Use of Gas Chromatography for Detecting Ornithine and Lysine Decarboxylase Activity in Bacteria

A gas-liquid chromatography (GLC) procedure for the detection of L-ornithine and L-lysine decarboxylase (EC 4.1.1.17 and EC 4.1.1.18, respectively) activities of bacteria was developed and evaluated against M?ller's method, a conventional biochemical test. Cultures were incubated for 2 to 4 h in a simple growth medium and tested by GLC for putrescine and cadaverine, the direct decarboxylation products of ornithine and lysine, respectively. Results obtained with various Enterobacteriaceae, pseudomonads, and vibrios showed that the GLC procedure was superior to the conventional test; clear, well-defined results were obtained within 3 to 5 h, even with cultures which gave weak, delayed, or variable reactions by M?ller's method. This GLC procedure for the determination of decarboxylase reactions would be useful in microbiological laboratories for culture identification and for various other enzymatic studies.     

Interference Between Two Adeno-associated Satellite Viruses: a Three-Component System

Adenovirus-associated satellite viruses interfere with the replication of their helper adenoviruses. According to a previous report, this interference is not mediated by interferon. A three-component system comprising simian adenovirus SV15 and satellites types 1 and 4 was studied to determine whether satellite viruses also interfere with one another. Satellite type 1 interfered with the replication of type 4 and vice versa. The degree of interference was directly proportional to the dose of interfering satellite. The events leading to mutual satellite interference were operative during the first 12 hr of replication, the period associated with active synthesis of viral deoxyribonucleic acid.     

pH-induced structural changes regulate histidine decarboxylase activity in Lactobacillus 30a

Histidine decarboxylase (HDC) from Lactobacillus 30a produces histamine that is essential to counter waste acids, and to optimize cell growth. The HDC trimer is active at low pH and inactive at neutral to alkaline pH. We have solved the X-ray structure of HDC at pH 8 and revealed the novel mechanism of pH regulation. At high pH helix B is unwound, destroying the substrate binding pocket. At acid pH the helix is stabilized, partly through protonation of Asp198 and Asp53 on either side of the molecular interface, acting as a proton trap. In contrast to hemoglobin regulation, pH has a large effect on the tertiary structure of HDC monomers and relatively little or no effect on quaternary structure.     

Expression and characterization of Lactobacillus 30a histidine decarboxylase in Escherichia coli

The genes coding for histidine decarboxylase from a wild-type strain and an autoactivation mutant strain of Lactobacillus 30a have been cloned and expressed in Escherichia coli. The mutant protein, G58D, has a single Asp for Gly substitution at position 58. The cloned genes were placed under control of the beta-galactosidase promoter and the products are natural length, not fusion proteins. The enzyme kinetics of the proteins isolated from E. coli are comparable to those isolated from Lactobacillus 30a. At pH 4.8 the Km of wild-type enzyme is 0.4 mM and the kcat = 2800 min-1; the corresponding values for G58D are 0.5 mM and 2750 min-1. The wild-type and G58D have autoactivation half-times of 21 and 9 h respectively under pseudophysiological conditions of 150 mM K+ and pH 7.0. At pH 7.6 and 0.8 M K+ the half-times are 4.9 and 2.9 h. The relatively slow rate of autoactivation for purified protein and the differences in cellular and non-cellular activation rates, coupled with the fact that wild-type protein is readily activated in wild-type Lactobacillus 30a but poorly activated in E. coli, suggest that wild-type Lactobacillus 30a contains a factor, possibly an enzyme, that enhances the activation rate.     

The Molecular Structure of Ornithine Acetyltransferase from Mycobacterium tuberculosis Bound to Ornithine, a Competitive Inhibitor

Mycobacterium tuberculosis ornithine acetyltransferase (Mtb OAT; E.C. 2.3.1.35) is a key enzyme of the acetyl recycling pathway during arginine biosynthesis. It reversibly catalyzes the transfer of the acetyl group from N-acetylornithine (NAORN) to l-glutamate. Mtb OAT is a member of the N-terminal nucleophile fold family of enzymes. The crystal structures of Mtb OAT in native form and in its complex with ornithine (ORN) have been determined at 1.7 and 2.4 Å resolutions, respectively. ORN is a competitive inhibitor of this enzyme against l-glutamate as substrate. Although the acyl-enzyme complex of Streptomyces clavuligerus ornithine acetyltransferase has been determined, ours is the first crystal structure to be reported of an ornithine acetyltransferase in complex with an inhibitor. ORN binding does not alter the structure of Mtb OAT globally. However, its presence stabilizes the three C-terminal residues that are disordered and not observed in the native structure. Also, stabilization of the C-terminal residues by ORN reduces the size of the active-site pocket volume in the structure of the ORN complex. The interactions of ORN and the protein residues of Mtb OAT unambiguously delineate the active-site residues of this enzyme in Mtb. Moreover, modeling studies carried out with NAORN based on the structure of the ORN-Mtb OAT complex reveal important interactions of the carbonyl oxygen of the acetyl group of NAORN with the main-chain nitrogen atom of Gly128 and with the side-chain oxygen of Thr127. These interactions likely help in the stabilization of oxyanion formation during enzymatic reaction and also will polarize the carbonyl carbon-oxygen bond, thereby enabling the side-chain atom O^γ1 of Thr200 to launch a nucleophilic attack on the carbonyl-carbon atom of the acetyl group of NAORN.     

Crystallization and molecular symmetry of ornithine decarboxylase from Lactobacillus 30a

Ornithine decarboxylase from Lactobacillus 30a is representative of the large subunit (80 kDa), oligomeric, pyridoxal phosphate-dependent amino-acid decarboxylases. Yellow crystals of ornithine decarboxylase are obtained from polyethylene glycol solutions and belong to space group P6 with unit cell constants a = b = 194.9 and c = 97.44 A, alpha = beta = 90 degrees and gamma = 120 degrees, V = 3.21 x 10(6) A3. Still photographs show reflections at better than 2.4-A resolution. Electron micrographs reported by Guirard and Snell (Guirard, B.M., and Snell, E.E. (1980) J. Biol. Chem. 255, 5960-5964) reveal that the ornithine decarboxylase dodecamer is a hexagonally shaped particle with a point-to-point distance of approximately 210 A and a thickness of approximately 70 A. The crystallographic unit cell can thus accommodate one 10(6)-Da dodecamer (Vm = 3.2 A3/Da), implying that a dimer occupies an asymmetric unit. Tanaka rotation function analysis, using native data (5-7 A) collected from three crystals, reveals that the particle has the expected 622 molecular symmetry with molecular 2-fold axes lying at 20 degrees and 50 degrees from a in the a-b plane. A search for suitable heavy atom derivatives is underway.     

Histidine Decarboxylaseless Mutants of Lactobacillus 30a: Isolation and Growth Properties

Mutants of Lactobacillus 30a deficient in their ability to form an inducible histidine decarboxylase (EC 4.1.1.22) were selected by plating nitrosoguanidine-treated cultures on a medium containing histidine and methyl red. Wild-type organisms produce histamine, thus raising the pH and forming yellow colonies; mutant colonies remain red. In the presence of added histidine, decarboxylase-producing cultures grow more heavily than mutant cultures when the initial pH of the growth medium is low or when the lactic acid produced lowers the pH to growth-limiting values. Addition of the decarboxylation products, histamine and carbon dioxide, did not favor growth in crude medium.     

Characterization of plantaricin KW30, a bacteriocin produced by Lactobacillus plantarum

A protease-sensitive antibacterial substance, produced by a strain of Lactobacillus plantarum isolated from fermented corn, was classified as a bacteriocin and designated plantaricin KW30. The bacteriocin was stable to heat, pH and treatment with surfactants, and unaffected by α-amylase, lipase or lysozyme. Plantaricin KW30 exhibited a bactericidal and non-bacteriolytic mode of action against indicator cells, and inhibitory activity was limited to other lactobacilli. Maximum production was in MRS broth, and coincided with the onset of stationary phase under conditions of low pH and high cell numbers. In a complex medium bacteriocin production was enhanced by the presence of sodium acetate and Tween 80. Curing experiments gave derivatives that no longer produced the bacteriocin but retained immunity to it. These Bac derivatives showed the same plasmid pattern as the parent strain suggesting a chromosomal location for the genes for bacteriocin production.     

Isotope effect studies of the pyruvate-dependent histidine decarboxylase from Lactobacillus 30a

The decarboxylation of histidine by the pyruvate-dependent histidine decarboxylase of Lactobacillus 30a shows a carbon isotope effect of k12/k13 = 1.0334 +/- 0.0005 and a nitrogen isotope effect k14/k15 = 0.9799 +/- 0.0006 at pH 4.8, 37 degrees C. The carbon isotope effect is slightly increased by deuteriation of the substrate and slightly decreased in D2O. The observed nitrogen isotope effect indicates that the imine nitrogen in the substrate-Schiff base intermediate complex is ordinarily protonated, and the pH dependence of the carbon isotope effect indicates that both protonated and unprotonated forms of this intermediate are capable of undergoing decarboxylation. As with the pyridoxal 5'-phosphate dependent enzyme, Schiff base formation and decarboxylation are jointly rate-limiting, with the intermediate histidine-pyruvate Schiff base showing a decarboxylation/Schiff base hydrolysis ratio of 0.5-1.0 at pH 4.8. The decarboxylation transition state is more reactant-like for the pyruvate-dependent enzyme than for the pyridoxal 5'-phosphate dependent enzyme. These studies find no particular energetic or catalytic advantage to the use of pyridoxal 5'-phosphate over covalently bound pyruvate in catalysis of the decarboxylation of histidine.     

Structure and cooperativity of a T-state mutant of histidine decarboxylase from Lactobacillus 30a

Histidine decarboxylase (HDC) from Lactobacillus 30a converts histidine to histamine, a process that enables the bacteria to maintain the optimum pH range for cell growth. HDC is regulated by pH; it is active at low pH and inactive at neutral to alkaline pH. The X-ray structure of HDC at pH 8 revealed that a helix was disordered, resulting in the disruption of the substrate-binding site. The HDC trimer has also been shown to exhibit cooperative kinetics at neutral pH, that is, histidine can trigger a T-state to R-state transition. The D53,54N mutant of HDC has an elevated Km, even at low pH, indicating that the enzyme assumes the low activity T-state. We have solved the structures of the D53,54N mutant at low pH, with and without the substrate analog histidine methyl ester (HME) bound. Structural analysis shows that the apo-D53,54N mutant is in the inactive or T-state and that binding of the substrate analog induces the enzyme to adopt the active or R-state. A mechanism for the cooperative transition is proposed.     

Evidence of a Restriction/Modification System in Lactobacillus delbrueckii subsp. lactis CNRZ 326

Lactobacillus delbrueckii subsp. lactis (Lb. lactis) CNRZ 326 is widely used in the propagation of Lb. delbrueckii bacteriophages. In this study, evidence is presented that this strain possesses a restriction-modification (R/M) system. The mitomycin C-induced temperate bacteriophage lb539 has a reduced efficiency of plaquing (EOP) on CNRZ 326 cells (EOP = 10⁻³), but after several passages on this strain, or on the indicator strain Lb. lactis LKT, the recovered phages (phages lb539.326 and lb539.LKT) have an EOP equal to 1. Restrictive development on CNRZ 326 was also observed after phage lb539.326 was propagated on the strain Lb. lactis CRL 934. The R/M system was also active against the virulent Lb. delbrueckii phage ll-h. Plasmid DNA was not detected in CNRZ 326, which suggests that the R/M system described is chromosomally encoded. Received: 11 September 1997 / Accepted: 21 October 1997     

Evidence for a Plasmid-Linked Restriction-Modification System in Lactobacillus helveticus

The presence of a restriction-modification (R/M) system against two bacteriophages, 328-B1 and hv, was demonstrated in three Lactobacillus helveticus strains, CNRZ 1094, CNRZ 1095, and CNRZ 1096. In addition, the burst size of phage 328-B1 in the three restrictive strains CNRZ 1094, CNRZ 1095, and CNRZ 1096 was reduced with respect to the values obtained in its propagating strain, CNRZ 328. Heating at 60°C did not inactivate the R/M system. Nonrestrictive variants from CNRZ 1094 were easily obtained under several culture conditions, but treatment with novobiocin at 42°C followed by storage at −20°C resulted in drastic elimination of the R⁺/M⁺ phenotype from all clones tested. Electrophoretic analysis of CNRZ 1094 nonrestrictive variants revealed the concomitant loss of a 34-kb plasmid. Four EcoRI fragments from the 34-kb plasmid were cloned in the Escherichia coli vector pACYC184. The use of one or several of these fragments as probes confirmed the plasmidic location of the genes responsible for the R/M system. These probes also showed the presence of R/M plasmids in the two other restrictive strains, CNRZ 1095 and CNRZ 1096. Lactose-fermenting ability and/or proteolytic capacity was not linked to the 34-kb plasmid.     

Structure determination of histidine decarboxylase from Lactobacillus 30a at 3.0 A resolution

The crystal structure of histidine decarboxylase from Lactobacillus 30a has been determined by X-ray diffraction methods to a resolution of 3.0 A. This protein is a pyruvoyl-dependent enzyme that is formed by an unusual self-activation process. The structure was determined from an electron density map calculated using multiple isomorphous replacement phases from two heavy-atom derivatives and included contributions from anomalous scattering measurements. The final mean figure of merit was 0.79, based on 28,805 independent reflections. The molecule has an (alpha beta)6 subunit composition and crystallizes in the space group 14122 with a = b = 221.7 A and c = 107.1 A. There is one (alpha beta)3 half molecule per asymmetric unit. The (alpha beta)6 particle is dumbbell-shaped, with each (alpha beta)3 unit being approximately spherical, with a diameter of about 65 A. There is a large central cavity approximately 30 A deep around the molecular 3-fold axis of the (alpha beta)3 unit. The 3-fold related active site pockets are located around the bottom of this cavity and are separated from each other by a distance of approximately 23 A. The inner portion of each (alpha beta) unit, which lies near the interface between the two (alpha beta)3 particles, consists mainly of random coil with several small helical and sheet regions. The outer region of each (alpha beta) unit has an unusual structure consisting of two overlapping, predominantly antiparallel beta-pleated sheets, lined on each side by an alpha-helix. The walls of the central cavity are formed by the 3-fold repeat of two strands from this beta-sandwich structure and one of the helices.     

Adding a Lysine Mimic in the Design of Potent Inhibitors of Histone Lysine Methyltransferases

Dynamic histone lysine methylation involves the activities of modifying enzymes (writers), enzymes removing modifications (erasers), and readers of the histone code. One common feature of these activities is the recognition of lysines in methylated and unmethylated states, whether they are substrates, reaction products, or binding partners. We applied the concept of adding a lysine mimic to an established inhibitor (BIX-01294) of histone H3 lysine 9 methyltransferases G9a and G9a-like protein by including a 5-aminopentyloxy moiety, which is inserted into the target lysine-binding channel and becomes methylated by G9a-like protein, albeit slowly. The compound enhances its potency in vitro and reduces cell toxicity in vivo. We suggest that adding a lysine or methyl-lysine mimic should be considered in the design of small-molecule inhibitors for other methyl-lysine writers, erasers, and readers.