Model construction for estimating potential vulnerability of Japanese soils to cadmium pollution based on intact soil properties.

Prediction of heavy metal bioavailability in intact soil is important to manage soil pollution risks. We developed a regression model for representative Japanese soils to judge their potential vulnerability to cadmium (Cd) pollution. We added four rates of Cd to 17 sample soils to mimic artificial contamination. After aging the contaminated soils, we measured Cd's bioavailability using the diffusive gradients in thin-films (DGT) technique. We then evaluated the relationships between bioavailability of Cd ([CdDGT]) and intact soil properties by statistical analyses. Cation exchange capacity (CEC) and pH emerged as significant factors to explain the cadmium bioavailability in Japanese soils. Specifically, lower CEC and lower pH were associated with higher [CdDGT], which poses a higher risk for soil ecosystems. The correlation between pH and [CdDGT] had a high dependence on [CdAdd], whereas that for CEC did not. Regression analysis also showed that the interaction between intact soil pH and spiked concentration ([CdAdd]) had a significant contribution to [CdDGT]. The regression model developed was rationally supported by a biotic ligand model. This simplified but realistic model would be useful in estimating the vulnerability of representative Japanese soils and determining the risk for Japanese soils in relation to Cd contamination.

Efficacy and safety of lomefloxacin on bacterial extraocular disease in the horse.

Lomefloxacin is a broad-spectrum fluoroquinolone antibiotic used for the treatment of bacterial extraocular disease. This study investigated the efficacy and safety of lomefloxacin eye drops for bacterial extraocular disease in horses. Lomefloxacin ophthalmic solution (0.3%) was instilled three times daily for 2-5 days in 65 horses diagnosed with bacterial extraocular disease based on clinical findings. Clinical observations and bacteriological examinations were performed at the start of treatment, 2 and 5 days after the start of treatment, and at the discontinuation or termination of treatment. Of the 65 horses, 64 were positive for bacteria, and 22 bacterial genera and 47 bacterial species were identified. The efficacy of lomefloxacin was evaluated in 63 horses; one horse with a negative culture and another with suspected bacterial contamination were excluded. Lomefloxacin was considered to be clinically effective in 54 horses. The major bacterial species identified were Staphylococcus aureus, Streptococcus equi subsp. zooepidemicus, Acinetobacter lwoffii, Staphylococcus xylosus, Staphylococcus vitulinus, Enterobacter agglomerans, Flavimonas oryzihabitans and Staphylococcus sciuri, with a cumulative disappearance rate of 80% or more at the termination of instillation. Excluding one horse that did not undergo a bacteriological examination, the remaining 62 horses were assessed for bacteriological outcome. Full or partial bacterial clearance was detected in 95% or more of the 62 horses. One of the 65 horses reported adverse events that had no causal relation with the eye drops. Our results showed that lomefloxacin is safe and effective for the treatment of bacterial extraocular disease in horses.

Construction of a novel expression vector in Pseudonocardia autotrophica and its application to efficient biotransformation of compactin to pravastatin, a specific HMG-CoA reductase inhibitor.

The novel plasmid vector (pTAOR4-Rev) suitable for gene expression in actinomycete strains of Pseudonocardia autotrophica was constructed from 2 P. autotrophica genetic elements, the novel replication origin and the acetone-inducible promoter. The replication origin was isolated from the endogenous plasmid of strain DSM 43082 and the acetone-inducible promoter was determined by analysis of the upstream region of an acetaldehyde dehydrogenase gene homologue in strain NBRC 12743. P. autotrophica strains transformed with pTAOR4-P450, carrying a gene for cytochrome P450 monooxygenase, expressed P450 from the acetone-inducible promoter, as verified by SDS-PAGE and spectral analysis. The biotransformation test of acetone-induced resting cells prepared from a strain of P. autotrophica carrying pTAOR4 that harbors a compactin (CP)-hydroxylating P450 gene revealed 3.3-fold increased production of pravastatin (PV), a drug for hypercholesterolemia. Biotransformation of CP by the same strain in batch culture yielded PV accumulation of 14.3 g/l after 100 h. The expression vector pTAOR4-Rev and its function-enhancing derivatives provide a versatile approach to industrial biotransformation by Pseudonocardia strains, which can be good hosts for P450 monooxygenase expression.

Structural evidence for enhancement of sequential vitamin D3 hydroxylation activities by directed evolution of cytochrome P450 vitamin D3 hydroxylase.

Vitamin D(3) hydroxylase (Vdh) isolated from actinomycete Pseudonocardia autotrophica is a cytochrome P450 (CYP) responsible for the biocatalytic conversion of vitamin D(3) (VD(3)) to 1α,25-dihydroxyvitamin D(3) (1α,25(OH)(2)VD(3)) by P. autotrophica. Although its biological function is unclear, Vdh is capable of catalyzing the two-step hydroxylation of VD(3), i.e. the conversion of VD(3) to 25-hydroxyvitamin D(3) (25(OH)VD(3)) and then of 25(OH)VD(3) to 1α,25(OH)(2)VD(3), a hormonal form of VD(3). Here we describe the crystal structures of wild-type Vdh (Vdh-WT) in the substrate-free form and of the highly active quadruple mutant (Vdh-K1) generated by directed evolution in the substrate-free, VD(3)-bound, and 25(OH)VD(3)-bound forms. Vdh-WT exhibits an open conformation with the distal heme pocket exposed to the solvent both in the presence and absence of a substrate, whereas Vdh-K1 exhibits a closed conformation in both the substrate-free and substrate-bound forms. The results suggest that the conformational equilibrium was largely shifted toward the closed conformation by four amino acid substitutions scattered throughout the molecule. The substrate-bound structure of Vdh-K1 accommodates both VD(3) and 25(OH)VD(3) but in an anti-parallel orientation. The occurrence of the two secosteroid binding modes accounts for the regioselective sequential VD(3) hydroxylation activities. Moreover, these structures determined before and after directed evolution, together with biochemical and spectroscopic data, provide insights into how directed evolution has worked for significant enhancement of both the VD(3) 25-hydroxylase and 25(OH)VD(3) 1α-hydroxylase activities.

Purification, characterization, and directed evolution study of a vitamin D3 hydroxylase from Pseudonocardia autotrophica.

Vitamin D(3) (VD(3)) is a fat-soluble prohormone that plays a crucial role in bone metabolism, immunity, and control of cell proliferation and cell differentiation in mammals. The actinomycete Pseudonocardia autotrophica is capable of bioconversion of VD(3) into its physiologically active forms, namely, 25(OH)VD(3) or 1alpha,25(OH)(2)VD(3). In this study, we isolated and characterized Vdh (vitamin D(3) hydroxylase), which hydroxylates VD(3) from P. autotrophica NBRC 12743. The vdh gene encodes a protein containing 403 amino acids with a molecular weight of 44,368Da. This hydroxylase was found to be homologous with the P450 belonging to CYP107 family. Vdh had the same ratio of the V(max) values for VD(3) 25-hydroxylation and 25(OH)VD(3) 1alpha-hydroxylation, while other enzymes showed preferential regio-specific hydroxylation on VD(3). We characterized a collection of Vdh mutants obtained by random mutagenesis and obtained a Vdh-K1 mutant by the combination of four amino acid substitutions. Vdh-K1 showed one-order higher VD(3) 25-hydroxylase activity than the wild-type enzyme. Biotransformation of VD(3) into 25(OH)VD(3) was successfully accomplished with a Vdh-expressed recombinant strain of actinobacterium Rhodococcus erythropolis. Vdh may be a useful enzyme for the production of physiologically active forms of VD(3) by a single cytochrome P450.

The effect of earthworms on copper fractionation of freshly and long-term polluted soils.

We investigated the effects of earthworm activity on the bioavailability of Cu in soil. The bioavailable fraction was estimated using sequential extraction, and the results of diethylenetriaminepentaacetic acid (DTPA) extraction were analyzed for comparison. Changes in the Cu fraction were compared in Cu-spiked soil (high bioavailability) and long-term polluted field soil (low bioavailability) with approximately equivalent total Cu concentrations. Earthworm activity decreased the bioavailable fraction in the Cu-spiked soil, where earthworm body Cu concentrations did not affect the bioavailable fraction. Soil pH was not a factor in the bioavailability differences between soils with and without earthworms in this study. The bioavailable fraction appears to be more heavily affected by biological and physical mechanisms than by soil pH. The two extraction methods showed different trends; the bioavailable fraction method was better than DTPA extraction, because the former gives clear insight into the aging process of Cu in soil.

Crystallization and preliminary X-ray diffraction studies of vitamin D3 hydroxylase, a novel cytochrome P450 isolated from Pseudonocardia autotrophica.

Vitamin D(3) hydroxylase (Vdh) is a novel cytochrome P450 monooxygenase isolated from the actinomycete Pseudonocardia autotrophica and consisting of 403 amino-acid residues. Vdh catalyzes the activation of vitamin D(3) via sequential hydroxylation reactions: these reactions involve the conversion of vitamin D(3) (cholecalciferol or VD3) to 25-hydroxyvitamin D(3) [25(OH)VD3] and the subsequent conversion of 25(OH)VD3 to 1alpha,25-dihydroxyvitamin D(3) [calciferol or 1alpha,25(OH)(2)VD3]. Overexpression of recombinant Vdh was carried out using a Rhodococcus erythropolis expression system and the protein was subsequently purified and crystallized. Two different crystal forms were obtained by the hanging-drop vapour-diffusion method at 293 K using polyethylene glycol as a precipitant. The form I crystal belonged to the trigonal space group P3(1), with unit-cell parameters a = b = 61.7, c = 98.8 A. There is one Vdh molecule in the asymmetric unit, with a solvent content of 47.6%. The form II crystal was grown in the presence of 25(OH)VD3 and belonged to the orthorhombic system P2(1)2(1)2(1), with unit-cell parameters a = 63.4, b = 65.6 c = 102.2 A. There is one Vdh molecule in the asymmetric unit, with a solvent content of 46.7%. Native data sets were collected to resolutions of 1.75 and 3.05 A for form I and form II crystals, respectively, using synchrotron radiation. The structure solution was obtained by the molecular-replacement method and model refinement is in progress for the form I crystal.

Efficient biotransformations using Escherichia coli with tolC acrAB mutations expressing cytochrome P450 genes.

We report here some efficient biotransformations using Escherichia coli strains with disruptions for the AcrAB-TolC efflux pump system. Biotransformations of compactin into pravastatin (6alpha-hydroxy-iso-compactin) were performed using E. coli strains with tolC and/or acrAB mutations expressing a cytochrome P450 (P450) gene. The production levels of pravastatin using strains with acrAB, tolC, and tolC acrAB mutations increased by 3.7-, 7.0-, and 7.1-fold, respectively. Likewise, the production levels of 25-hydroxy vitamin D3 and 25-hydroxy 4-cholesten 3-one using tolC acrAB mutant strains expressing an individual P450 gene increased by 2.2- and 16-fold, respectively. The enhancement of this biotransformation efficiency could be explained by increases in the intracellular amounts of substrates and the concentrations of active P450s. These results demonstrate that we have achieved versatile methods for efficient biotransformations using E. coli strains with tolC acrAB mutations expressing P450 genes.

Crystal structure of cytochrome P450 MoxA from Nonomuraea recticatena (CYP105).

Cytochrome P450 MoxA (P450moxA) from a rare actinomycete Nonomuraea recticatena belongs to the CYP105 family and exhibits remarkably broad substrate specificity. Here, we demonstrate that P450moxA acts on several luciferin derivatives, which were originally identified as substrates of the human microsomal P450s. We also describe the crystal structure of P450moxA in substrate-free form. Structural comparison with various bacterial and human microsomal P450s reveals that the P450moxA structure is most closely related to that of the fungal nitric oxide reductase P450nor (CYP55A1). Final refined model of P450moxA comprises almost all the residues, including the "BC-loop" and "FG-loop" regions pivotal for substrate recognition, and the current structure thus defines a well-ordered substrate-binding pocket. Clear electron density map reveals that the MES molecule is bound to the substrate-binding site, and the sixth coordination position of the heme iron is not occupied by a water molecule, probably due to the presence of MES molecule in the vicinity of the heme. The unexpected binding of the MES molecule might reflect the ability of P450moxA to accommodate a broad range of structurally diverse compounds.

Hydroxylation of oleanolic acid to queretaroic acid by cytochrome P450 from Nonomuraea recticatena.

A gene for cytochrome P450 (moxA) from Nonomuraea recticatena, coexpressed with camAB for pseudomonad redox partners in Escherichia coli, hydroxylated oleanolic acid to produce queretaroic acid. When we used the P450-induced whole-cell as a catalyst, only a small amount of queretaroic acid was produced, probably due to poor permeability of oleanolic acid into the E. coli cell. In an alternative approach with the cell-free reaction system, the conversion ratio increased up to 17%.

Hydroxylation of testosterone by bacterial cytochromes P450 using the Escherichia coli expression system.

Two hundred thirteen cytochrome P450 (P450) genes were collected from bacteria and expressed based on an Escherichia coli expression system to test their hydroxylation ability to testosterone. Twenty-four P450s stereoselectively monohydroxylated testosterone at the 2alpha-, 2beta-, 6beta-, 7beta-, 11beta-, 12beta-, 15beta-, 16alpha-, and 17-positions (17-hydroxylation yields 17-ketoproduct). The hydroxylation site usage of the P450s is not the same as that of human P450s, while the 2alpha-, 2beta-, 6beta-, 11beta-, 15beta-, 16alpha-, and 17-hydroxylation are reactions common to both human and bacterial P450s. Most of the testosterone hydroxylation catalyzed by bacterial P450s is on the beta face.

5-keto-D-gluconate production is catalyzed by a quinoprotein glycerol dehydrogenase, major polyol dehydrogenase, in gluconobacter species.

Acetic acid bacteria, especially Gluconobacter species, have been known to catalyze the extensive oxidation of sugar alcohols (polyols) such as D-mannitol, glycerol, D-sorbitol, and so on. Gluconobacter species also oxidize sugars and sugar acids and uniquely accumulate two different keto-D-gluconates, 2-keto-D-gluconate and 5-keto-D-gluconate, in the culture medium by the oxidation of D-gluconate. However, there are still many controversies regarding their enzyme systems, especially on D-sorbitol and also D-gluconate oxidations. Recently, pyrroloquinoline quinone-dependent quinoprotein D-arabitol dehydrogenase and D-sorbitol dehydrogenase have been purified from G. suboxydans, both of which have similar and broad substrate specificity towards several different polyols. In this study, both quinoproteins were shown to be identical based on their immuno-cross-reactivity and also on gene disruption and were suggested to be the same as the previously isolated glycerol dehydrogenase (EC 1.1.99.22). Thus, glycerol dehydrogenase is the major polyol dehydrogenase involved in the oxidation of almost all sugar alcohols in Gluconobacter sp. In addition, the so-called quinoprotein glycerol dehydrogenase was also uniquely shown to oxidize D-gluconate, which was completely different from flavoprotein D-gluconate dehydrogenase (EC 1.1.99.3), which is involved in the production of 2-keto-D-gluconate. The gene disruption experiment and the reconstitution system of the purified enzyme in this study clearly showed that the production of 5-keto-D-gluconate in G. suboxydans is solely dependent on the quinoprotein glycerol dehydrogenase.