Bacterial Bioluminescence Reaction Research Articles

Increased Autonomous Bioluminescence Emission from Mammalian Cells by Enhanced Cofactor Synthesis

The bacterial bioluminescence system has been successfully implemented in mammalian cell lines, enabling the substrate-free luminescence imaging of living cells. One of the major limitations of the system is its comparatively low brightness. To improve light emission, we aimed to increase the cellular production of FMNH2 and NADPH, which serve as cosubstrates in the bacterial bioluminescence reaction. We coexpressed different proteins involved in the synthesis of these two cofactors together with the proteins of the bacterial bioluminescence system in different mammalian cell lines. The combined expression of a riboflavin kinase (RFK) and a constitutively active Akt2 variant (Akt2CA) that participate in the cellular production of FMN and NADP+, respectively, increased bioluminescence emission up to 2.4-fold. The improved brightness allows autonomous bioluminescence imaging of mammalian cells at a higher signal-to-noise ratio and enhanced spatiotemporal resolution.

Cryo-EM structure of the fatty acid reductase LuxC–LuxE complex provides insights into bacterial bioluminescence

The discovery of reduced flavin mononucleotide and fatty aldehydes as essential factors of light emission facilitated study of bacterial luminescence. Although the molecular mechanisms underlying bacterial luminescence have been studied for more than 60 years, the structure of the bacterial fatty acid reductase complex remains unclear. Here, we report the cryo-EM structure of the Photobacterium phosphoreum fatty acid reductase complex LuxC–LuxE to a resolution of 2.79 Å. We show that the active site Lys238/Arg355 pair of LuxE is >30 Å from the active site Cys296 of LuxC, implying that catalysis relies on a large conformational change. Furthermore, mutagenesis and biochemical experiments support that the L-shaped cleft inside LuxC plays an important role in substrate binding and reaction. We obtained a series of mutants with significantly improved activity as measured by in vitro bioluminescence assays and demonstrated that the double mutant W111A/F483K displayed the highest activity (370% of the WT). Our results indicated that the activity of LuxC significantly affects the bacterial bioluminescence reaction. Finally, we expressed this mutated lux operon in Escherichia coli but observed that the in vivo concentrations of ATP and NADPH limited the enzyme activity; thus, we conclude that the luminous intensity mainly depends on the level of metabolic energy.

Mechanisms of Viscous Media Effects on Elementary Steps of Bacterial Bioluminescent Reaction.

Enzymes activity in a cell is determined by many factors, among which viscosity of the microenvironment plays a significant role. Various cosolvents can imitate intracellular conditions in vitro, allowing to reduce a combination of different regulatory effects. The aim of the study was to analyze the media viscosity effects on the rate constants of the separate stages of the bacterial bioluminescent reaction. Non-steady-state reaction kinetics in glycerol and sucrose solutions was measured by stopped-flow technique and analyzed with a mathematical model developed in accordance with the sequence of reaction stages. Molecular dynamics methods were applied to reveal the effects of cosolvents on luciferase structure. We observed both in glycerol and in sucrose media that the stages of luciferase binding with flavin and aldehyde, in contrast to oxygen, are diffusion-limited. Moreover, unlike glycerol, sucrose solutions enhanced the rate of an electronically excited intermediate formation. The MD simulations showed that, in comparison with sucrose, glycerol molecules could penetrate the active-site gorge, but sucrose solutions caused a conformational change of functionally important Glu175 of luciferase. Therefore, both cosolvents induce diffusion limitation of substrates binding. However, in sucrose media, increasing enzyme catalytic constant neutralizes viscosity effects. The activating effect of sucrose can be attributed to its exclusion from the catalytic gorge of luciferase and promotion of the formation of the active site structure favorable for the catalysis.

The Effect of Osmolytes on the Bioluminescent Reaction of Bacteria: Structural and Dynamic Properties

The effects of viscous media with glycerol and sucrose (10–40%) on the kinetics of the bacterial bioluminescent reaction have been investigated by stopped-flow technique. Increment of quantum yield in media with 10% of both osmolytes was shown. Higher concentrations of glycerol, up to 30–40%, were found to reduce the efficiency of the reaction, while this effect was not observed in the media with sucrose. The molecular dynamics simulation was used to study the structure of bacterial luciferase surrounded by either water molecules solely or by mixture of water with various numbers of glycerol/sucrose molecules. It was found that both cosolvents at studied concentrations did not cause a significant change in conformation of bacterial luciferase. The calculated root-mean-square fluctuation for Cα-atoms of bacterial luciferase α-subunit indicated that the higher flexibility of the enzyme mobile loop could be responsible for increment of quantum yield in the presence of 10% of both osmolytes. The active site of bacterial luciferase was found to be accessible for glycerol molecules while sucrose did not enter catalytic gorge. Moreover, at 30 and 40% concentration the glycerol molecules were found to locate in the active site of bacterial luciferase throughout the whole simulation time.

Viscous Media Slow Down the Decay of the Key Intermediate in Bacterial Bioluminescent Reaction.

The effects of medium viscosity on the decay rate of the 4a-hydroperoxyflavin intermediate of the bioluminescent reaction was investigated. It was found that at low concentrations of glycerol or sucrose (viscosity 1.1-1.3 cP) the decay rate rises, whereas a further increase in viscosity to 6.2 cP leads to a decrease in the decay rate following a power function with an exponent of 0.82-0.84. Using molecular dynamics methods, it was shown that the presence of glycerol and sucrose molecules causes a change in the mobility of the amino acid residues in the active center of luciferase, particularly those responsible for binding of flavin. The results obtained are indicative of two opposite effects of viscous media with glycerol and sucrose: (1) destabilization of 4a-hydroperoxyflavin due to a change in the structural and dynamic properties of the protein and (2) stabilization of this intermediate by the decrease in the diffusion rate of its decay products.

ВЛИЯНИЕ ОСМОЛИТОВ НА БИОЛЮМИНЕСЦЕНТНУЮ РЕАКЦИЮ БАКТЕРИЙ: СТРУКТУРНО-ДИНАМИЧЕСКИЕ АСПЕКТЫ

The effects of viscous media with glycerol and sucrose (10-40%) on the kinetics of the bacterial bioluminescent reaction have been investigated by stopped-flow technique. Increment of quantum yield in media with 10% of both osmolytes was shown. Higher concentrations of glycerol, up to 30-40%, were found to reduce the efficiency of the reaction, while this effect was not observed in the media with sucrose. The molecular dynamics simulation was used to study the structure of bacterial luciferase surrounded by either water molecules solely or by mixture of water with various numbers of glycerol/sucrose molecules. It was found that both cosolvents at studied concentrations did not cause a significant change in conformation of bacterial luciferase. The calculated root mean square fluctuations for Cα-atoms of bacterial luciferase α-subunit indicated that the higher flexibility of the enzyme mobile loop could be responsible for increment of quantum yield in the presence of 10% of both osmolytes. The active site of bacterial luciferase was found to be accessible for glycerol molecules while sucrose did not enter catalytic gorge. Moreover, at 30% and 40% concentration the glycerol molecules were found to locate in the active site of bacterial luciferase throughout the whole simulation time (40 ns) and to exclude water molecules, which can explain the experimentally obtained reaction quantum yield decrease.

Evidence for the generation of myristylated FMN by bacterial luciferase.

The genes responsible for the light production in bioluminescent bacteria are present as an operon, luxCDABEG. Many strains of Photobacteria carry an additional gene, termed luxF. X-ray crystallographic analysis of LuxF revealed the presence of four molecules of a flavin derivative, i.e. 6-(3'-(R)-myristyl) flavin adenine mononucleotide (myrFMN) non-covalently bound to the homodimer. In the present study, we exploited the binding of myrFMN to recombinant apo-LuxF to explore the occurrence of myrFMN in various bioluminescent bacteria. MyrFMN was detected in all bacterial strains tested including Vibrio and Aliivibrio indicating that it is more widely occurring in bioluminescent bacteria than previously assumed. We also show that apo-LuxF captures myrFMN and thereby relieves the inhibitory effect on luciferase activity. Thus our results provide support for the hypothesis that LuxF acts as a scavenger of myrFMN in bioluminescent bacteria. However, the source of myrFMN remained obscure. To address this issue, we established a cofactor regeneration enzyme-catalyzed cascade reaction that supports luciferase activity in vitro for up to 3 days. This approach enabled us to unambiguously demonstrate that myrFMN is generated in the bacterial bioluminescent reaction. Based on this finding we postulate a reaction mechanism for myrFMN generation that is based on the luciferase reaction.

Abstracts of the 17th International Symposium on Bioluminescence and Chemiluminescence ‐ (ISBC 2012)

WARNING : The light-emitting molecular structures responsible for the chemiluminescence and fluorescence phenomena are not necessarily the same!

The Mechanism of Electronic Excitation in the Bacterial Bioluminescent Reaction

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Identity of the Emitter in the Bacterial Luciferase Luminescence Reaction: Binding and Fluorescence Quantum Yield Studies of 5-Decyl-4a-hydroxy-4a,5-dihydroriboflavin-5‘-phosphate as a Model

The excited state of 4a-hydroxy-4a,5-dihydroFMN has been postulated to be the emitter in the bacterial bioluminescence reaction. However, while the bioluminescence quantum yield of the luciferase emitter is about 0.16, chemiluminescence and fluorescence quantum yields of earlier flavin models mimicking the luciferase emitter were no more than 10(-5). To further examine the proposed chemical identity of the luciferase emitter, 5-decyl-4a-hydroxy-4a,5-dihydroFMN was prepared as a new flavin model. Both the wild-type Vibrio harveyi luciferase and a catalytically active alphaC106A mutant formed complexes with the flavin model at a 1:1 molar ratio with K(d) values at 2.4 and 1.2 microM, respectively. This flavin model inhibited the activity of both luciferases, suggesting that it was bound to the enzyme active center. While the free flavin model was itself only very weakly fluorescent, its binding to either luciferase species resulted in markedly enhanced fluorescence, peaking at 440 nm. The fluorescence quantum yields of 5-decyl-4a-hydroxy-4a,5-dihydroFMN bound to wild-type and alphaC106A luciferases were 0.08 and 0.05, respectively, which are about 50% of the respective emitter bioluminescence quantum yields of these two luciferases. The present findings clearly demonstrated that the luciferase active site was suitable for marked enhancement of fluorescence of 4a-hydroxyflavin and, hence, provides a strong support to the proposed identity of 4a-hydroxy-4a,5-dihydroFMN, in its exited state, as the luciferase emitter.

Hyperactivity and interactions of a chimeric myristoryl-ACP thioesterase from the lux system of luminescent bacteria

A chimeric myristoyl-ACP thioesterase with much higher catalytic efficiency than the parental enzymes has been generated by ligating the N-terminal half of the lux-specific thioesterase (LuxD) from Photobacterium phosphoreum with the C-terminal half of LuxD from Vibrio harveyi. The LuxD chimera had the same rate-limiting step and specificity, but cleaved esters and thioesters over eight times faster than the native enzymes. LuxD, along with acyl-protein synthetase (LuxE) and reductase (LuxC), comprise a multienzyme complex channeling activated fatty acids into the aldehyde substrate for the bacterial bioluminescence reaction. As P. phosphoreum LuxD and LuxE modulate each of their respective activities, the effects of mixing V. harveyi and the chimeric LuxD with P. phosphoreum LuxE were investigated. The chimeric LuxD stimulated acylation of LuxE to the same extent as V. harveyi LuxD, but to a lower level than that caused by P. phosphoreum LuxD. Conversely, P. phosphoreum LuxE stimulated the thioesterase activity of V. harveyi LuxD by 30% and the chimeric LuxD by 20% while the activity of P. phosphoreum LuxD was increased by over 140%. These results show that the stimulatory effects are unrelated to the level of thioesterase activity and indicate that the carboxyl terminal region of LuxD interacts with LuxE and causes a conformational change.

Mutation of the Nucleophilic Elbow of the Lux-Specific Thioesterase from Vibrio harveyi

Myristoyl-ACP thioesterase (LuxD) from Vibrio harveyi causes the slow release of fatty acids for reduction into the aldehyde substrate required for the bacterial bioluminescence reaction. The active site Ser nucleophile (S114) of the LuxD thioesterase is in a γ-turn with a sequence (AXS114XS) quite different from the standard motif of GXSXG found in almost all (thio) esterases and lipases. The presence of an Arg residue (R118) in the first turn of the helix after the γ-turn also distinguishes LuxD from other enzymes. Mutation of R118 to Leu inactivated the enzyme and prevented acylation of the Ser114 nucleophile, while even a conservative replacement with Lys resulted in over 75% loss of the same functions, suggesting that R118 helps maintain the configuration of the active site. In contrast, replacement of S116 with Gly but not Ala stimulated the esterase and deacylation rates by over threefold. Purification of the S116G mutant to homogeneity and analyses of its intrinsic fluorescence on acylation with myristoyl-CoA clearly demonstrated that this mutant was much more active than wild-type LuxD. The presence of S116 rather than the expected Gly residue in the γ-turn containing the Ser nucleophile may function so that release of fatty acids from LuxD is restricted allowing a more efficient delivery of fatty acids to the luminescent system.

Practical enzymology course based on bioluminescence.

We describe our experience with laboratory courses in enzymology based on the phenomenon of bioluminescence. The soluble and immobilized enzymes of luminous bacteria are used and the practical enzymological course consists of four main courses: (1) training in measuring the activities of soluble and immobilized enzymes; (2) the investigation of kinetic characteristics (kinetic constants) and enzyme-substrate and enzyme-inhibitor interactions in the bacterial bioluminescent reaction; (3) The testing of physico-chemical characteristics of enzymes (pH, temperature, ion strength, etc.); (4) the effect of inhibitors on enzymes. Training is possible in groups of about ten persons. Our practice work has been introduced in the biological, pedagogical and physical departments of Krasnoyarsk State University. Students of the pedagogical department have created a popular and interesting series of laboratory works for high school children aged 14-17 years.

Computational Analysis of the Oxygen Addition at the C4aSite of Reduced Flavin in the Bacterial Luciferase Bioluminescence Reaction

The energetic characteristics of selected reaction steps in the bacterial luciferase-catalyzed luminescence reaction were examined by computation using the MNDO-PM3 method. Specifically, a three-step model was proposed to account for the reaction between oxygen and reduced riboflavin 5'-phosphate (1,5H2-FMN) to generate first the 5-hydroFMN-4a-peroxide (5H-FMN-4aOO-) and then the 5-hydro-4a-hydroperoxyFMN (5H-FMN-4aOOH) intermediates. Lysine (Lys-H+) and aspartate (Asp-) were chosen as representative catalytic residues involved in the protonation and deprotonation processes. Results show that deprotonation at the N1 site of 1,5H2-FMN by a basic amino acid residue at the luciferase active site would efficiently accelerate the reaction rate of O2 addition to form 5H-FMN-4aOO-. The most favored site of oxygen attack is at the flavin C4a. With the aid of a catalytic acid group, the 5H-FMN-4aOO- so formed tends to undergo a spontaneous protonation reaction to yield the 5H-FMN-4aOOH.

Computational Analysis of the Oxygen Addition at the C4a Site of Reduced Flavin in the Bacterial Luciferase Bioluminescence Reaction

Computational Analysis of the Oxygen Addition at the C4a Site of Reduced Flavin in the Bacterial Luciferase Bioluminescence Reaction

Cysteine-286 as the site of acylation of the Lux-specific fatty acyl-CoA reductase

The channelling of fatty acids into the fatty aldehyde substrate for the bacterial bioluminescence reaction is catalyzed by a fatty acid reductase multienzyme complex, which channels fatty acids through the thioesterase (LuxD), synthetase (LuxE) and reductase (LuxC) components. Although all three components can be readily acylated in extracts of different luminescent bacteria, this complex has been successfully purified only from Photobacterium phosphoreum and the sites of acylation identified on LuxD and LuxE. To identify the acylation site on LuxC, the nucleotide sequence of P. phosphoreum luxC has been determined and the gene expressed in a mutant Escherichia coli strain. Even in crude extracts, the acylated reductase intermediate as well as acyl-CoA reductase activity could be readily detected, providing the basis for analysis of mutant reductases. Comparison of the amino-acid sequences of LuxC from P. phosphoreum, P. leiognathi and other luminescent bacteria, showed that only three cysteine residues (C 171, C 279, and C 286) were conserved. As a cysteine residue on LuxC has been implicated in fatty acyl transfer, each of the conserved cysteine residues of the P. phosphoreum and P. leiognathi reductases was converted to a serine residue, and the properties of the mutant proteins examined. Only mutation of C 286-blocked reductase activity and prevented formation of the acylated reductase intermediate, showing that C 286 is the site of acylation on LuxC.

Interaction of Photobacterium leiognathi and Vibrio fischeri Y1 luciferases with fluorescent (antenna) proteins: bioluminescence effects of the aliphatic additive.

The kinetics of the bacterial bioluminescence reaction is altered in the presence of the fluorescent (antenna) proteins, lumazine protein (LumP) from Photobacterium or the yellow fluorescence proteins (YFP) having FMN or Rf bound, from Vibrio fischeri strain Y1. Depending on reaction conditions, the bioluminescence intensity and its decay rate may be either enhanced or strongly quenched in the presence of the fluorescent proteins. These effects can be simply explained on the basis of the same protein-protein complex model that accounts for the bioluminescence spectral shifts induced by these fluorescent proteins. In such a complex, where the fluorophore evidently is in proximity to the luciferase active site, it is expected that the on-off rate of certain aliphatic components of the reaction should be altered with a consequent shift in the equilibria among the luciferase intermediates, as recently elaborated in a kinetic scheme. These aliphatic components are the bioluminescence reaction substrate, tetradecanal or other long-chain aldehyde, its carboxylic acid product, or dodecanol used as a stabilizer of the luciferase peroxyflavin. No evidence can be found for the protein-protein interaction in the absence of the aliphatic component.

DITHIONITE TREATMENT OF FLAVINS: SPECTRAL EVIDENCE FOR COVALENT ADDUCT FORMATION and EFFECT ON in vitro BACTERIAL BIOLUMINESCENCE

Intrigued by the apparent requirement of dithionite for FMN reduction (as opposed to photoreduction or catalytic hydrogenation) in the H2O2-initiated bacterial bioluminescence reaction, we chose 5-ethyl-3-methyllumiflavinium cation I as a model to investigate possible flavin adduct formation by treatment with dithionite or (bi)sulfite. In the range of pH 5-8, the reaction of dithionite with 5-ethyl-3-methyllumiflavinium cation, which is in equilibrium with the 5-ethyl-4a-hydroxy-3-methyl-4a, 5-dihydrolumiflavin pseudobase II (X = OH), is not limited to the formation of flavosemiquinone and dihydroflavin following two one-electron steps. Several parallel and sequential reactions may take place involving the intermediacy of covalent flavin adducts. Addition of (bi)sulfite gave a 4a-sulfiteflavin adduct II (X = SO3-). Consistent with the S2O4(2-) in equilibrium with 2 SO2-. equilibrium, the reaction of dithionite and II (X = OH; SO3-) gave rise to two flavin adducts in competitive nucleophilic displacements: a 4a-sulfoxylate-flavin radical (II, X = SO2.) and a 4a-dithioniteflavin adduct (II, X = S2O4-), respectively. On increasing the (S2O4(2-), SO2.-)/flavin ratio under N2, the formation of the 4a-sulfoxylate-flavin radical became predominant. The II (X = SO2.) so formed was in equilibrium with the flavosemiquinone and bisulfate and can be trapped by reacting with hydroxylamine. In the initial presence of oxygen, II (X = SO2.) was highly reactive toward O2, giving a fast oxidation to II (X = SO3-) and effectively suppressing the formation of the flavosemiquinone.(ABSTRACT TRUNCATED AT 250 WORDS)

Proposed mechanism for the bacterial bioluminescence reaction involving a dioxirane intermediate

We propose here a verifiable mechanism for the bacterial bioluminescence reaction involving a dioxirane intermediate. Participation of the dioxirane predicts either formation of an excited carbonyl, rather than the flavin, as the primary excited state in the reaction, or, through a CIEEL mechanism, the C4a hydroxyflavin or the chromophore of a secondary emitter protein could become excited. We propose energy transfer from the primary excited state to the C4a hydroxyflavin in the absence of the lumazine protein or the yellow fluorescence protein, while in the presence of either of the secondary emitter proteins, excitation energy would be transferred to the second protein-bound chromophore. The mechanism is similar to other currently discussed mechanisms, except in the final steps leading to the primary excited state. The mechanism is consistent with the known details of the reactions of dioxiranes and of flavins and with recent studies of the secondary emitter proteins and bacterial luciferases.

Two-phase flow cell for chemiluminescence and bioluminescence measurements

A new approach to two-phase CL (chemiluminescence) measurements is reported. A magnetically stirred reagent phase is separated from the analyte phase by a dialysis membrane so that only smaller molecules can go from one phase to the other. The system is designed so that the analyte phase flows through a spiral groove on an aluminum block that is flush against the dialysis membrane. As solution flows through the spiral grove, analyte diffuses into the reagent phase where it reacts to produce light. A simple model is developed to predict how this system will behave. Experimentally, the system is evaluated by using the luminol reaction catalyzed by peroxidase, the firefly reaction, and the bacterial bioluminescence reaction. 10 references, 4 tables, 6 figures.