Chemical aspects of bioluminescence

Systematic Theoretical Study on the pH-Dependent Absorption and Fluorescence Spectra of Flavins

Flavins are a class of organic compounds with the basic structure of 7,8-dimethy-10-alkyl isoalloxazine. They are ubiquitous in nature and participate in many biochemical reactions. Due to various existing forms, there is a lack of systematic research on the absorption and fluorescence spectra of flavins. In this study, employing the density functional theory (DFT) and time-dependent (TD) DFT, we calculated the pH-dependent absorption and fluorescence spectra of flavin of three redox states (quinone, semiquinone, and hydroquinone) in solvents. The chemical equilibrium of three redox states of flavins and the pH effect on the absorption spectra and fluorescence spectra of flavins were carefully discussed. The conclusion helps with identifying the existing forms of flavins in solvent with different pH values.

Chemistry in Fungal Bioluminescence: Theoretical Studies on Biosynthesis of Luciferin from Caffeic Acid and Regeneration of Caffeic Acid from Oxidized Luciferin

Fungal bioluminescence is widely distributed in the terrestrial environment. At a specific stage of growth, luminescent fungi shine green light at the fruiting body or mycelium. From the viewpoint of chemistry, fungal bioluminescence involves an in vivo cycle of caffeic acid. The complete cycle is composed of three stages: biosynthesis of luciferin from caffeic acid, luminescence process from luciferin to oxidized luciferin, and regeneration of caffeic acid from oxidized luciferin. Experimental studies roughly proposed this cycle but not the detailed reaction process and mechanism. Our previous theoretical study clearly described the mechanism of the middle stage. The present article attempts to describe the reaction processes and mechanisms of the other two stages by theoretical calculations. A complete theoretical study on the chemistry in the entire process of fungal bioluminescence is helpful to deeply understand fungal bioluminescence.

The Sensitized Bioluminescence Mechanism of Bacterial Luciferase

After more than one-half century of investigations, the mechanism of bioluminescence from the FMNH₂ assisted oxygen oxidation of an aliphatic aldehyde on bacterial luciferase continues to resist elucidation. There are many types of luciferase from species of bioluminescent bacteria originating from both marine and terrestrial habitats. The luciferases all have close sequence homology, and in vitro, a highly efficient light generation is obtained from these natural metabolites as substrates. Sufficient exothermicity equivalent to the energy of a blue photon is available in the chemical oxidation of the aldehyde to the corresponding carboxylic acid, and a luciferase-bound FMNH-OOH is a key player. A high energy species, the source of the exothermicity, is unknown except that it is not a luciferin cyclic peroxide, a dioxetanone, as identified in the pathway of the firefly and the marine bioluminescence systems. Besides these natural substrates, variable bioluminescence properties are found using other reactants such as flavin analogs or aldehydes, but results also depend on the luciferase type. Some rationalization of the mechanism has resulted from spatial structure determination, NMR of intermediates and dynamic optical spectroscopy. The overall light path appears to fall into the sensitized class of chemiluminescence mechanism, distinct from the dioxetanone types.

Perspectives on Bioluminescence Mechanisms

The molecular mechanisms of the bioluminescence systems of the firefly, bacteria and those utilizing imidazopyrazinone luciferins such as coelenterazine are gradually being uncovered using modern biophysical methods such as dynamic (ns-ps) fluorescence spectroscopy, NMR, X-ray crystallography and computational chemistry. The chemical structures of all reactants are well defined, and the spatial structures of the luciferases are providing important insight into interactions within the active cavity. It is generally accepted that the firefly and coelenterazine systems, although proceeding by different chemistries, both generate a dioxetanone high-energy species that undergoes decarboxylation to form directly the product in its S₁ state, the bioluminescence emitter. More work is still needed to establish the structure of the products completely. In spite of the bacterial system receiving the most research attention, the chemical pathway for excitation remains mysterious except that it is clearly not by a decarboxylation. Both the coelenterazine and bacterial systems have in common of being able to employ "antenna proteins," lumazine protein and the green-fluorescent protein, for tuning the color of the bioluminescence. Spatial structure information has been most valuable in informing the mechanism of the Ca²⁺ -regulated photoproteins and the antenna protein interactions.

Decomposition reaction of dioxetanone in firefly bioluminescence by computer experiment

Firefly luciferin (Ln) reacts with molecular oxygen in the presence of the enzyme luciferase (E), the Mg(+2) ion and ATP to form a four-membered cyclic peroxide, so-called dioxetanone, which has not yet been observed by spectrophotometric techniques. Subsequently, dioxetanone decomposes into carbon dioxide (CO(2)) and electronically excited oxyluciferin (Oxyln(-∗)), emitting yellow-green light. In order to clarify the characteristics of the elementary reaction path from dioxetanone to Oxyln(-∗), the potential energy curve of the singlet ground-state (S(0)-PEC) along the reaction coordinate was obtained by the intrinsic reaction coordinate (IRC) calculations using the AM1 Hamiltonian. Furthermore, the potential energy curve of the singlet excited-state (S(1)-PEC) was calculated, because dioxetanone decomposes to Oxyln(-∗) along the reaction coordinate. The S(1)-PEC relative to S(0)-PEC was estimated at each point of the reaction coordinate using the INDO/S, where only the singly-excited configuration interactions (CI) constructed from 20 occupied and 20 unoccupied molecular orbitals (MOs) were considered. As a result of these calculations, it was concluded that (1) firefly dioxetanone might not be an intermediate but rather be in an unstable transition state; (2) the S(0)-PEC has an activation barrier of 37.5 kcal/mol for dioxetanone formation and the reaction is exothermic along the S(0)-PEC; (3) the S(1)-PEC approaches the S(0)-PEC in a concave manner where dioxetanone decomposes to efficiently produce Oxyln(-∗); and (4) rupturing of an O-O bond in dioxetanone can trigger the coming and going of electrons in a "cradle" motion mediated by S(0)- and S(1)-PECs in the chemiexcitation step toward Oxyln(-∗).

Evidence for the presence of a FAD pyrophosphatase and a FMN phosphohydrolase in yeast mitochondria: a possible role in flavin homeostasis

Despite the crucial roles of flavin cofactors in metabolism, we know little about the enzymes responsible for the turnover of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) and their subcellular localization. The mechanism by which mitochondria obtain their own flavin cofactors is an interesting point of investigation, because FMN and FAD are mainly located in mitochondria, where they act as redox cofactors of a number of dehydrogenases and oxidases that play a crucial function in both bioenergetics and cellular regulation. In this context, the capability of yeast mitochondria to metabolize externally added and endogenous FAD and FMN was investigated and use was made of purified and bioenergetically active mitochondria prepared starting from the Saccharomyces cerevisiae cell. To determine whether flavin metabolism can occur, the amounts of flavins in aliquots of neutralized perchloric extracts of both spheroplasts and mitochondria were measured by HPLC, and the competence of S. cerevisiae mitochondria to metabolize FAD and FMN was investigated both spectroscopically and via HPLC. FAD deadenylation and FMN dephosphorylation were studied with respect to dependence on substrate concentration, pH profile and inhibitor sensitivity. The existence of two novel mitochondrial FAD pyrophosphatase (diphosphatase) (EC 3.6.1.18) and FMN phosphohydrolase (EC 3.1.3.2) activities, which catalyse the reactions FAD + H₂O → FMN + AMP and FMN + H₂O → riboflavin + Pi respectively, is here shown by fractionation studies. Considering cytosolic riboflavin, FMN and FAD concentrations, as calculated by measuring both spheroplast and mitochondrial contents via HPLC, probably mitochondria play a major role in regulating the flavin pool in yeast and in relation to flavin homeostasis.

The diverse roles of flavin coenzymes--nature's most versatile thespians

Flavin coenzymes play a variety of roles in biological systems. This Perspective highlights the chemical versatility of flavins by reviewing research on five flavoenzymes that have been studied in our laboratory. Each of the enzymes discussed in this review [the acyl-CoA dehydrogenases (ACDs), CDP-6-deoxy-l-threo-d-glycero-4-hexulose-3-dehydrase reductase (E3), CDP-4-aceto-3,6-dideoxygalactose synthase (YerE), UDP-galactopyranose mutase (UGM), and type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2)] utilizes flavin in a distinct role. In particular, the catalytic mechanisms of two of these enzymes, UGM and IDI-2, may involve novel flavin chemistry.

Codon-Optimized Gaussia Luciferase cDNA for Mammalian Gene Expression in Culture and in Vivo

Photoproteins have played a major role in advancing our understanding of biological processes. A broader array of biocompatible, nontoxic, and novel reporters can serve to expand this potential. Here we describe the properties of a luciferase from the copepod marine organism Gaussia princeps. It is a monomeric protein composed of 185 aa (19.9 kDa) with a short coding sequence (555 bp) making it suitable for viral vectors. The humanized form of Gaussia luciferase (hGLuc) was efficiently expressed in mammalian cells following delivery by HSV-1 amplicon vectors. It was found to be nontoxic and naturally secreted, with flash bioluminescence characteristics similar to those of other coelenterazine luciferases. hGLuc generated over 1000-fold higher bioluminescent signal intensity from live cells together with their immediate environment and over 100-fold higher intensity from viable cells alone (not including secreted luciferase) or cell lysates, compared to humanized forms of firefly (hFLuc) and Renilla (hRLuc) luciferases expressed under similar conditions. Furthermore, hGLuc showed 200-fold higher signal intensity than hRLuc and intensity comparable to that of hFLuc in vivo under standard imaging conditions. Gaussia luciferase provides a sensitive means of imaging gene delivery and other events in living cells in culture and in vivo, with a unique combination of features including high signal intensity, secretion, and ATP independence, thus being able to report from the cells and their environment in real time.

Bacterial luminescence: luminescence mechanism with cyclic peroxide participation and dependence on reactive oxygen species (a hypothesis)

Chemically initiated exchange (CIEE) luminescence reactions were reviewed and a new mechanism of luminescence with peracid as an intermediate is proposed; bacterial luminescence is generally considered to be a case of dioxetane luminescence, or, to be more precise, CIEE-luminescence which includes the generation of a cyclic peroxide. In the hypothesis the monooxygenase reaction (aldehyde -->fatty acid) should not be coupled with emitter generation as is usually believed, but only with the generation of peracid. As to the generation of the emitter, excited flavin, it is likely to occur later, during the interaction of flavin with cyclic peroxide. Its consequence is the breaking of two chemical bonds (O-O and C-C) in the cyclic peroxide and simultaneous generation of 4alpha-hydroxyflavin in exited state. In general, the generation of light includes three stages: 1) the monooxygenase reaction and the concurrent production of peracid; 2) the conversion of peracid to cyclic peroxide; and 3) the interaction of cyclic peroxide with flavin (through the CIEE mechanism).

Bioluminescence

Bioluminescence has evolved independently many times; thus the responsible genes are unrelated in bacteria, unicellular algae, coelenterates, beetles, fishes, and others. Chemically, all involve exergonic reactions of molecular oxygen with different substrates (luciferins) and enzymes (luciferases), resulting in photons of visible light (approximately 50 kcal). In addition to the structure of luciferan, several factors determine the color of the emissions, such as the amino acid sequence of the luciferase (as in beetles, for example) or the presence of accessory proteins, notably GFP, discovered in coelenterates and now used as a reporter of gene expression and a cellular marker. The mechanisms used to control the intensity and kinetics of luminescence, often emitted as flashes, also vary. Bioluminescence is credited with the discovery of how some bacteria, luminous or not, sense their density and regulate specific genes by chemical communication, as in the fascinating example of symbiosis between luminous bacteria and squid.