Xanthobacter Py2 Research Articles

Antibacterial properties of the extract of Abelmoschus esculentus

In this study, antimicrobial properties of both lyophilized and fresh water extracts of the okra pods were assessed against Rhodococcus erythropolis and R. opacus, Mycobacterium sp. and M. aurum, Staphylococcus aureus, Escherichia coli, and Xanthobacter Py2. The extracts were effective against all bacterial strains tested, except R. erythropolis and the fresh extract displayed better antimicrobial properties than the lyophilized extract. A fresh extract concentration of 97.7 mg/mL was sufficient to kill all S. aureus cells, which is a worldwide source of nosocomial infection. The extract was also effective in inhibiting the growth of both Mycobacterium strains, X. Py2 and S. aureus, but was ineffective against R. erythropolis and E. coli. The lipid fraction of the okra gum was found to be responsible for the antibacterial properties and the protein and polysaccharide fractions displayed no antimicrobial activity. The two major constituents of the lipid fraction, palmitic and stearic acids, were apparently responsible for the antimicrobial properties of the okra extract.

Solubility of Ethene in Water and in a Medium for the Cultivation of a Bacterial Strain

The solubility of ethene in water and in the fermentation medium of Xanthobacter Py2 was determined with a Ben-Naim−Baer type apparatus. The solubility measurements were carried out in the temperature range of (293.15 to 323.15) K and at atmospheric pressure with a precision of about ± 0.3 %. The Ostwald coefficients, the mole fractions of the dissolved ethene, at the gas partial pressure of 101.325 kPa, and the Henry coefficients, at the water vapor pressure, were calculated using accurate thermodynamic relations. A comparison between the solubility of ethene in water and in the cultivation medium has shown that this gas is about 2.4 % more soluble in pure water. On the other hand, from the solubility temperature dependence, the Gibbs energy, enthalpy, and entropy changes for the process of transferring the solute from the gaseous phase to the liquid solutions were also determined. Moreover, the perturbed-chain statistical associating fluid theory equation of state (PC-SAFT EOS) model was used for the pr...

Principal component analysis applied to bacterial cell behaviour in the presence of organic solvents

The behaviour of cells of Rhodococcus erythropolis DCL14, Xanthobacter Py2, Arthrobacter simplex and Mycobacterium sp. NRRL B-3805, in biphasic systems containing different organic solvents was evaluated and compared. The data, obtained mainly by fluorescence microscopy and image analysis, was interpreted using principal components analysis (PCA). With this technique, the variability of the data could be summarised in 7 components, representing 75.8% of the variance of the data. Over a third of the variance could be explained by the first two principal components which represent solvent toxicity. Apparently this is the major factor influencing cell behaviour in an organic:aqueous system. However, factors such as substrate concentration, cell adaptation ability (resulting in morphological changes and aggregation or separation of cells) and membrane composition (specific to each strain) also play an important role in cell resistance to solvent toxicity. The results regarding cell shape indicate that loss of viability occurs, in the tested bacterial strains, after incorporation of molecules of solvent in the cellular membrane. This should result in an increase in membrane fluidity, and thus, in an alteration of cell shape. The ability to form “self-defence” clusters was observed to be different amongst the four strains. X. Py2 showed, in general, a low tendency to form aggregates under the tested conditions; A. simplex and R. erythropolis aggregated mainly in the presence of low log P solvents; and Mycobacterium. sp. cells showed a high ability to aggregate.

Solubility of 1-butene in water and in a medium for cultivation of a bacterial strain

Solubility measurements of 1-butene in water, from 20 to 50°C and at atmospheric pressure, were carried out using a Ben-Naim/Baer-type apparatus. The experimental results have a precision of about ±0.3%. Using accurate thermodynamic relations, the Ostwald coefficients at the experimental conditions and at infinite dilution, the mole fractions of the dissolved gas at the gas partial pressure of 101.325 kPa and the Henry coefficients at the water vapor pressure were calculated. The mole fraction of dissolved gas were fitted to the Clarke, Glew, and Weiss equation and thermodynamic quantities, standard molar Gibbs energy, entropy, and enthalpy changes, for the process of transferring the 1-butene molecules from the gaseous to the water phase, were computed. Moreover, solubility measurements of 1-butene in an aqueous medium for the cultivation of Xanthobacter Py2 in the same temperature range were also performed at atmospheric pressure. These solubility data are approximately 2.6% lower than those observed in pure water.

Two short-chain dehydrogenases confer stereoselectivity for enantiomers of epoxypropane in the multiprotein epoxide carboxylating systems of Xanthobacter strain Py2 and Nocardia corallina B276.

Epoxide carboxylase from the bacterium Xanthobacter strain Py2 is a multicomponent enzyme system which catalyzes the pyridine nucleotide-dependent carboxylation of aliphatic epoxides to beta-ketoacids as illustrated by the reaction epoxypropane + CO2 + NADPH + NAD+ --> acetoacetate + H+ + NADP+ + NADH. The combination of four distinct proteins, designated components I-IV, are required for the reconstitution of epoxide carboxylase activity with racemic mixtures of short-chain (C3-C5) terminal epoxyalkanes. In this work, components III and IV of the epoxide carboxylase system are shown to confer specificity for epoxyalkane enantiomers. Components I-III supported the carboxylation of (R)-epoxypropane, while components I, II, and IV supported the carboxylation of (S)-epoxypropane. At fixed concentrations of components I and II, the rates of (R)- and (S)-epoxypropane carboxylation saturated with increasing concentrations of component III or IV to give identical maximal rates for the two epoxide substrates. (S)-Epoxypropane was an inactivator of (R)-epoxypropane carboxylation by components I- III, while (R)-epoxypropane was an inactivator of (S)-epoxypropane carboxylation by components I, II, and IV. These inactivating effects were fully reversed upon the addition of the correct complementing dehydrogenase component. Amino acid sequence analysis of components III and IV demonstrates that they belong to the short-chain dehydrogenase/reductase (SDR) family of enzymes. Both components contain highly conserved residues within the coenzyme binding fold and catalytic regions found in SDR enzymes. Components III and IV are proposed to catalyze the NAD+-dependent abstraction of a hydride from a chiral secondary alcohol-like intermediate bound to the active site component of the enzyme system to form the corresponding beta-ketone intermediate. A multicomponent epoxide carboxylase system was purified to homogeneity from Nocardia corallina B276, a bacterium phylogenetically unrelated to Xanthobacter Py2, and found to consist of four proteins with functions identical to those of the Xanthobacter Py2 system. The stereoselective dehydrogenases of the Xanthobacter epoxide carboxylase system were able to substitute for the corresponding components of the N. corallina system when using (R)- and (S)-epoxypropane as substrates, and vice versa. These results provide the first demonstration of the involvement of stereospecific dehydrogenases in aliphatic epoxide metabolism and provide new insights into microbial strategies for the utilization of chiral organic molecules.

Purification and characterization of a flavoprotein involved in the degradation of epoxyalkanes by Xanthobacter Py2.

Recently a newly discovered pyridine nucleotide-disulfide oxidoreductase was reported to be essential for the degradation of epoxyalkanes by the Xanthobacter Py2 [Swaving, J., De Bont, J. A. M., Westphal, A. & De Kok, A. (1996) J. Bacteriol. 178, 6644-6646]. The disulfide oxidoreductase has now been purified from propene-grown Xanthobacter Py2. This enzyme (component II) is a NADPH-dependent FAD-containing homodimeric protein. The physiological substrate for this enzyme is unknown. The enzyme was active with the following dithiol substrates in decreasing order: 1,3-propanedithiol, reduced lipoamide and dithiothreitol, and inactive with glutathione and monothiols. In the reversed direction, only activity with 5,5'-dithiobis(2-nitrobenzoate) could be measured. Compared with other disulfide reductases it has a high activity with 5,5'-dithiobis(2-nitrobenzoate) and a low diaphorase and oxidase activity. Steady-state kinetic studies at pH 8.5 with 1,3-propanedithiol show that the enzyme operates by a ternary complex mechanism in the direction of NADP+ reduction. Anaerobic incubation of the enzyme with 1,3-propanedithiol resulted in slow reduction of the enzyme to yield the thiolate-FAD charge-transfer complex, the rate depending on the pH. At pH 7, where reduction was not detectable within 2 h, rapid mixing of NADP+ with the enzyme-propanedithiol mixture resulted in the formation of a complex between the reduced enzyme and NADP+ within the dead time of the instrument (5.6 ms). This is followed by slow formation of NADPH, concomitant with the appearance of the flavin C(4a)-thiol adduct, as judged from the spectral changes. This suggests that the rate-limiting step is the transfer of a hydride ion from the half-reduced enzyme to NADP+. Stopped-flow experiments involving reduction by NADPH show a biphasic behavior. The rapid formation (k(obs) = 40 s(-1)) of a transient intermediate with little absorption decrease at 460 nm and long wavelength absorption was followed by the slow formation (k(obs) = 4 s(-1)) of a species characterized as the thiolate-FAD charge-transfer complex with bound NADP+. Some formation of the FAD C(4a)-thiol adduct was also observed. Photoreduction in the presence of deazaflavin results in rapid bleaching at 450 nm, followed by the slow formation of a stable semiquinone. Full reduction could not be achieved, either by photoreduction or with NADPH, and was incomplete even with dithionite or NADPH in the presence of arsenite. The results indicate a low redox potential of the FAD and a slow rate of electron transfer from the pyridine nucleotide to the redox active disulfide and vice versa. From a sequence alignment with other disulfide reductases, it appears that the active site His-Glu diad is absent in this enzyme. The kinetic and spectral features described above will be discussed in this context.

The alkene monooxygenase from Xanthobacter Py2 is a binuclear non-haem iron protein closely related to toluene 4-monooxygenase

The genes encoding the six polypeptide components of the alkene monooxygenase from Xanthobacter Py2 have been sequenced. The predicted amino acid sequence of the first ORF shows homology with the iron binding subunits of binuclear non-haem iron containing monooxygenases including benzene monooxygenase, toluene 4-monooxygenase (>60% sequence similarity) and methane monooxygenase (>40% sequence similarity) and that the necessary sequence motifs associated with iron co-ordination are also present. Secondary structure prediction based on the amino acid sequence showed that the predominantly α-helical structure that surrounds the binuclear iron binding site was conserved allowing the sequence to be modelled on the co-ordinates of the methane monooxygenase α-subunit. Significant differences in the residues forming the hydrophobic cavity which forms the substrate binding site are discussed with reference to the differences in reaction specificity and stereospecificity of binuclear non-haem iron monooxygenases.

Purification to Homogeneity and Reconstitution of the Individual Components of the Epoxide Carboxylase Multiprotein Enzyme Complex from Xanthobacter Strain Py2

Epoxide metabolism in the aerobic bacterium Xanthobacter strain Py2 proceeds by an NADPH- and NAD+-dependent carboxylation reaction that forms beta-keto acids as products. Epoxide carboxylase, the enzyme catalyzing this reaction, was resolved from the soluble fraction of cell-free extracts into four protein components that are obligately required for functional reconstitution of epoxide carboxylase activity. One of these components, component II, has previously been purified and characterized as an NADPH:disulfide oxidoreductase. In the present study, the three additional epoxide carboxylase components have been purified to homogeneity and characterized. These component proteins are as follows: component I, a homohexameric protein consisting of 41.7-kDa subunits; component III, a dimeric protein consisting of 26.0- and 26.2-kDa polypeptides; and component IV, a dimeric protein consisting of a single 25.4-kDa polypeptide. Component I contained 5 mol of tightly bound zinc per mol of protein. Component I was specifically inactivated by methylepoxypropane, a time-dependent irreversible inactivator of epoxide carboxylase activity, suggesting that this component plays an integral role in epoxide binding and activation. No metals or organic cofactors were detected for components III and IV. The molecular weights, N-terminal sequences, and amino acid compositions of the purified epoxide carboxylase components were determined and found to correlate with open reading frames within and adjacent to a cloned fragment of DNA that complements Xanthobacter Py2 mutants defective in epoxide degradation. Using the purified epoxide carboxylase system, epoxide carboxylation was found to be stoichiometrically coupled to the transhydrogenation of pyridine nucleotide cofactors according to the following equation: epoxypropane + CO2 + NADPH + NAD+ --> acetoacetate + H+ + NADP+ + NADH.

Alkene Monooxygenase from Xanthobacter Strain Py2

Alkene monooxygenase from Xanthobacter strain Py2 is an inducible enzyme that catalyzes the O2- and NADH-dependent epoxidation of short chain (C2 to C6) alkenes to their corresponding epoxides as the initial step in the utilization of aliphatic alkenes as carbon and energy sources. In the present study, alkene monooxygenase has been resolved from the soluble fraction of cell-free extracts into four components, each of which has been purified to homogeneity, that are obligately required for alkene epoxidation activity. The four required components are 1) a monomeric 35.5-kDa protein containing 1 mol of FAD and a probable 2Fe-2S center; 2) a 13.3-kDa ferredoxin containing a Rieske-type 2Fe-2S cluster; 3) an 11-kDa monomeric protein that contains no detectable cofactors; and 4) a 212-kDa alpha2beta2gamma2 multimeric protein containing four atoms of nonheme iron. The 35.5-kDa protein has been characterized as an NADH reductase. The physiological electron acceptor for the reductase was the Rieske-type ferredoxin, which is proposed to be an intermediate electron carrier between the reductase and terminal catalytic component of the system. The 212-kDa protein was specifically inactivated in cell-free extracts by the mechanism-based inactivator propyne, suggesting that it is the catalytic component and contains the active site(s) for O2 activation and alkene epoxidation. The subunit structure and metal analysis of this component suggest that it contains two diiron centers, one for each alphabetagamma protomeric unit. No specific enzymatic activities could be assigned for the 11-kDa protein, but this component was obligately required for steady-state alkene epoxidation. The alkene monooxygenase components were expressed during growth of Xanthobacter Py2 on aliphatic alkenes or epoxides and repressed during growth on other carbon sources. The electron transfer components of alkene monooxygenase were highly specific: other reductase activities present in Xanthobacter were incapable of transferring electrons to the Rieske-type ferredoxin or substituting for the reductase in the alkene monooxygenase complex. Likewise, other bacterial and plant ferredoxins were unable to substitute for the Rieske-type ferredoxin in mediating electron transfer to the oxygenase. The biochemical properties of alkene monooxygenase described in this study suggest that this enzyme combines elements of both the well-characterized aromatic dioxygenase (two-component electron transfer scheme) and methane monooxygenase (small regulatory protein and diiron oxygenase) multicomponent enzyme systems.

Biofiltration of Air Containing Low Concentrations of Propene Using a Membrane Bioreactor

AbstractVolatiles with a low water solubility are difficult to remove from air by biofiltration, especially when present in low concentrations, because the driving force for mass transfer into the aqueous phase is very small. We have used a microporous hydrophobic membrane as a support for biofilms that remove the poorly soluble propene from air. Two bacterial strains were compared, and the faster growing strain, Xanthobacter Py2, was selected to study biofilm formation and reactor performance at propene concentrations in the range encountered in off‐gas treatment. With a concentration of 200–350 ppm of propene in the gas phase a 20‐day start‐up period was required for the formation of a biofilm on the membrane. Once the biofilm had been established, continuous propene removal was tested over a range of concentrations. The amount of active biomass adapted to the amount of propene available. When the membrane bioreactor was operated with propene concentrations as low as 9–30 ppm in the gas phase, the propene removal rate was stable for several weeks, without the supply of any other source of carbon or energy to the microbial population.

Purification and characterization of two components of epoxypropane isomerase/carboxylase from Xanthobacter Py2.

Epoxypropane isomerase from Xanthobacter Py2 has been resolved into at least two components (A and B) by ion-exchange chromatography. Both components were required for the degradation of epoxypropane and were purified further. Component A was apparently homohexameric with a subunit M(r) of about 44,000, and possessed NAD(+)-dependent dihydrolipoamide dehydrogenase activity and lipoamide reductase activity. It was sensitive to inhibition by o-phenanthroline and the thiol-specific reagents N-ethylmaleimide(NEM)and p-chloromercuribenzoate. Component B was homodimeric with a subunit M(r), of 62,170 and contained 2 mol.mol-1 FAD. It had an NADPH-dependent lipoamide reductase activity which was sensitive to NEM and p-chloromercuribenzoate. The N-terminal amino acid sequences and monomer sizes of components A and B correspond to those of ORF1 and ORF3 respectively (ORF = open reading frame) of a recently published sequence of a clone which complements mutants unable to degrade epoxypropane. NADPH was found to replace the need for a low-M(r), fraction in epoxypropane degradation assays containing components A and B and NAD+. The predicted amino acid sequence of component A (ORF1) has been analysed and shown to contain a potential ADP binding site near the N-terminus and putative cofactor binding domain near the C-terminus, with sequence similarity to the biotinyl and lipoyl binding domains of biotin-dependent carboxylases and 2-oxoacid dehydrogenases respectively. A reaction mechanism for epoxypropane degradation, incorporating recent evidence for combined isomerization and carboxylation to acetoacetate, is discussed.

Propene removal from synthetic waste gas using a hollow-fibre membrane bioreactor

Hollow-fibre modules containing microporous membrane material were evaluated as bioreactors for waste gas treatment. The reactors were inoculated with the propene-utilizing strain Xanthobacter Py2, which formed a biofilm on the inner side of the fibres. The removal of the poorly soluble volatile propene from synthetic waste gas was monitored for up to 170 days. The maximum removal rates were 70–110 g propene per m3 reactor per hour. A gas residence time of 80 s was required to remove 95% of an initial propene concentration of 0.84 g/m3. The presence of ammonium in the liquid medium resulted in the development of an additional population of nitrifying organisms. Therefore, nitrate was used as the source of nitrogen in later experiments. During long-term operation, the propene removal rates gradually decreased. At low liquid velocities (1–5 cm/s) clogging of individual fibres with excess biomass was observed. Elevation of the liquid velocity in the fibres to 90 cm/s resulted in the formation of a dense biofilm and prevented clogging of the fibres. However, also at this high liquid velocity a gradual decrease in propene removal rate was observed. These results suggest that aging of biofilms is a very important factor in long-term operation of hollow-fibre bioreactors.

Cloning and expression of the genes encoding the propene monooxygenase from Xanthobacter, Py2

Xanthobacter Py2 grows on propene as sole carbon source, converting propene to propene oxide (epoxypropane) using an alkene-specific monooxygenase, as the first step in catabolism. Four mutants, NZ1–4, with a propene− propene oxide+ phenotype were isolated by 1-methyl-3-nitro-1-nitrosoguanidine mutagenesis or by enrichment with the suicide substrate vinylidene chloride, and were shown to have lost the ability to convert alkenes to epoxides. All four mutants were complemented by a number of clones of Xanthobacter Py2 chromosomal DNA in the broad-host-range cosmid pLAFR5, some of which appeared to be non-overlapping. Representatives of the different clones obtained were transferred into Xanthobacter autotrophicus JW33 and one, pNY2, the most frequently isolated clone, was shown to express an inducible, fully functional propene monooxygenase. Subcloning revealed that all four mutants were complemented by a 2.4-kb EcoRI-PstI fragment situated at one end of the cosmid insert. However, activity in X. autotrophicus JW33 could only be expressed from pNY2, containing the complete insert (25 kb), suggesting a large operon or some form of long-range control. pNY2 failed to express in E. coli. In X. autotrophicus JW33 [pNY2] at least three new polypeptides were evident after induction with propene compared with a control carrying only the cosmid pLAFR5.

Complementation of Xanthobacter Py2 mutants defective in epoxyalkane degradation, and expression and nucleotide sequence of the complementing DNA fragment.

Three Xanthobacter Py2 mutants (M3, M8 and M10) lacking epoxyalkane-degrading activity were isolated and characterized. All mutants were able to grow on acetone, the degradation product of 1,2-epoxypropane conversions. Furthermore, they contained the unidentified 'low molecular mass fraction' (LMF) necessary for epoxyalkane-degrading activity. Three cosmids from a gene bank complemented the mutation in M10 and M8 but not in mutant M3. Epoxyalkane-degrading activity in crude extracts of 1,2-epoxypropane-grown complemented mutants was similar to the wild-type activity. Surprisingly, M10 transformed with complementing cosmid pEP9 showed a constitutively expressed epoxyalkane-degrading activity, which was not observed in the wild-type strain. The cosmid pEP9 was conjugated into Xanthobacter autotrophicus GJ10, which is not able to degrade 1,2-epoxypropane. In crude extracts of X. autotrophicus GJ10(pEP9), epoxyalkane-degrading activity was demonstrated, but only after the addition of the LMF from Xanthobacter Py2. Hybridization experiments demonstrated an overlap on complementing cosmids pEP1, pEP3 and pEP9. Subcloning revealed a 4.8 kb EcoRI-HindIII fragment to be necessary for complementing the mutant M10. In the sequence of this fragment four different ORFs were found.

Membrane bioreactor with a porous hydrophobic membrane as a gas–liquid contactor for waste gas treatment

A novel type of bioreactor for waste gas treatment has been designed. The reactor contains a microporous hydrophobic membrane to create a large interface between the waste gas and the aqueous phase. To test the new reactor, propene was chosen because of its high air/water partition coefficient, which causes a low water concentration and hampers its removal from air. Propene transfer from air to a suspension of propene-utilizing Xanthobacter Py2 cells in the membrane bioreactor proved to be controlled by mass transfer in the liquid phase. The resistance of the membrane was negligible. Simulated propene transfer rates agreed well with the experimental data. A stable biofilm of Xanthobacter Py2 developed on the membrane during prolonged operation. The propene flux into the biofilm was 1 x 10(-6) mol m(-2) s(-1) at a propene concentration of 9.3 x 10(-2) mol m(-3) in the gas phase. (c) 1995 John Wiley & Sons, Inc.

Dithiol- and NAD-dependent degradation of epoxyalkanes by Xanthobacter Py2

A broad range of epoxyalkanes was converted into the corresponding ketones by cell extracts of Xanthobacter Py2. Both 1,2- and 2,3-epoxyalkanes were degraded and in addition, the degradation of 2,3-epoxyalkanes in all cases was highly enantioselective. Conversion of a deuterium-labelled substrate indicated that the ketone product was probably formed indirectly via an hydroxy intermediate. Degradation of epoxyalkanes by Xanthobacter Py2 was dependent on both NAD and another, not yet identified, cofactor that was present in the low-molecular-mass fraction (LMF) of propene-grown cells. It is proposed that the LMF was involved in a reductive reaction step since it could be replaced by dithiothreitol (DTT) and various other dithiol compounds. Epoxyalkane-degrading activity was inhibited by the sulphhydryl blocking reagent N-ethylmaleimide (NEM). Inhibition by NEM and stimulation by LMF, DTT and other dithiols was effective only in the simultaneous presence of NAD.

Dithiol- and NAD-dependent degradation of epoxyalkanes by Xanthobacter Py2

Dithiol- and NAD-dependent degradation of epoxyalkanes by Xanthobacter Py2

Batch cultivation of Xanthobacter Py2 on 1-pentene

The propene isolated strain Xanthobacter Py2 was able to grow on 1-pentene. The biomass yield for growth under 1-pentene limiting conditions was 0.48 (Ceq/Ceq). Upon storage at both +4°C and -20°C no loss of enzymatic epoxide degrading activity in resting cell suspensions was observed after a month. However, activity decay was pronounced during the stationary phase of growth as well as under reaction conditions.

Initial Characterization of the Enzyme and Cloning of Genes Involved in the Enantioselective Epoxyalkane Degradation by Xanthobacter PY2

The epoxyalkane-degrading enzyme of Xanthobacter Py2 was studied in crude extracts. NAD and a low molecular weight fraction which can be replaced by DTT are necessary for the conversion of epoxyalkanes into ketones. The genes responsible for the epoxyalkane-degrading enzyme were cloned and expressed in Xanthobacter autotrophics GJ10.

Chiral resolution of 2,3-epoxyalkanes by Xanthobacter Py2

With propene-grown cells of Xanthobacter Py2 it was possible to resolve racemic mixtures of 2,3-epoxyalkanes. Only 2S-forms were metabolized by this organism, resulting in pure 2R-2,3-epoxyalkanes. Chiral resolution was obtained with trans-2,3-epoxybutane, trans-2,3-epoxypentane and cis-2,3-epoxypentane. Xanthobacter Py2 was however not able to discriminate between the enantiomeric forms of 1,2-epoxyalkanes, resulting in the complete degradation of both chiral forms of 1,2-epoxyalkanes.