The elusive relationship between structure and colour emission in beetle luciferases

Exploring the Light-Emitting Agents in Renilla Luciferases by an Effective QM/MM Approach

Bioluminescence is a fascinating natural phenomenon, wherein organisms produce light through specific biochemical reactions. Among these organisms, Renilla luciferase (RLuc) derived from the sea pansy Renilla reniformis is notable for its blue light emission and has potential applications in bioluminescent tagging. Our study focuses on RLuc8, a variant of RLuc with eight amino acid substitutions. Recent studies have shown that the luminescent emitter coelenteramide can adopt multiple protonation states, which may be influenced by nearby residues at the enzyme's active site, demonstrating a complex interplay between protein structure and bioluminescence. Herein, using the quantum mechanical consistent force field method and the semimacroscopic protein dipole-Langevin dipole method with linear response approximation, we show that the phenolate state of coelenteramide in RLuc8 is the primary light-emitting species in agreement with experimental results. Our calculations also suggest that the proton transfer (PT) from neutral coelenteramide to Asp162 plays a crucial role in the bioluminescence process. Additionally, we reproduced the observed emission maximum for the amide anion in RLuc8-D120A and the pyrazine anion in the presence of a Na+ counterion in RLuc8-D162A, suggesting that these are the primary emitters. Furthermore, our calculations on the neutral emitter in the engineered AncFT-D160A enzyme, structurally akin to RLuc8-D162A but with a considerably blue-shifted emission peak, aligned with the observed data, possibly explaining the variance in emission peaks. Overall, this study demonstrates an effective approach to investigate chromophores' bimolecular states while incorporating the PT process in emission spectra calculations, contributing valuable insights for future studies of PT in photoproteins.

Bioluminescence - The Vibrant Glow of Nature and its Chemical Mechanisms

Bioluminescence, the mesmerizing natural phenomenon where living organisms produce light through chemical reactions, has long captivated scientists and laypersons alike, offering a rich tapestry of insights into biological function, ecology, evolution as well as the underlying chemistry. This comprehensive introductory review systematically explores the phenomenon of bioluminescence, addressing its historical context, geographic dispersion, and ecological significance with a focus on their chemical mechanisms. Our examination begins with terrestrial bioluminescence, discussing organisms from different habitats. We analyze thefireflies of Central Europe's meadows and the fungi in the Atlantic rainforest of Brazil. Additionally, we inspect bioluminescent species in New Zealand, specifically river-dwelling snails and mosquito larvae found in Waitomo Caves. Our exploration concludes in the Siberian Steppes, highlighting the area's luminescent insects and annelids. Transitioning to the marine realm, the second part of this review examines marine bioluminescent organisms. We explore this phenomenon in deep-sea jellyfish and their role in the ecosystem. We then move to Toyama Bay, Japan, where seasonal bioluminescence of dinoflagellates and ostracods present a unique case study. We also delve into the bacterial world, discussing how bioluminescent bacteria contribute to symbiotic relationships. For each organism, we contextualize its bioluminescence, providing details about its discovery, ecological function, and geographical distribution. A special focus lies on the examination of the underlying chemical mechanisms that enables these biological light displays. Concluding this review, we present a series of practical bioluminescence and chemiluminescence experiments, providing a resource for educational demonstrations and student research projects. Our goal with this review is to provide a summary of bioluminescence across the diverse ecological contexts, contributing to the broader understanding of this unique biological phenomenon and its chemical mechanisms serving researchers new to the field, educators and students alike.

Discovery of Red-Shifting Mutations in Firefly Luciferase Using High-Throughput Biochemistry

Photinus pyralis luciferase (FLuc) has proven a valuable tool for bioluminescence imaging, but much of the light emitted from the native enzyme is absorbed by endogenous biomolecules. Thus, luciferases displaying red-shifted emission enable higher resolution during deep-tissue imaging. A robust model of how protein structure determines emission color would greatly aid the engineering of red-shifted mutants, but no consensus has been reached to date. In this work, we applied deep mutational scanning to systematically assess 20 functionally important amino acid positions on FLuc for red-shifting mutations, predicting that an unbiased approach would enable novel contributions to this debate. We report dozens of red-shifting mutations as a result, a large majority of which have not been previously identified. Further characterization revealed that mutations N229T and T352M, in particular, bring about unimodal emission with the majority of photons being >600 nm. The red-shifting mutations identified by this high-throughput approach provide strong biochemical evidence for the multiple-emitter mechanism of color determination and point to the importance of a water network in the enzyme binding pocket for altering the emitter ratio. This work provides a broadly applicable mutational data set tying FLuc structure to emission color that contributes to our mechanistic understanding of emission color determination and should facilitate further engineering of improved probes for deep-tissue imaging.

Expedient Synthesis and Characterization of π-Extended Luciferins

Bioluminescence imaging enables the sensitive tracking of cell populations and the visualization of biological processes in living systems. Bioluminescent luciferase/luciferin pairs with far-red and near-infrared emission benefit from the reduced competitive absorption by blood and tissue while also facilitating multiplexing strategies. Luciferins with extended π-systems, such as AkaLumine and recently reported CouLuc-1 and -3, can be used for bioluminescence imaging in this long wavelength regime. Existing synthetic routes to AkaLumine and similar π-extended compounds require a multistep sequence to install the thiazoline heterocycle. Here we detail the development of a two-step strategy for accessing these molecules via a Horner-Wadsworth-Emmons reaction and cysteine condensation sequence from readily available aldehyde starting materials. We detail an improved synthesis of AkaLumine, as well as the corresponding two-carbon homologues, Tri- and Tetra-AkaLumine. We then extended this approach to prepare coumarin- and naphthalene-derived luciferins. These putative luciferins were tested against a panel of luciferases to identify capable emitters. Of these, an easily prepared naphthalene derivative exhibits photon emission on par with that of the broadly used Akaluc/AkaLumine pair with similar emission maxima. Overall, this chemistry provides efficient access to several bioluminescent probes for a variety of imaging applications.

Preparation and Spectroscopic Identification of the Cyclic CO2 Dimer 1,2-Dioxetanedione

We report the preparation and infrared spectroscopic identification of 1,2-dioxetanedione, which is one of the two possible cyclic dimers of carbon dioxide. We prepared this hitherto experimentally incompletely characterized species in a solid nitrogen matrix at 3 K from the reaction of oxalyl dichloride with the urea·hydrogen peroxide complex. Surprisingly, irradiation at 254 nm does not lead to its dissociation into carbon dioxide but rather yields cyclic carbon trioxide. We further assert our spectroscopic assignments by 18O isotopic labeling and high-level N-electron valence state perturbation theory and coupled-cluster computations. The successful isolation of 1,2-dioxetanedione supports its viability as the postulated high-energy intermediate in the well-known and ubiquitously exploited "peroxyoxalate" chemiluminescent system.

Computational Investigation of Substituent Effects on the Fluorescence Wavelengths of Oxyluciferin Analogs

Oxyluciferin, which is the light emitter for firefly bioluminescence, has been subjected to extensive chemical modifications to tune its emission wavelength and quantum yield. However, the exact mechanisms for various electron-donating and withdrawing groups to perturb the photophysical properties of oxyluciferin analogs are still not fully understood. To elucidate the substituent effects on the fluorescence wavelength of oxyluciferin analogs, we applied the absolutely localized molecular orbitals (ALMO)-based frontier orbital analysis to assess various types of interactions (i.e. permanent electrostatics/exchange repulsion, polarization, occupied-occupied orbital mixing, virtual-virtual orbital mixing, and charge-transfer) between the oxyluciferin and substituent orbitals. We suggested two distinct mechanisms that can lead to red-shifted oxyluciferin emission wavelength, a design objective that can help increase the tissue penetration of bioluminescence emission. Within the first mechanism, an electron-donating group (such as an amino or dimethylamino group) can contribute its highest occupied molecular orbital (HOMO) to an out-of-phase combination with oxyluciferin's HOMO, thus raising the HOMO energy of the substituted analog and narrowing its HOMO-LUMO gap. Alternatively, an electron-withdrawing group (such as a nitro or cyano group) can participate in an in-phase virtual-virtual orbital mixing of fragment LUMOs, thus lowering the LUMO energy of the substituted analog. Such an ALMO-based frontier orbital analysis is expected to lead to intuitive principles for designing analogs of not only the oxyluciferin molecule, but also many other functional dyes.

Spectrochemistry of Firefly Bioluminescence

The chemical reactions underlying the emission of light in fireflies and other bioluminescent beetles are some of the most thoroughly studied processes by scientists worldwide. Despite these remarkable efforts, fierce academic arguments continue around even some of the most fundamental aspects of the reaction mechanism behind the beetle bioluminescence. In an attempt to reach a consensus, we made an exhaustive search of the available literature and compiled the key discoveries on the fluorescence and chemiluminescence spectrochemistry of the emitting molecule, the firefly oxyluciferin, and its chemical analogues reported over the past 50+ years. The factors that affect the light emission, including intermolecular interactions, solvent polarity, and electronic effects, were analyzed in the context of both the reaction mechanism and the different colors of light emitted by different luciferases. The collective data points toward a combined emission of multiple coexistent forms of oxyluciferin as the most probable explanation for the variation in color of the emitted light. We also highlight realistic research directions to eventually address some of the remaining questions related to firefly bioluminescence. It is our hope that this extensive compilation of data and detailed analysis will not only consolidate the existing body of knowledge on this important phenomenon but will also aid in reaching a wider consensus on some of the mechanistic details of firefly bioluminescence.

Intrinsic fluorescence from firefly oxyluciferin monoanions isolated in vacuo

Fireflies, click beetles, and railroad worms glow in the dark. The color varies from green to red among the insects and is associated with an electronically excited oxyluciferin formed catalytically by the luciferase enzyme. The actual color tuning mechanism has been, and still is, up for much debate. One complication is that oxyluciferin can occur in different charge states and isomeric forms. We present here emission spectra of oxyluciferin monoanions in vacuo at both room temperature and at 100 K recorded with a newly developed and unique mass-spectroscopy setup specially designed for gas-phase ion fluorescence spectroscopy. Ions are limited to the phenolate-keto and phenolate-enol forms that account for natural bioluminescence. At 100 K, fluorescence band maxima are at 599 ± 2 nm and 563 ± 2 nm for the keto and enol forms, respectively, and at 300 K about 5 nm further to the red. The bare-ion spectra, free from solvent effects, serve as important references as they reveal whether a protein microenvironment redshifts or blueshifts the emission, and they serve as important benchmarks for nontrivial excited-state calculations.

Bioluminescence Color-Tuning Firefly Luciferases: Engineering and Prospects for Real-Time Intracellular pH Imaging and Heavy Metal Biosensing

Firefly luciferases catalyze the efficient production of yellow-green light under normal physiological conditions, having been extensively used for bioanalytical purposes for over 5 decades. Under acidic conditions, high temperatures and the presence of heavy metals, they produce red light, a property that is called pH-sensitivity or pH-dependency. Despite the demand for physiological intracellular biosensors for pH and heavy metals, firefly luciferase pH and metal sensitivities were considered drawbacks in analytical assays. We first demonstrated that firefly luciferases and their pH and metal sensitivities can be harnessed to estimate intracellular pH variations and toxic metal concentrations through ratiometric analysis. Using Macrolampis sp2 firefly luciferase, the intracellular pH could be ratiometrically estimated in bacteria and then in mammalian cells. The luciferases of Macrolampis sp2 and Cratomorphus distinctus fireflies were also harnessed to ratiometrically estimate zinc, mercury and other toxic metal concentrations in the micromolar range. The temperature was also ratiometrically estimated using firefly luciferases. The identification and engineering of metal-binding sites have allowed the development of novel luciferases that are more specific to certain metals. The luciferase of the Amydetes viviani firefly was selected for its special sensitivity to cadmium and mercury, and for its stability at higher temperatures. These color-tuning luciferases can potentially be used with smartphones for hands-on field analysis of water contamination and biochemistry teaching assays. Thus, firefly luciferases are novel color-tuning sensors for intracellular pH and toxic metals. Furthermore, a single luciferase gene is potentially useful as a dual bioluminescent reporter to simultaneously report intracellular ATP and/or luciferase concentrations luminometrically, and pH or metal concentrations ratiometrically, providing a useful tool for real-time imaging of intracellular dynamics and stress.

Luciferin Synthesis and Pesticide Detection by Luminescence Enzymatic Cascades

D-Luciferin (D-LH₂ ), a substrate of firefly luciferase (Fluc), is important for a wide range of bioluminescence applications. This work reports a new and green method using enzymatic reactions (HELP, HadA Enzyme for Luciferin Preparation) to convert 19 phenolic derivatives to 8 D-LH₂ analogues with ≈51 % yield. The method can synthesize the novel 5'-methyl-D-LH₂ and 4',5'-dimethyl-D-LH₂ , which have never been synthesized or found in nature. 5'-Methyl-D-LH₂ emits brighter and longer wavelength light than the D-LH₂ . Using HELP, we further developed LUMOS (Luminescence Measurement of Organophosphate and Derivatives) technology for in situ detection of organophosphate pesticides (OPs) including parathion, methyl parathion, EPN, profenofos, and fenitrothion by coupling the reactions of OPs hydrolase and Fluc. The LUMOS technology can detect these OPs at parts per trillion (ppt) levels. The method can directly detect OPs in food and biological samples without requiring sample pretreatment.

Identification of 2-Benzylidene-tetralone Derivatives as Highly Potent and Reversible Firefly Luciferase Inhibitors

The extensive applications of Firefly luciferase (Fluc) in numerous biological, biomedical, and clinical investigations rendered an urgent need for efficient and biocompatible Fluc inhibitors for the construction of novel assay platforms. Herein we describe the identification of 2-benzylidene-tetralone derivatives as highly potent and reversible Firefly luciferase inhibitors by competing with d-luciferin. The most active compound 48 was found to have >7000 fold higher potency (IC50 = 0.25 nM) than that of the well-known luciferase inhibitor resveratrol (IC50 = 1.9 μM) biochemically with sub- to low nanomolar IC50 values, and it can efficiently block the Fluc generated bioluminescence in vivo.

Cultural Significance of Beetles in Sub-Saharan Africa

An overview is given of how beetles are utilised, perceived, and experienced in daily life across sub-Saharan Africa. More than 300 people from 27 countries were interviewed and the results were compared with literature findings. Both the adults and larvae of many beetle species are eaten, mainly from the families Curculionidae, Buprestidae, Cerambycidae, Dytiscidae and Scarabaeidae. Some beetle species are used for medicinal purposes. The use of breast-shaped water beetles by adolescent girls to stimulate breast growth could be due to superstition or the effect of the defensive secretion containing steroid hormones. Blister beetles contain cantharidin, which influences the urinary tract, and is therefore used as an aphrodisiac and for treating venereal disease. Throughout Africa children play with beetles by letting them fly on a string. In the Sahel, the hard work of dung beetles is an inspiration for stories. Fireflies are generally associated with ghosts and witches, likely because the glowing of the beetles is interpreted as magical. Many beetle groups are brightly and attractively coloured and are therefore used in ceremonies and commerce. This type of indigenous knowledge, revealed in stories provided by older people, is rapidly disappearing due to urbanisation.

Elucidating the chemiexcitation of dioxetanones by replacing the peroxide bond with S–S, N–N and C–C bonds

Replacing the peroxide bond of dioxetanone prevents chemiluminescence by making its thermolysis energetically unfavorable and without a singlet chemiexcitation pathway.