The binding and spectral alterations of oxidized flavin mononucleotide by bacterial luciferase

The binding of oxidized flavin mononucleotide (FMN) to bacterial luciferase was studied by equilibrium dialysis. A Scatchard plot of the data indicates a single FMN binding site per luciferase molecule, with a dissociation constant of 2.4 × 10^?4 M at 2° in 0.05 M Bis-Tris, 0.2 M NaCl, pH 7.0. The visible absorbance spectrum of luciferase-bound FMN is altered considerably relative to the spectrum of free FMN. The spectrum of the bound flavin shows an apparent splitting of the 443-nm peak yielding well-defined maxima at 458 nm and 434 nm.     

Fatty acid-enhanced binding of flavin mononucleotide to bacterial luciferase measured by steady-state fluorescence.

Bacterial luciferase catalyzes the oxidation of reduced flavin mononucleotide and tetradecanal resulting in the emission of light. We have investigated the interactions of a recombinant luciferase from a terrestrial bacterium Xenorhabdus luminescens with the reaction products, FMN and myristic acid, using steady-state fluorescence spectroscopy. Quenching of the intrinsic fluorescence and FMN fluorescence on binding of FMN to luciferase was found to be greatly stimulated in the presence of myristic acid, corresponding to a reduction of more than 30-fold in the FMN dissociation constant of the enzyme. In addition, the FMN-luciferase complex exhibits distinct fatty acid-dependent fluorescence properties. These results indicate that luciferase forms a ternary complex with FMN and myristic acid with a significantly different conformation from that of the binary FMN-luciferase complex.     

Effect of quinone on the fluorescence decay dynamics of endogenous flavin bound to bacterial luciferase

The interaction of quinone with luciferase from Photobacterium leiognathi was studied based on the fluorescence decay measurements of the endogenous flavin bound to the enzyme. Homologous 1,4-quinones, 1,4-benzoquinone, methyl-1,4-benzoquinone, 2-methyl-5-isopropyl-1,4-benzoquine and 1,4-naphthoquinone, were investigated. In the absence of quinone, the fluorescence intensity and anisotropy decays of the endogenous flavin exhibited two intensity decay lifetimes (~ 1 and 5 ns) and two anisotropy decay lifetimes (~ 0.2 and 20 ns), suggesting a heterogeneous quenching and a rotational mobility microenvironment of the active site of the luciferase, respectively. In the presence of quinone, the intensity decay heterogeneity was largely maintained, whereas the fraction of the short anisotropy decay component and the averaged rotational rate of FMN increased with the increasing hydrophobicity of the quinone. We hypothesize that the hydrophobicity of the quinone plays a role in the non-specific inhibition mechanism of xenobiotic molecules in the bacterial bioluminescence system via altering the rotational mobility of the endogenous flavin in the luciferase.     

Isolation of bacterial luciferases by affinity chromatography on 2,2-diphenylpropylamine-Sepharose: phosphate-mediated binding to an immobilized substrate analogue

A covalently immobilized form of an inhibitor of bacterial luciferase, 2,2-diphenylpropylamine (D phi PA), was an effective affinity resin for purifying this enzyme from several distinct bacterial species. The inhibitor is competitive with the luciferase aldehyde substrate but enhances binding of the flavin substrate FMNH2 (reduced riboflavin 5'-phosphate); comparable binding interactions occur with luciferase, the immobilized inhibitor D phi PA-Sepharose, and the substrates [Holzman, T. F., & Baldwin, T. O. (1981) Biochemistry 20, 5524-5528]. The effect of FMNH2 on the binding of luciferase to D phi PA-Sepharose was mimicked by inorganic phosphate; the luciferase-phosphate complex had a greater affinity for D phi PA-Sepharose than did luciferase. This observation led to the development of a method using D phi PA-Sepharose to purify bacterial luciferase. When crude enzyme in a high-phosphate buffer was applied to a column of the affinity matrix, the luciferase activity was removed from solution. After the column was washed with the same buffer to remove unbound protein, the luciferase was eluted with a non-phosphate cationic buffer. The affinity column has proven useful for rapid purification of luciferase in much greater yield than has been previously possible with standard ion-exchange techniques. This approach has allowed one-step purification of luciferases from ammonium sulfate precipitates of Vibrio harveyi, Vibrio fischeri, and Photobacterium phosphoreum. The dissociation constants in 0.10 M phosphate for the affinity ligand: luciferase complexes were 0.49 micro M, 0.28 micro M, and 0.15 micro M, respectively, for the three species. The dissociation constant for the V. harveyi mutant AK-6, which has normal aldehyde binding but greatly reduced affinity for FMNH2, was 0.30 micro M, while that for the V. harveyi mutant AK-20, which has greatly reduced affinity for aldehyde but a slightly increased affinity for FMNH2, was 1.2 microM. Preliminary experiments indicated that the yellow fluorescence protein (YFP) that participates, through energy transfer, in bioluminescent emission in V. fischeri strain Y-1 could be separated from the luciferase in this strain by chromatography on the affinity matrix, whereas other methods of separating luciferase and YFP have had limited success because of the binding of YFP to luciferase.     

Differential transfers of reduced flavin cofactor and product by bacterial flavin reductase to luciferase

It is believed that the reduced FMN substrate required by luciferase from luminous bacteria is provided in vivo by NAD(P)H-FMN oxidoreductases (flavin reductases). Our earlier kinetic study indicates a direct flavin cofactor transfer from Vibrio harveyi NADPH-preferring flavin reductase P (FRP(H)) to the luciferase (L(H)) from the same bacterium in the in vitro coupled luminescence reaction. Kinetic studies were carried out in this work to characterize coupled luminescence reactions using FRP(H) and the Vibrio fischeri NAD(P)H-utilizing flavin reductase G (FRG(F)) in combination with L(H) or luciferase from V. fischeri (L(F)). Comparisons of K(m) values of reductases for flavin and pyridine nucleotide substrates in single-enzyme and luciferase-coupled assays indicate a direct transfer of reduced flavin, in contrast to free diffusion, from reductase to luciferase by all enzyme couples tested. Kinetic mechanisms were determined for the FRG(F)-L(F) and FRP(H)-L(F) coupled reactions. For these two and the FRG(F)-L(H) coupled reactions, patterns of FMN inhibition and effects of replacement of the FMN cofactor of FRP(H) and FRG(F) by 2-thioFMN were also characterized. Similar to the FRP(H)-L(H) couple, direct cofactor transfer was detected for FRG(F)-L(F) and FRP(H)-L(F). In contrast, despite the structural similarities between FRG(F) and FRP(H) and between L(F) and L(H), direct flavin product transfer was observed for the FRG(F)-L(H) couple. The mechanism of reduced flavin transfer appears to be delicately controlled by both flavin reductase and luciferase in the couple rather than unilaterally by either enzyme species.     

Mapping ligand binding domains in chimeric fibroblast growth factor receptor molecules. Multiple regions determine ligand binding specificity

Fibroblast growth factors (FGFs) mediate essential cellular functions by activating one of four alternatively spliced FGF receptors (FGFRs). To determine the mechanism regulating ligand binding affinity and specificity, soluble FGFR1 and FGFR3 binding domains were compared for activity. FGFR1 bound well to FGF2 but poorly to FGF8 and FGF9. In contrast, FGFR3 bound well to FGF8 and FGF9 but poorly to FGF2. The differential ligand binding specificity of these two receptors was exploited to map specific ligand binding regions in mutant and chimeric receptor molecules. Deletion of immunoglobulin-like (Ig) domain I did not effect ligand binding, thus localizing the binding region(s) to the distal two Ig domains. Mapping studies identified two regions that contribute to FGF binding. Additionally, FGF2 binding showed positive cooperativity, suggesting the presence of two binding sites on a single FGFR or two interacting sites on an FGFR dimer. Analysis of FGF8 and FGF9 binding to chimeric receptors showed that a broad region spanning Ig domain II and sequences further N-terminal determines binding specificity for these ligands. These data demonstrate that multiple regions of the FGFR regulate ligand binding specificity and that these regions are distinct with respect to different members of the FGF family.     

Subunit exchange between and specific activities of mutant bacterial luciferases

Complementation has been demonstrated between two mutant bacterial luciferases which possess low activities due to different structural defects in different subunits. Activity characteristic of the wild type dimer was obtained by incubating under non-denaturing conditions. The specific activities of the two mutant enzymes were determined by using specific antiserum made against the wild type luciferase.     

Characterization of the peptide-bound flavin of a bacterial sarcosine dehydrogenase.

As in the case of the succinate and sarcosine dehydrogenases of liver mitochondria, the flavin prosthetic group of the bacterial sarcosine dehydrogenase can be released from the enzyme by proteolytic digestion with trypsin and chymotrypsin. The flavin, isolated in the dinucleotide form and covalently bound to a peptide fragment, is converted to the mononucleotide and purified by sequential chromatography on Sephadex G-25, DEAE-Sephadex A-25, followed by preparative paper chromatography and high voltage electrophoresis.The absorption maxima of the purified flavin at pH 7 are found at 268, 350, and 447 nm, with 268:447 nm and 350:447 nm ratios of 3.08 and 0.79, respectively. The fluorescence excitation and emission maxima, 450 and 530 nm, respectively, are similar to those of flavin mononucleotide. The fluorescence of the flavin-peptide is maximal at pH 3.0–3.1.Amino acid analysis of the flavin-peptide (riboflavin form) gave the following molar ratios of amino acids to flavin: Lys(1), Asp(2), Thr(1), Ser(1), Glu(1), Gly(1), and Ala(1). Aspartic acid was the N-terminal amino acid. Upon more extensive hydrolysis, histidine was obtained in 71–84% yields. Employing aminopeptidase M, the partial sequence of amino acids in the flavin-peptide was determined to be as follows: Flavin

-Asp-Lys-Ser-Glu-Gly-His-(Asp,Ala,Thr)-Evidence is presented that the isoalloxazine ring is linked covalently via its 8 α-methyl group to N-3 of histidine.     

Engineering of monomeric bacterial luciferases by fusion of luxA and luxB genes in Vibrio harveyi

Luciferase (Lux)-encoding sequences are very useful as reporter genes. However, a drawback when applying Vibrio harveyi Lux as a reporter enzyme in eukaryotic cells, is that it is a heterodimeric enzyme, thus requiring simultaneous synthesis of both Lux subunits to be active. To overcome this disadvantage, luxA and luxB genes encoding the A and B subunits of this light-emitting heterodimeric Lux, were fused and expressed in Escherichia coli. Comparative analysis of four fused monomeric Lux enzymes by in vivo enzyme assay, immunoblotting and partial enzyme purification, showed that the fused Lux were active both as AB or as BA monomers, albeit at different levels (up to 80% activity for AB and up to 2% for BA, as compared with the wild type binary A + B construct). One of the LuxAB fusion proteins was stably expressed in calli of Nicotiana tabacum, and displayed very high Lux activity, thus demonstrating its potential as a reporter enzyme in eukaryotic systems.     

Examination of the activity of carboxyl-terminal chimeric constructs of human and yeast ferrochelatases

Insertion of ferrous iron into protoporphyrin IX is catalyzed by ferrochelatase (EC 4.99.1.1). Human and Schizosaccharomyces pombe forms of ferrochelatase contain a [2Fe-2S] cluster with three of the four coordinating cysteine ligands located within the 30 carboxyl-terminal residues. Saccharomyces cerevisiae ferrochelatase contains no cluster, but has comparable activity. Truncation mutants of S. cerevisiae lacking either the last 37 or 16 amino acids have no enzyme activity. Chimeric mutants of human, S. cerevisiae, and Sc. pombe ferrochelatase have been created by switching the terminal 10% of the carboxy end of the enzyme. Site-directed mutagenesis has been used to introduce the fourth cysteinyl ligand into chimeric mutants that are 90% S. cerevisiae. Activity was assessed by rescue of Deltahem H, a ferrochelatase deficient strain of Escherichia coli, and by enzyme assays. UV-visible and EPR spectroscopy were used to investigate the presence or absence of the [2Fe-2S] cluster. Only 2 of the 13 chimeric mutants that were constructed produced active enzymes. HYB, which is predominately human with the last 40 amino acids being that of S. cerevisiae, is an active protein which does not contain a [2Fe-2S] cluster. The other active chimeric mutant, HSp, is predominately human ferrochelatase with the last 38 amino acids being that of Sc. pombe ferrochelatase. This active mutant contains a [2Fe-2S] cluster, as verified by UV-visible and EPR spectroscopic techniques. No other chimeric proteins had detectable enzyme activity or a [2Fe-2S] cluster. The data are discussed in terms of structural requirements for cluster stability and the role that the cluster plays for ferrochelatase.     

Use of bacterial and firefly luciferases as reporter genes in DEAE-dextran-mediated transfection of mammalian cells.

The aim of this study was to compare three different luciferase genes by placing them in a single reporter vector and expressing them in the same mammalian cell type. The luciferase genes investigated were the luc genes from the fireflies Photinus pyralis (PP) and Luciola mingrelica (LM) and the lux AB5 gene, a translational fusion of the two subunits of the bacterial luciferase from Vibrio harveyi (VH). The chloramphenicol acetyltransferase (CAT) gene was also included in this study for comparison. The performances of the assay methods of the corresponding enzymes were evaluated using reference materials and the results of the expressed enzymes following transfection were calculated using calibration curves. All of the bioluminescent assays possess high reproducibility both within and between the batches (less than 15%). The comparison of the assay methods shows that firefly luciferases have the highest detection sensitivity (0.05 and 0.08 amol for PP and LM, respectively) whereas the VH bacterial luciferase has 5 amol and CAT 100 amol. On the other hand, the transfection of the various plasmids shows that the content of the expressed enzyme within the cells is much higher for CAT than for the other luciferase genes. VH luciferase is expressed at very low levels in mammalian cells due to the relatively high temperature of growing of the mammalian cells that seems to impair the correct folding of the active enzyme. PP and LM luciferases are both expressed at picomolar level but usually 10 to 70 times less in content with respect to CAT within the transfected cells. On the basis of these results the overall improvement in sensitivity related to the use of firefly luciferases as reporter genes in mammalian cells is about 30 to 50 times with respect to that of CAT.     

Role of the carboxyl-terminal region of arrestin in binding to phosphorylated rhodopsin.

The structural and functional properties of arrestin were studied by subjecting the protein to limited proteolysis. Limited proteolysis by trypsin cleaves arrestin (48 kDa), producing 20-25-kDa fragments. Prior to this stage of proteolysis, trypsin produced 46.6-, 45.4-, and 42-kDa fragments. Structural analysis of the proteolytic fragments demonstrated major cleavage at the carboxyl terminus, indicating that the carboxyl terminus is highly exposed. We found that forms of arrestin truncated at their carboxyl terminus maintained their functional properties and bound to phosphorylated rhodopsin. Native arrestin binds only to photoexcited phosphorylated rhodopsin, whereas the truncated arrestin binds to phosphorylated rhodopsin independent of its exposure to light. The truncated forms of arrestin were separated from native arrestin by a chromatographic procedure and subsequently characterized in functional studies. The binding of the truncated forms of arrestin to phosphorylated photoexcited rhodopsin is more tight than the binding of native arrestin as determined by a direct binding assay and the phosphodiesterase assay. We suggest that the acidic carboxyl-terminal region of arrestin may act as a regulator for light-dependent binding to phosphorylated rhodopsin.     

Activity coupling and complex formation between bacterial luciferase and flavin reductases.

Luminous bacteria contain several species of flavin reductases, which catalyze the reduction of FMN using NADH and/or NADPH as a reductant. The reduced FMN (i.e. FMNH(2)) so generated is utilized along with a long-chain aliphatic aldehyde and molecular oxygen by luciferase as substrates for the bioluminescence reaction. In this report, the general properties of luciferases and reductases from luminous bacteria are briefly summarized. Earlier and more recent studies demonstrating the direct transfer of FMNH(2) from reductases to luciferase are surveyed. Using reductases and luciferases from Vibrio harveyi and Vibrio fischeri, two mechanisms were uncovered for the direct transfer of reduced flavin cofactor and reduced flavin product of reductase to luciferase. A complex of an NADPH-specific reductase (FRP(Vh)) and luciferase from V. harveyi has been detected in vitro and in vivo. Both constituent enzymes in such a complex are catalytically active. The reduction of FRP(Vh)-bound FMN cofactor by NADPH is reversible, allowing the cellular contents of NADP(+) and NADPH as a factor for the regulation of the production of FMNH(2) by FRP(Vh) for luciferase bioluminescence. Other regulations of the activity coupling between reductase and luciferase are also discussed.     

Active site residues critical for flavin binding and 5,6-dimethylbenzimidazole biosynthesis in the flavin destructase enzyme BluB

The "flavin destructase" enzyme BluB catalyzes the unprecedented conversion of flavin mononucleotide (FMN) to 5,6-dimethylbenzimidazole (DMB), a component of vitamin B(12). Because of its unusual chemistry, the mechanism of this transformation has remained elusive. This study reports the identification of 12 mutant forms of BluB that have severely reduced catalytic function, though most retain the ability to bind flavin. The "flavin destructase" BluB is an unusual enzyme that fragments the flavin cofactor FMNH(2) in the presence of oxygen to produce 5,6-dimethylbenzimidazole (DMB), the lower axial ligand of vitamin B(12) (cobalamin). Despite the similarities in sequence and structure between BluB and the nitroreductase and flavin oxidoreductase enzyme families, BluB is the only enzyme known to fragment a flavin isoalloxazine ring. To explore the catalytic residues involved in this unusual reaction, mutants of BluB impaired in DMB biosynthesis were identified in a genetic screen in the bacterium Sinorhizobium meliloti. Of the 16 unique point mutations identified in the screen, the majority were located in conserved residues in the active site or in the unique "lid" domain proposed to shield the active site from solvent. Steady-state enzyme assays of 12 purified mutant proteins showed a significant reduction in DMB synthesis in all of the mutants, with eight completely defective in DMB production. Ten of these mutants have weaker binding affinities for both oxidized and reduced FMN, though only two have a significant effect on complex stability. These results implicate several conserved residues in BluB's unique ability to fragment FMNH(2) and demonstrate the sensitivity of BluB's active site to structural perturbations. This work lays the foundation for mechanistic studies of this enzyme and further advances our understanding of the structure-function relationship of BluB.