.

Study of Parameters of Biological Rhythms of Plankton Communities in Natural Conditions

The change in the intensity of bioluminescence fields in the coastal area of the western shelf of the Crimea in the dark time of day was discussed. It is noted, that the biomass of luminous organisms closely correlate with the biomass of plankton and other pelagic creatures, including commercial pelagic fish. The parameters of the basic biological rhythms of plankton communities are found using method of Fourier series. These rhythms leads to change of intensity of the bioluminescence field. It is shown, that the change of the intensity of bioluminescence field with a 14 hours period due to duration of photo- and dark- periods. Changes in the intensity of the bioluminescence fields with periods of 4.7 and 2.8 hours due to endogenous circadian rhythms of plankton community. An original method for evaluation of errors of periods found of biological rhythms was proposed. The correlation coefficient between measured and calculated values of the intensity of the bioluminescence fields was estimated, taking into account the influence of three main biological rhythms, was r = 0.906, that confirms the correctness of the assumptions made.

Bioluminescence of the Largest Luminous Vertebrate, the Kitefin Shark, Dalatias licha: First Insights and Comparative Aspects

Bioluminescence has often been seen as a spectacular yet uncommon event at sea but considering the vastness of the deep sea and the occurrence of luminous organisms in this zone, it is now more and more obvious that producing light at depth must play an important role structuring the biggest ecosystem on our planet. Three species of deepwater sharks (Dalatias licha,Etmopterus lucifer, andEtmopterus granulosus) were collected from the Chatham Rise, off New Zealand, and for the first time, we documented their luminescence. Comparison of glowing shark pictures, combined with histological description of light organs and hormonal control analysis, highlight the evolutive conservation of the bioluminescence process within Dalatiidae and Etmopteridae. A special emphasis is placed on the luminescence ofD. licha, the largest known luminous vertebrate. This first experimental study of three luminous shark species from New Zealand provides an insight into the diversity of shark bioluminescence and highlights the need for more research to help understand these unusual deep-sea inhabitants: the glowing sharks.

IBLP: An XGBoost-Based Predictor for Identifying Bioluminescent Proteins.

Bioluminescent proteins (BLPs) are a class of proteins that widely distributed in many living organisms with various mechanisms of light emission including bioluminescence and chemiluminescence from luminous organisms. Bioluminescence has been commonly used in various analytical research methods of cellular processes, such as gene expression analysis, drug discovery, cellular imaging, and toxicity determination. However, the identification of bioluminescent proteins is challenging as they share poor sequence similarities among them. In this paper, we briefly reviewed the development of the computational identification of BLPs and subsequently proposed a novel predicting framework for identifying BLPs based on eXtreme gradient boosting algorithm (XGBoost) and using sequence-derived features. To train the models, we collected BLP data from bacteria, eukaryote, and archaea. Then, for getting more effective prediction models, we examined the performances of different feature extraction methods and their combinations as well as classification algorithms. Finally, based on the optimal model, a novel predictor named iBLP was constructed to identify BLPs. The robustness of iBLP has been proved by experiments on training and independent datasets. Comparison with other published method further demonstrated that the proposed method is powerful and could provide good performance for BLP identification. The webserver and software package for BLP identification are freely available at http://lin-group.cn/server/iBLP.

Multi-level convergence of complex traits and the evolution of bioluminescence.

Evolutionary convergence provides natural opportunities to investigate how, when, and why novel traits evolve. Many convergent traits are complex, highlighting the importance of explicitly considering convergence at different levels of biological organization, or 'multi-level convergent evolution'. To investigate multi-level convergent evolution, we propose a holistic and hierarchical framework that emphasizes breaking down traits into several functional modules. We begin by identifying long-standing questions on the origins of complexity and the diverse evolutionary processes underlying phenotypic convergence to discuss how they can be addressed by examining convergent systems. We argue that bioluminescence, a complex trait that evolved dozens of times through either novel mechanisms or conserved toolkits, is particularly well suited for these studies. We present an updated estimate of at least 94 independent origins of bioluminescence across the tree of life, which we calculated by reviewing and summarizing all estimates of independent origins. Then, we use our framework to review the biology, chemistry, and evolution of bioluminescence, and for each biological level identify questions that arise from our systematic review. We focus on luminous organisms that use the shared luciferin substrates coelenterazine or vargulin to produce light because these organisms convergently evolved bioluminescent proteins that use the same luciferins to produce bioluminescence. Evolutionary convergence does not necessarily extend across biological levels, as exemplified by cases of conservation and disparity in biological functions, organs, cells, and molecules associated with bioluminescence systems. Investigating differences across bioluminescent organisms will address fundamental questions on predictability and contingency in convergent evolution. Lastly, we highlight unexplored areas of bioluminescence research and advances in sequencing and chemical techniques useful for developing bioluminescence as a model system for studying multi-level convergent evolution.

Terrestrial and marine bioluminescent organisms from the Indian subcontinent: a review.

The inception of bioluminescence by Harvey (1952) has led to a Nobel Prize to Osamu Shimomura (Chemistry, 2008) in biological research. Consequently, in recent years, bioluminescence-based assays to monitor toxic pollutants as a real-time marker, to study various diseases and their propagation in plants and animals, are developed in many countries. The emission ability of bioluminescence is improved by gene modification, and also, search for novel bioluminescent systems is underway. Over 100 species of organisms belonging to different taxa are known to be luminous in India. However, the diversity and distribution of luminous organisms and their applications are studied scarcely in the Indian scenario. In this context, the present review provides an overview of the current understanding of various bioluminescent organisms, functions, and applications. A detailed checklist of known bioluminescent organisms from India's marine, terrestrial, and freshwater ecosystems is detailed. This review infers that Indian scientists are needed to extend their research on various aspects of luminescent organisms such as biodiversity, genomics, and chemical mechanisms for conservation, ecological, and biomedical applications.

Self‐powered bioluminescence in a marine tube worm

An increasing number of luminous organisms are being found in the ocean, presenting opportunities to discover new biochemical reactions associated with light production, and thus new bioreporter systems for biotechnology and biomedicine. The marine parchment tube worm Chaetopterus sp. is of particular interest because it secretes a luminous mucus that glows for a long time (hours, possibly days), although in seawater and isolated from any continuous metabolic support. This contrasts with the short flashes, or the bacterial, metabolically driven glow that are more typical for naturally observed bioluminescence. We have recently found that the light production in this mucus is activated by Fe2+ and that the long‐lasting glow may therefore be supported by the proven presence of the iron storage protein ferritin.We have also observed a temporary increase in the bioluminescence after exposure of the mucus to blue light specifically, which is capable of triggering Fe2+ release from ferritin through a photo‐reduction process. Since the mucus bioluminesces in the blue region of visible light, we are investigating whether it could be powering its own light production.Support or Funding InformationThis research is supported by the Air Force Office of Scientific Research (grant # FA955017 0189 to D. D. Deheyn).

Selected Least Studied but not Forgotten Bioluminescent Systems.

Bioluminescence is a form of chemiluminescence generated by luminous organisms. Luminous taxa have currently been reported from about 800 genera and probably over 10 000 species in the world. On the other hand, their bioluminescent systems, including chemical structures of luciferins/chromophores and the genes encoding luciferases/photoproteins, have been elucidated from only a few taxonomic groups, for example beetles, bacteria, dinoflagellates, ostracods and some cnidarians. Research efforts to understand unknown bioluminescence systems are being conducted around the world, and recently, for example, novel luciferin structures of luminous enchytraeid potworms and fungi were identified by the authors. In this study, we review the current status and perspectives, in the context of postgenomic era, of most likely novel but less-revealed bioluminescence systems of ten selected organisms: earthworm, parchment tubeworm, fireworm, scaleworm, limpet, millipede, brittle star, acorn worms, tunicate and shark, which indeed are the next focus of our international collaboration.

Evaluation of parameters of a plankton community's biological rhythms under the natural environment of the Black Sea using the Fourier transform method.

Night-time changes in bioluminescence intensity in the coastal area of the Black Sea were recorded. It was noted that the biomass of luminous organisms is closely correlated with the biomass of plankton and other pelagic organisms, including commercial pelagic fish. The parameters of plankton communities' basic biological rhythms were determined using the discrete Fourier transform method. These rhythms were manifest as spatial and temporal changes in the bioluminescence intensity. It was shown that changes in the bioluminescence intensity over a 14.0-h period were due to the duration of the light/dark cycles. By contrast, changes in bioluminescence intensity with periods of 4.7 and 2.8h were due to the endogenous rhythms of the plankton community (feeding and cell division). An original method for evaluating of errors in the calculated periods of the biological rhythms was proposed. A strong correlation (r=0.906) was observed between the measured and calculated values for the bioluminescence intensity, which provided support for the assumptions made.

Transient-state kinetic analysis of complex formation between photoprotein clytin and GFP from jellyfish Clytia gregaria.

Luminous organisms use different protein-mediated strategies to modulate light emission color. Here, we report the transient-state kinetic studies of the interaction between photoprotein clytin from Clytia gregaria and its antenna protein, cgreGFP. We propose that cgreGFP forms a transient complex with Ca(2+)-bound clytin before the excited singlet state of the coelenteramide product is formed. From the spectral distribution and donor-acceptor separation distance, we infer that clytin reaction intermediates may interact only with the middle side part of cgreGFP.

Coelenterazine-dependent luciferases.

Bioluminescence is a widespread natural phenomenon. Luminous organisms are found among bacteria, fungi, protozoa, coelenterates, worms, molluscs, insects, and fish. Studies on bioluminescent systems of various organisms have revealed an interesting feature - the mechanisms underlying visible light emission are considerably different in representatives of different taxa despite the same final result of this biochemical process. Among the several substrates of bioluminescent reactions identified in marine luminous organisms, the most commonly used are imidazopyrazinone derivatives such as coelenterazine and Cypridina luciferin. Although the substrate used is the same, bioluminescent proteins that catalyze light emitting reactions in taxonomically remote luminous organisms do not show similarity either in amino acid sequences or in spatial structures. In this review, we consider luciferases of various luminous organisms that use coelenterazine or Cypridina luciferin as a substrate, as well as modifications of these proteins that improve their physicochemical and bioluminescent properties and therefore their applicability in bioluminescence imaging in vivo.

Propensity scores for prediction and characterization of bioluminescent proteins from sequences.

Bioluminescent proteins (BLPs) are a class of proteins with various mechanisms of light emission such as bioluminescence and fluorescence from luminous organisms. While valuable for commercial and medical applications, identification of BLPs, including luciferases and fluorescent proteins (FPs), is rather challenging, owing to their high variety of protein sequences. Moreover, characterization of BLPs facilitates mutagenesis analysis to enhance bioluminescence and fluorescence. Therefore, this study proposes a novel methodological approach to estimating the propensity scores of 400 dipeptides and 20 amino acids in order to design two prediction methods and characterize BLPs based on a scoring card method (SCM). The SCMBLP method for predicting BLPs achieves an accuracy of 90.83% for 10-fold cross-validation higher than existing support vector machine based methods and a test accuracy of 82.85%. A dataset consisting of 269 luciferases and 216 FPs is also established to design the SCMLFP prediction method, which achieves training and test accuracies of 97.10% and 96.28%, respectively. Additionally, four informative physicochemical properties of 20 amino acids are identified using the estimated propensity scores to characterize BLPs as follows: 1) high transfer free energy from inside to the protein surface, 2) high occurrence frequency of residues in the transmembrane regions of the protein, 3) large hydrophobicity scale from the native protein structure, and 4) high correlation coefficient (R = 0.921) between the amino acid compositions of BLPs and integral membrane proteins. Further analyzing BLPs reveals that luciferases have a larger value of R (0.937) than FPs (0.635), suggesting that luciferases tend to locate near the cell membrane location rather than FPs for convenient receipt of extracellular ions. Importantly, the propensity scores of dipeptides and amino acids and the identified properties facilitate efforts to predict, characterize, and apply BLPs, including luciferases, photoproteins, and FPs. The web server is available at http://iclab.life.nctu.edu.tw/SCMBLP/index.html.

Bioluminescence: living lights, lights for living

Bioluminescence is everywhere on earth--most of all in the ocean, from angler fish in the depths to the flashing of dinoflagellates at the surface. Here, Therese Wilson and Woody Hastings explore the natural history, evolution, and biochemistry of the diverse array of organisms that emit light. While some bacteria, mushrooms, and invertebrates, as well as fish, are bioluminescent, other vertebrates and plants are not. The sporadic distribution and paucity of luminous forms calls for explanation, as does the fact that unrelated groups evolved completely different biochemical pathways to luminescence. The authors explore the hypothesis that many different luciferase systems arose in the early evolution of life because of their ability to remove oxygen, which was toxic to life when it first appeared on earth. As oxygen became abundant and bioluminescence was no longer adequate for oxygen removal, other antioxidant mechanisms evolved and most luminous species became extinct. Those light-emitting species that avoided extinction evolved uses with survival value for the light itself. Today's luminous organisms use bioluminescence for defense from predators, for their own predatory purposes, or for communication in sexual courtship. Bioluminescence was earlier viewed as a fascinating feature of the living world, but one whose study seemed unlikely to contribute in any practical way. Today, bioluminescence is no longer an esoteric area of research. Applications are numerous, ranging from the rapid detection of microbial contamination in beef and water, to finding the location of cancer cells, to working out circuitry in the brain.