Structure of bacterial luciferase.

The generation of light by living organisms such as fireflies, glow-worms, mushrooms, fish, or bacteria growing on decaying materials has been a subject of fascination throughout the ages, partly because it occurs without the need for high temperatures. The chemistry behind the numerous bioluminescent systems is quite varied, and the enzymes that catalyze the reactions, the luciferases, are a large and evolutionarily diverse group. The structure of the best understood of these intriguing enzymes, bacterial luciferase, has recently been determined, allowing discussion of features of the protein in structural terms for the first time.

Firefly luciferase: the structure is known, but the mystery remains.

The structure of firefly luciferase reveals a new protein fold which may be representative of a growing family of homologous enzymes.

Studies on the complex formed between bacitracin A and divalent cations.

Bacitracin A is a peptide antibiotic which forms stoichiometric complexes with divalent cations, including Ni2+ and Zn2+. In this paper it is shown that the metal-bacitracin complex contains a group which has a pKa near pH 5.5. Deprotonation of the group is concomitant with the aggregation and precipitation of the metal-bacitracin complex. Bacitracin A, in the absence of metals, does not contain any group which has a pKa in this range. It is postulated that this group is the N-terminal amino of isoleucine, which was previously postulated not to be directly involved in metal coordination based on proton release measurements. An attempt was made to demonstrate directly that the N-terminal amino group is not coordinated to the metal by examining the reactivity of this group with 2,4,6-trinitrobenzene sulfonate. It was clearly shown that bound metals protect the N-terminal amino group from reacting with this reagent. It is speculated that this metal-protection results from a combination of factors, including steric hindrance.

Luciferase from the east European firefly Luciola mingrelica: cloning and nucleotide sequence of the cDNA, overexpression in Escherichia coli and purification of the enzyme.

We have cloned cDNA encoding luciferase in Luciola mingrelica, fireflies living near the Black Sea in southern Russia, and obtained high level expression of the cloned sequences in Escherichia coli. The nucleotide sequences of two isolated clones were determined; five single base differences were observed, but none resulted in a change in the encoded amino acid residue. The cDNA encoded a protein of 548 amino acid residues. The overall amino acid sequence identity with the luciferase from Photinus pyralis, the North American firefly, was 67%, while comparison of the L. mingrelica luciferase with L. cruciata and L. lateralis, both indigenous to Japan, showed about 80% of the residues were strictly conserved. A novel overexpression system which employs the regulatory genes of the luminous bacterium Vibrio fischeri allowed growth of cultures to high cell density and high luciferase content, facilitating purification of the enzyme. Luciferase was purified to homogeneity in good yield from lysates of recombinant E. coli by ammonium sulfate fractionation and chromatography on columns of DEAE Sephadex and Blue Sepharose. The physicochemical properties of the luciferases from the available recombinant sources are significantly different and should allow detailed investigations into the mechanism of the bioluminescence reaction and the physical basis of the differences in the color of light emitted from the various enzymes.

GroE modulates kinetic partitioning of folding intermediates between alternative states to maximize the yield of biologically active protein.

The central issue of chaperone function is the mechanism whereby partitioning of folding polypeptides along the productive pathway may be maximized, while non-productive folding pathways are minimized. We have found that the GroE chaperone is capable of accelerating the rate of the productive pathway of bacterial luciferase alphabeta heterodimer formation. At intermediate temperatures at which the productive pathway and non-productive pathways leading to dimerization-incompetent monomeric forms of the subunits coexist, GroE enhances the yield of native enzyme while minimizing the yield of misfolded protein. These results suggest that GroE releases the subunits in forms capable of achieving the native structure faster than the forms initially bound by the chaperone. At higher temperatures, at which the native enzyme is stable but the dimerization reaction is diminished, GroE is unable to force the productive folding reaction to occur. However, the chaperone decreases the rate of formation of the heterodimerization-incompetent species, thereby enhancing the final yield of active enzyme when the temperature is reduced to the permissive range. Our results suggest a mechanism by which the chaperone functions to maximize the yield of the biologically active form of the protein while maintaining or even accelerating the essential rapid kinetics of folding reactions.

Implications of N and C-terminal proximity for protein folding.

We have investigated the proximity of the N and C termini in protein structures, and developed a model to test the theoretical possibility that proteins fold with their termini closely associated. On average, the distance between the termini is not significantly different from what would be expected based on chance. However, the theoretical model indicated that it is possible to greatly decrease the N-to-C terminal distance by allowing small (approximately six amino acid residues) solvent-accessible terminal fragments to move. Subsequent to this distance minimization method, more than 90% of the proteins studied had smaller-than-expected N-to-C distances, but only minor structural modification.

Process of biosynthetic protein folding determines the rapid formation of native structure.

Biosynthetic folding, beginning with the growing nascent chain and leading to the biologically active structure within its proper cellular context, is one function shared by all proteins. We show that the bacterial luciferase beta subunit reaches its final native form in the alphabeta heterodimer much more rapidly during biosynthetic folding than during refolding from urea. The rate of formation of active enzyme is determined by a short-lived folding intermediate, which is able to associate with the alpha subunit very rapidly following release from the ribosome. This intermediate appears to involve a transient interaction of the C-terminal region of the beta subunit, a region distant from the subunit interface, but intimately involved in heterodimerization. Refolding of the beta subunit under similar conditions proceeds much more slowly. We have characterized both pathways and show that the basic difference between biosynthetic folding and refolding from urea is that the newly synthesized beta subunit enters the folding pathway at a point beyond the slow, rate-determining step that limits the rate of the renaturation process and constitutes a kinetic trap. This mechanism embodies a major strategy, the avoidance of slow-folding intermediates and kinetic traps, that may be employed by many proteins to achieve fast and efficient biosynthetic folding.

Structure of the beta 2 homodimer of bacterial luciferase from Vibrio harveyi: X-ray analysis of a kinetic protein folding trap.

Luciferase, as isolated from Vibrio harveyi, is an alpha beta heterodimer. When allowed to fold in the absence of the alpha subunit, either in vitro or in vivo, the beta subunit of enzyme will form a kinetically stable homodimer that does not unfold even after prolonged incubation in 5 M urea at pH 7.0 and 18 degrees C. This form of the beta subunit, arising via kinetic partitioning on the folding pathway, appears to constitute a kinetically trapped alternative to the heterodimeric enzyme (Sinclair JF, Ziegler MM, Baldwin TO. 1994. Kinetic partitioning during protein folding yields multiple native states. Nature Struct Biol 1: 320-326). Here we describe the X-ray crystal structure of the beta 2 homodimer of luciferase from V. harveyi determined and refined at 1.95 A resolution. Crystals employed in the investigational belonged to the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions of a = 58.8 A, b = 62.0 A, and c = 218.2 A and contained one dimer per asymmetric unit. Like that observed in the functional luciferase alpha beta heterodimer, the major tertiary structural motif of each beta subunit consists of an (alpha/beta)8 barrel (Fisher AJ, Raushel FM, Baldwin TO, Rayment I. 1995. Three-dimensional structure of bacterial luciferase from Vibrio harveyi at 2.4 A resolution. Biochemistry 34: 6581-6586). The root-mean-square deviation of the alpha-carbon coordinates between the beta subunits of the hetero- and homodimers is 0.7 A. This high resolution X-ray analysis demonstrated that "domain" or "loop" swapping has not occurred upon formation of the beta 2 homodimer and thus the stability of the beta 2 species to denaturation cannot be explained in such simple terms. In fact, the subunit:subunit interfaces observed in both the beta 2 homodimer and alpha beta heterodimer are remarkably similar in hydrogen-bonding patterns and buried surface areas.

A plasmid vector and quantitative techniques for the study of transcription termination in Escherichia coli using bacterial luciferase.

We have developed a plasmid expression vector for the study of transcription terminators in Escherichia coli that utilizes the lux genes coding for the enzyme luciferase of the bioluminescent marine bacterium, Vibrio harveyi. The pBR322-derived plasmid, called pHV100, contains the E. coli lac promoter, the polylinker regions from the plasmid vector pUC18, and the V. harveyi lux genes. Insertion of transcription termination sites into the polylinker region results in decreased luciferase expression. Because the bioluminescence genes are not indigenous to E. coli, their expression can be studied in virtually any host strain without the complications of background activity. This facilitates sensitive measurements of terminator efficiency in hosts containing termination factor mutations. Bioluminescence can be easily monitored with high sensitivity, using a rapid photographic technique or a more quantitative photometric assay.

Individual alpha and beta subunits of bacterial luciferase exhibit bioluminescence activity.

The alpha subunit of luciferase, encoded by the luxA gene, and the beta subunit, encoded by the luxB gene, have been expressed independently in Escherichia coli. We have found that the individual subunits of the heterodimeric (alpha beta) enzyme have bioluminescence activity. Overexpression of the individual subunits in Escherichia coli at 37 degrees resulted in accumulation of large amounts of the specific subunit in the insoluble fraction, while expression at lower temperatures (20 degrees-26 degrees) resulted in accumulation of high levels of the individual subunits in the soluble fraction of the cell lysates. We were surprised to find that addition of n-decanal to extracts of cells carrying either the luxA gene or the luxB gene followed by injection of FMNH2, conditions of the standard luciferase assay, resulted in emission of significant bioluminescence. The occurrence of the activity in lysates of E. coli cells carrying the gene for only one subunit showed that the activity of the isolated subunits is not due to contamination of one subunit with trace amounts of the other. The observed bioluminescence activity is the result of reactions catalyzed by the alpha subunit in the absence of beta subunit and also by the beta subunit in the absence of the alpha subunit.

Active center studies on bacterial luciferase: modification of the enzyme with 2,4-dinitrofluorobenzene.

Bacterial luciferase catalyzes the mixed-function oxidation of a long-chain saturated aldehyde and FMNH2 to yield the carboxylic acid, FMN, and blue-green light. The enzyme was inactivated by 2,4-dinitrofluorobenzene (FDNB) with an observed second-order rate constant (k2(obsd) of 157 M-1 min-1 at pH 7.0, 25 degrees C; activity was not recovered upon treatment with 2-mercaptoethanol (thiolysis), demonstrating that the inactivation was the result of reaction with one or more amino groups. The dinitrophenyl (DNP) moiety was incorporated into the alpha subunit approximately twice as fast as it was incorporated into the beta subunit; the rate of inactivation was nearly identical with the rate of incorporation into the alpha beta dimer. The incorporation of 1 mol of DNP/alpha beta resulted in complete inactivation, demonstrating that modification of either alpha or beta is sufficient to cause inactivation. Incorporation of DNP into one subunit appeared to either block or decrease the rate of incorporation of DNP into the other subunit. The luciferase was protected from inactivation by binding of long-chain aldehydes or FMN. Following modification by FDNB, the enzyme had lost measurable FMNH2 binding. The apparent pKa of the amino groups, determined by analysis of the pH dependence of the inactivation reaction, was 9.4. This value is too high to allow correlation with the pH-activity profile of the enzyme [Nicoli, M. Z., Meighen, E. A., & Hastings, J. W. (1974) J. Biol. Chem. 249, 2385-2392]. The catalytic function, if any, for the reactive amino groups remains unknown.

Contribution of cotranslational folding to the rate of formation of native protein structure.

To compare the process of protein folding in the cell with refolding following denaturation in vitro, we have investigated and compared the kinetics of renaturation of a full-length protein upon dilution from concentrated urea with the rate of folding in the course of biosynthesis. Formation of enzymatically active bacterial luciferase, an alpha beta heterodimer, occurred 2 min after completion of beta-subunit synthesis in an Escherichia coli cell-free system. Renaturation of urea-denatured beta subunit, either in the presence of the cell-free protein synthesis system or in buffer solutions, proceeded more slowly. Cellular components present in the cell-free protein synthesis system slightly accelerated the rate of refolding of urea-unfolded beta subunit. The results indicate that the luciferase beta subunit begins the folding process cotranslationally and that cotranslational folding contributes to the rapid formation of the native structure in the cell.

Proteolytic inactivation of luciferases from three species of luminous marine bacteria, Beneckea harveyi, Photobacterium fischeri, and Photobacterium phosphoreum: evidence of a conserved structural feature.

Upon limited proteolysis of luciferases from the luminous marine bacteria Photobacterium fischeri, Photobacterium phosphoreum, and Beneckea harveyi, the rate of loss of luciferase activity is the same as the rate of loss of the heavier subunit of all three enzymes. It thus appears that the larger subunit of the luciferase from P. phosphoreum should be designated alpha based on its apparent homology with the alpha subunits of the luciferases from B. harveyi and P. fischeri. The luciferase from B. harveyi is more sensitive to chymotrypsin than to trypsin; the luciferases of the Photobacterium species are more sensitive to trypsin than to chymotrypsin. Proteolytic inactivation of all three luciferases results from hydrolysis of a few peptide bonds in the alpha subunit; the proteolytic fragments from the three luciferases in 0.50 M phosphate are approximately the same size, indicating that the three enzymes have a protease-labile region at about the same position in the primary structure of their alpha subunits. Phosphate stabilizes all three luciferases against inactivation by proteases. Formation and degradation of intermediate species derived from the alpha subunits are readily observable in all three luciferases. Phosphate alters both the rate of product formation and the sites of peptide bond scission. The beta subunits of the luciferases from the two Photobacterium species, unlike the enzyme of B. harveyi, appear to be degraded in buffers containing low concentrations of phosphate; in high-phosphate buffers, the beta subunits of all three luciferases appear to resist proteases. Analysis of native and chymotrypsin-inactivated P. fischeri and P. phosphoreum luciferases in the analytical ultracentrifuge indicates that, as with B. harveyi luciferase, the products of limited proteolysis do not dissociate under nondenaturing conditions. The fact that the luciferases from evolutionarily diverse species of luminous bacteria have protease-sensitive bonds in the same region of the alpha subunit that are stabilized by anions strongly suggests that the protease-labile region of the alpha subunit is either an integral component of or in close proximity to the active center.