Improvement of 2'-hydroxybiphenyl-2-sulfinate desulfinase, an enzyme involved in the dibenzothiophene desulfurization pathway, from Rhodococcus erythropolis KA2-5-1 by site-directed mutagenesis

In the microbial dibenzothiophene desulfurization pathway, 2'-hydroxybiphenyl-2-sulfinate is converted to 2-hydroxybiphenyl and sulfinate by desulfinase (DszB) at the last step, and this reaction is rate-limiting for the whole pathway. The catalytic activity and thermostability of DszB were enhanced by the two amino acid substitutions. Based on information on the 3-D structure of DszB and a comparison of amino acid sequences between DszB and reported thermophilic and thermostable homologs (TdsB and BdsB), two amino acid residues, Tyr63 and Gln65, were selected as targets to mutate and improve DszB. These two residues were replaced by several amino acids, and the promising mutant enzymes were purified and their properties were examined. Among the wild-type and mutant enzymes, Y63F had higher catalytic activity but similar thermostability, and Q65H showed higher thermostability but less catalytic activity and affinity for the substrate. To compensate for these drawbacks, the double mutant enzyme Y63F-Q65H was purified and its properties were investigated. This mutant enzyme showed higher thermostability without loss of catalytic activity or affinity for the substrate. These superior properties of the mutant enzyme have also been confirmed with resting cells harboring the mutant gene.     

Crystal structure and desulfurization mechanism of 2'-hydroxybiphenyl-2-sulfinic acid desulfinase

The desulfurization of dibenzothiophene in Rhodococcus erythropolis is catalyzed by two monooxygenases, DszA and DszC, and a desulfinase, DszB. In the last step of this pathway, DszB hydrolyzes 2'-hydroxybiphenyl-2-sulfinic acid into 2-hydroxybiphenyl and sulfite. We report on the crystal structures of DszB and an inactive mutant of DszB in complex with substrates at resolutions of 1.8A or better. The overall fold of DszB is similar to those of periplasmic substrate-binding proteins. In the substrate complexes, biphenyl rings of substrates are recognized by extensive hydrophobic interactions with the active site residues. Binding of substrates accompanies structural changes of the active site loops and recruits His(60) to the active site. The sulfinate group of bound substrates forms hydrogen bonds with side chains of Ser(27), His(60), and Arg(70), each of which is shown by site-directed mutagenesis to be essential for the activity. In our proposed reaction mechanism, Cys(27) functions as a nucleophile and seems to be activated by the sulfinate group of substrates, whereas His(60) and Arg(70) orient the syn orbital of sulfinate oxygen to the sulfhydryl hydrogen of Cys(27) and stabilize the negatively charged reaction intermediate. Cys, His, and Arg residues are conserved in putative proteins homologous to DszB, which are presumed to constitute a new family of desulfinases.     

Metabolic oxidation of the ethynyl group in 4-ethynylbiphenyl.

1. 4-Ethynylbiphenyl undergoes extensive metabolism in the rat and the rabbit, involving aromatic hydroxylation and oxidation of the ethynyl group. No metabolites containing the intact ethynyl group were detected. 2. In the rat unchanged 4-ethynylbiphenyl was concentrated initially in the adipose tissue. No other tissues accumulated significant amounts of radioactivity. 3. The major metabolites were the same in both the rat and the rabbit, namely 4'-hydroxybiphenyl-4-ylacetic acid (90-95% of dose) and biphenyl-4-ylacetic acid (2-10% of dose). 4. Excretion was slower in the rat than in the rabbit, probably because of greater biliary and faecal excretion in the rat. Biliary excretion and enterohepatic circulation of biphenyl-4-ylacetic acid and 4'-hydroxybiphenyl-4-ylacetic acid were demonstrated in the rat.     

Demonstration of the carbon-sulfur bond targeted desulfurization of benzothiophene by thermophilic Paenibacillus sp. strain A11-2 capable of desulfurizing dibenzothiophene

Paenibacillus sp. strain A11-2, which had been primarily isolated as a bacterial strain capable of desulfurizing dibenzothiophene to produce 2-hydroxybiphenyl at high temperatures, was found to desulfurize benzothiophene more efficiently than dibenzothiophene. The desulfurized product was identified as o-hydroxystyrene by GC-MS and 1H-NMR analysis. Benzothiophene was assumed to be degraded in a way analogous to the 4S pathway, which has been well-known as a mode of dibenzothiophene degradation. These results suggest that benzothiophene desulfurization may share at least partially the reaction mechanism with dibenzothiophene desulfurization.     

Biodegradation by immobilized bacteria in an airlift-loop reactor-influence of biofilm diffusion limitation

Naphthalene-2-sulfonate was degraded by submerse growing Pseudomonads in a chemostat culture. The kinetic parameters for the Monod equation, including Pirts maintenance energy, were calculated from these experiments regarding naphthalene-2-sulfonate as substrate and oxygene as cosubstrate. By immobilizing the bacteria on sand particles, the degradation of naphthalene-2-sulfonate was carried out in a specialy designed three-phase airlift-loop reactor in a completely fluidized state. From these experiments, the influence of biofilm diffusion limitation on reaction kinetics and criteria for stable biofilm formation on sand particles were obtained.     

Mineralization of the dibenzothiophene biodegradation products 3-hydroxy-2-formyl benzothiophene and dibenzothiophene sulfone.

Dibenzothiophene is degraded to 3-hydroxy-2-formyl benzothiophene by various bacteria, including a strain of Pseudomonas putida that also forms dibenzothiophene sulfone via an alternate pathway. By using these end products as substrates, mixed enrichment cultures that could degrade 3-hydroxy-2-formyl benzothiophene and dibenzothiophene sulfone with the formation of CO2 were established.     

Mineralization of the dibenzothiophene biodegradation products 3-hydroxy-2-formyl benzothiophene and dibenzothiophene sulfone

Dibenzothiophene is degraded to 3-hydroxy-2-formyl benzothiophene by various bacteria, including a strain of Pseudomonas putida that also forms dibenzothiophene sulfone via an alternate pathway. By using these end products as substrates, mixed enrichment cultures that could degrade 3-hydroxy-2-formyl benzothiophene and dibenzothiophene sulfone with the formation of CO2 were established.     

Reversible structural changes in a hydrophobic protein,elastin, as indicated by fluorescence probe analysis

Fluorescent probe analysis of purified elastin using 1-anilinonaphthalene-8-sulfonate has been used to investigate reversible structural changes that accompany stretching of this rubberlike protein. There is a specific binding of 1-anilinonaphthalene-8-sulfonate to elastin with a single dye molecule attached per 74,000 molecular-weight protein subunit. When labeled elastin is stretched, the intensity of the 1-anilinonaphthalene-8-sulfonate fluorescence decreases reversibly, and this decrease appears to be linked to an increase in the environmental polarity in the immediate vicinity of the bound dye molecule. The results of experiments carried out in H₂O and D₂O indicate that this polarity change is due to an increase in the exposure of the 1-anilinonaphthalene-8-sulfonate to water as the hydrophobic interior of the protein subunit is unfolded during stretching. The data are consistent with the proposal that the elastin network is a two-phase system of hydrophobic protein globules surrounded by free solvent spaces.     

Co-operative mutagenic actions of bisulfite and nitrogen nucleophiles.

The combined effect of bisulfite and a nitrogen nucleophile, i.e. semicarbazide, methoxyamine or hydroxylamine, to chemically modify cytosine and to cause mutation and inactivation of bacteriophage lambda was investigated. A rapid transamination of cytidine with each of the amines took place in the presence of bisulfite, and the reaction product was solely the N(4)-transaminated 5,6-dihydrocytidine-6-sulfonate. Modifications of cytidine with bisulfite alone and with the nitrogen nucleophile alone were much slower reactions than those using a combination of bisulfite and the nucleophile. Whereas the product of the modification with the bisulfite/semicarbazide, 5,6-dihydro-4-semicarbazido-2-ketopyrimidine ribofuranoside-6-sulfonate, is convertible to 4-semicarbazido-2-ketopyrimidine ribofuranoside by treatment with a phosphate buffer, the products of the modification with the bisulfite/methoxyamine and with the bisulfite/hydroxylamine, i.e. 4-methoxy-5,6-dihydrocytidine-6-sulfonate and 4-hydroxy-5,6-dihydrocytidine-6-sulfonate, were stable in phosphate buffer.Inactivation and the “clear” mutation of bacteriophage lambda were observed when the phage was treated with sodium bisulfite in the presence of semicarbazide, methoxyamine or hydroxylamine. Under the conditions used, only very small increases in the mutation frequency were obtained by treatment of the phage with bisulfite alone or with the base alone. It was concluded that the residues, 5,6-dihydro-4-semicarbazido-2-ketopyrimidine-6-sulfonate, 4-methoxy-5, 6-dihydrocytosine-6-sulfonate and 4-hydroxy-5,6-dihydrocytosine-6-sulfonate in DNA are the causes of the mutation.When phage that had been inactivated by the semicarbazide/bisulfite reagent was subsequently treated with a phosphate buffer, a reactivation took place. The rate of the reactivation increased as the concentration of phosphate in the buffer increased. This reactivation was not accompanied by change in the mutation frequency. No reactivation was observed after a similar incubation when the prior inactivation had been induced by either methoxyamine/bisulfite or hydroxylamine/bisulfite. These results indicate that the 4-semicarbazido-2-ketopyrimidine residue is also mutagenic but is less lethal than the corresponding 5,6-dihydro-6-sulfonate structure.These results offer the first clear example of the co-operative mutagenic action of two different reagents.     

Binding of Streptomyces pepsin inhibitor (acetyl-pepstatin) with chymosin (Rennin)

Chymosin (Rennin) was effectively purified using an AH-Sepharose 4B column. Binding of Streptomyces pepsin inhibitor (acetul-pepstatin) with chymosin was studied spectroscopically. The binding caused ultraviolet difference and CD spectral changes suggesting microenvironmental changes around tryptophan and/or tyrosine residue(s) in chymosin. The fluorescence intensity of a hydrophobic probe, 2-p-toluidinylnaphthalene-6-sulfonate, increased in the presence of chymosin and was further amplified when Streptomyces pepsin inhibitor was added to the chymosin-2-p-toluidinylnaphthalene-6-sulfonate solution. The binding and dissociation-rate constants between chymosin and the inhibitor were determined using 2-p-toluidinylhnaphthalene-6-sulfonate as a probe. The binding constant was determined from the binding and dissociation-rate constants, to be 3.1 . 10(7) M-1 at 25 degrees C, pH 5.5.     

O-esters of N-acylhydroxylamines: toxicity and enhancement of sister-chromatid exchange in chinese hamster ovary cells

2-Naphthohydroxamic acid, 4-N-butoxyphenylacetohydroxamic acid, and their O-sulfonate, O-formate, O-acetate, and O-propionate derivatives were studied for cytotoxicity and sister chromatid exchange (SCE) induction in Chinese hamster ovary (CHO) cells. 2-Naphthylisocyanate, 2-aminonaphthalene (2 Lossen rearrangement products of the O-sulfonate derivative of 2-naphthohydroxamic acid), and N-methyl-2-naphthohydroxamic acid were also studied. All of these chemicals were cytotoxic and significantly increased SCE frequency, although there was a lack of correlation between these 2 effects. 2-Naphthylisocyanate and 2-aminonaphthalene were not as cytotoxic nor as active in inducing SCEs as the O-sulfonate ester of 2-naphthohydroxamic acid suggesting that the cytotoxicity and SCE induction of the latter are not due to its decomposition products.     

Degradation of dibenzothiophene by Brevibacterium sp.DO

Dibenzothiophene, a polycyclic aromatic sulfur heterocycle, represents as a model compound the organic sulfur integrated in the macromolecular coal matrix. A pure culture of a Brevibacterium species was isolated, which is able to use dibenzothiophene as sole source of carbon, sulfur and energy for growth. During dibenzothiophene utilization sulfite was released in a stoichiometrical amount and was further oxidized to sulfate. Three metabolites of dibenzothiophene degradation were isolated and identified as dibenzothiophene-5-oxide, dibenzothiophene-5-dioxide and benzoate by cochromatography, UV spectroscopy and gas chromatographymass spectrometry analyses. Based on the identified metabolites a pathway for the degradation of dibenzothiophene by Brevibacterium sp. DO is proposed.Non-standard abbreviations DBT dibenzothiophene - PASH polycyclic aromatic sulfur heterocycle - PAH polycyclic aromatic hydrocarbons - GC-MS gas chromatography-mass spectrometry - HPLC high pressure liquid chromatography - IC ion chromatography     

Desulfurization of alkylated forms of both dibenzothiophene and benzothiophene by a single bacterial strain

Thirty-five bacterial strains capable of converting dibenzothiophene into 2-hydroxybiphenyl were isolated. Among them Rhodococcus erythropolis KA2-5-1 was chosen for further characterization because of its ability to retain high desulfurization activity stably. PCR cloning and DNA sequencing of a KA2-5-1 genomic DNA fragment showed that it was practically identical with dszABC genes from Rhodococcus sp. IGTS8, a representative carbon-sulfur-bond-targeted dibenzothiophene-degrading bacterium. KA2-5-1 desulfurized a variety of alkyl dibenzothiophenes through the specific cleavage of their C-S bonds. In addition, unexpectedly, KA2-5-1 also attacked alkyl benzothiophenes in a C-S-bond-targeted fashion. The purified monooxygenase, encoded by dszC of KA2-5-1, converted benzothiophene and dibenzothiophene into benzothiophene sulfone and dibenzothiophene sulfone, respectively, with the aid of an NADH-dependent oxidoreductase. This result raises the possibility that the same enzymatic step may be involved in desulfurization of alkylated forms of both dibenzothiophene and benzothiophene in KA2-5-1 cells.     

The interaction of collagen with the hydrophobic fluorescent probe-2-p-toluidinylnaphthalene-6-sulfonate.

Three kinds of fluorescence enhancement result from the interaction of 2-p-toluidinylnaphthalene-6-sulfonate and calf-skin collagen. They are negatively cooperative, independent, and highly cooperative fluorescence enhancement. In the independent region at pH 3.7, the binding number is about 36 moles of 2-p-toluidinylnaphthalene-6-sulfonate per mole of tropocollagen with a binding constant of 2.0 × 10⁴ M^?1; with ΔG = ?5.7 kcal/mole, ΔH = ?4.0 kcal/mole, and ΔS = 6 e.u. The pH dependence of fluorescence of native collagen shows that the deprotonated forms of the β and γ carboxyl groups of aspartic and glutamic acid decrease the intensity, possibly by charge repulsion of the negatively charged sulfonate group of 2-p-toluidinylnaphthalene-6-sulfonate. The positive charge of lysine is found to be unimportant in the interaction of 2-p-toluidinylnaphthalene-6-sulfonate with collagen. Fluorescence enhancement is caused mainly by the hydrophobic interactions of 2-p-toluidinylnaphthalene-6-sulfonate and collagen. Salt bridge formation between basic and acidic side chains in very low salt concentration may be detectable by 2-p-toluidinylnaphthalene-6-sulfonate fluorescence.     

The role of bisulfite in the debromination of 5-bromouracil. The debromination of 5-bromo-5,6-dihydrouracil-6-sulfonate

5-Bromouracil is dehalogenated in the presence of bisulfite buffers to yield uracil which subsequently adds bisulfite to form 5,6-dihydrouracil-6-sulfonate. Presumably, 5-bromo-5,6-dihydrouracil-6-sulfonate is an intermediate in uracil formation. Kinetic data indicate that the disappearance of 5-bromouracil in the presence of bisulfite buffers is second order with respect to total bisulfite concentration, thus indicating the participation of 2 moles of either sulfite or bisulfite in the overall reaction, Iodometric titrations of total bisulfite combined with spectral analysis of the various pyrimidine and dihydropyrimidine species present indicate that, in addition to the total bisulfite required to form 5,6-dihydrouracil-6-sulfonate, an additional mole of sulfite is consumed per mole of 5-bromouracil dehalogenated. These data combined with the finding that sulfate is generated during dehalogenation are indicative of a pathway for the dehalogenation of the intermediate 5-bromo-5,6-dihydro-uracil-6-sulfonate which involves the attack of sulfite either directly or via an intervening molecule of water to yield uracil. Subsequent reactions of halogen-containing intermediates yield sulfate and bromide as final products of the reaction.     

Identification of Disulfides from the Biodegradation of Dibenzothiophene

Several investigations have identified benzothiophene-2,3-dione in the organic solvent extracts of acidified cultures degrading dibenzothiophene via the Kodama pathway. In solution at neutral pH, the 2,3-dione exists as 2-mercaptophenylglyoxylate, which cyclizes upon acidification and is extracted as the 2,3-dione. The fate of these compounds in microbial cultures has never been determined. This study investigated the abiotic reactions of 2-mercaptophenylglyoxylate incubated aerobically in mineral salts medium at neutral pH. Oxidation led to the formation of 2-oxo-2-(2-thiophenyl)ethanoic acid disulfide, formed from two molecules of 2-mercaptophenylglyoxylate. Two sequential abiotic, net losses of both a carbon and an oxygen atom produced two additional disulfides, 2-oxo-2-(2-thiophenyl)ethanoic acid 2-benzoic acid disulfide and 2,2′-dithiosalicylic acid. The methods developed to extract and detect these three disulfides were then used for the analysis of a culture of Pseudomonas sp. strain BT1d grown on dibenzothiophene as its sole carbon and energy source. All three of the disulfides were detected, indicating that 2-mercaptophenylglyoxylate is an important, short-lived intermediate in the breakdown of dibenzothiophene via the Kodama pathway. The disulfides eluded previous investigations because of (i) their high polarity, being dicarboxylic acids; (ii) the need to lower the pH of the aqueous medium to <1 to extract them into an organic solvent such as dichloromethane; (iii) their poor solubility in organic solvents, (iv) their removal from organic extracts of cultures during filtration through the commonly used drying agent anhydrous sodium sulfate; and (v) their high molecular masses (362, 334, and 306 Da) compared to that of dibenzothiophene (184 Da).     

Effect of sulfonates on the esterase activity of carboxypeptidase A

The effects of sulfonates on the carboxypeptidase A catalyzed hydrolysis of the ester substrate benzoylglycyl-L-phenyllactate were determined. The modifiers examined were benzenesulfonate, p-toluenesulfonate, 2-phenylethane-sulfonate, methanesulfonate, ethanesulfonate, propanesulfonate, butanesulfonate, pentanesulfonate, hexanesulfonate, heptanesulfonate, and 2,2-dimethyl-2-silapentane-5-sulfonate. Sulfonate activators of peptide hydrolysis were inhibitors of esterase activity. Of the sulfonates studied, 2,2-dimethyl-2-silapentane-5-sulfonate was the most effective inhibitor. 2-Phenylethanesulfonate, hexanesulfonate, heptanesulfonate, and 2,2-dimethyl-2-silapentane-5-sulfonate exhibited uncompetitive inhibition. The remaining sulfonates either did not inhibit or the inhibition was too weak to properly characterize.     

Biodesulfurization of dibenzothiophene by Gordonia sp. AHV-01 and optimization by using of response surface design procedure

A novel desulfurizing bacterium has been isolated from oil-contaminated soils in Khuzestan. The ability for dibenzothiophene desulfurization and its biochemical pathway were investigated. The bacterium was identified as Gordonia sp. AHV-01 (Genbank Accession No HQ607780) by 16S rRNA gene sequencing. HPLC results and Gibb's assay were shown that dibenzothiophene desulfurized via 4S-pathway Maximum growth (0.426 g dry cells/L) and produced 2-hydroxybiphenyl (63.1 microM) were observed at 120 h of cultivation. By using of response surface design procedure the optimization of pH, temperature and rotary shaker round on the desulfurization reaction of isolate AHV-01 were performed. The optimum conditions were determined at pH of 7.0, temperature of 30 degrees C and rotary shaker round of 180 rpm. At these conditions, the dibenzothiophene desulfurization activity was increased and maximum 2-hydroxybiphenyl production was detected 70.29 microM at 96 h. According to these results, Isolate AHV-01 was capable to desulfurize dibenzothiophene via 4S-pathway and likely it can be useful to reduce organic sulfur contents of crude oil.     

Superoxide anion and drug-induced hemolysis.

Superoxide anion, either generated during the autooxidation of dihydroxyfumaria acid or by the interaction of 1,4-naphthoquinone-2-sulfonate and intracellular hemoglobin in red cells pretreated with the intracellular superoxide dismutase inhibitor, diethyldithiocarbamate, produces structural changes in red cells hemoglobin and hypotonic lysis. No evidence for lipid peroxidation was found in red cells exposed to either 1,4 naphthoquinone-2-sulfonate in the presence of diethyldithiocarbamate or to dihydroxyfumaric acid, although the membranes of these cells exposed to either 1,4 naphthoquinone-2-sulfonate in the presence of diethyldithiocarbamate or to dihydroxyfumaric acid, although the membranes of these cells retained a green pigment. These results suggest that superoxide anion reacts with cellular hemoglobin to form hemoglobin breakdown products which bind to the red cell membrane and thereby increase the osmotic fragility of the cell.     

Isolation and characterization of an apoprotein from the d less than 1.006 lipoproteins of human and canine lymph homologous with the rat A-IV apoprotein.

The singlet oxygen traps, 2,5-diphenylfurane and 1,3-diphenylisobenzofurane were oxidized to cis-benzoylethylene and o-dibenzoylbenzene during the decomposition of diisopropyl-N-nitrosamine catalyzed by peroxidase. Singlet oxygen quenchers inhibited this conversion and also the chemiluminescence accompaying the catalyzed reaction. The chemiluminescence is enhanced by 1,4-diazobicyclo (2.2.2) octane, fluorescein, eosin rhodamine B and rose bengal but little effect was detected in the presence of 9,10-dibromoanthracene-2-sulfonate, 9,10-diphenylanthracene-2-sulfonate and anthracene-2-sulfonate. An emission spectrum of the unsensitized reaction in 560 – 600 nm region was observed. It is concluded that singlet oxygen is formed during peroxidase catalyzed degradation of diisopropyl-N-nitrosamine.