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PubMed1998

The catalytic mechanism of amidase also involves nitrile hydrolysis.

The amidase from Rhodococcus rhodochrous J1, which hydrolyzes an amide to an acid and ammonium, was surprisingly found to catalyze the hydrolytic cleavage of the C-N triple bond in a nitrile to form an acid and ammonium stoichiometrically. The amidase exhibited a Km of 3.26 mM for benzonitrile in contrast to that of 0.15 mM for benzamide as the original substrate, but the Vmax for benzonitrile was about 116000 of that for benzamide. A mutant amidase containing alanine instead of Ser195, which is essential for amidase catalytic activity, showed no nitrilase activity, demonstrating that this residue plays a crucial role in the hydrolysis of nitriles as well as amides.

Amidohydrolases↗

PubMed2003

Molecular cloning and characterization of an amidase from Arabidopsis thaliana capable of converting indole-3-acetamide into the plant growth hormone, indole-3-acetic acid.

Acylamidohydrolases from higher plants have not been characterized or cloned so far. AtAMI1 is the first member of this enzyme family from a higher plant and was identified in the genome of Arabidopsis thaliana based on sequence homology with the catalytic-domain sequence of bacterial acylamidohydrolases, particularly those that exhibit indole-3-acetamide amidohydrolase activity. AtAMI1 polypeptide and mRNA are present in leaf tissues, as shown by immunoblotting and RT-PCR, respectively. AtAMI1 was expressed from its cDNA in enzymatically active form and exhibits substrate specificity for indole-3-acetamide, but also some activity against L-asparagine. The recombinant enzyme was characterized further. The results show that higher plants have acylamidohydrolases with properties similar to the enzymes of certain plant-associated bacteria such as Agrobacterium-, Pseudomonas- and Rhodococcus-species, in which these enzymes serve to synthesize the plant growth hormone, indole-3-acetic acid, utilized by the bacteria to colonize their host plants. As indole-3-acetamide is a native metabolite in Arabidopsis thaliana, it can no longer be ruled out that one pathway for the biosynthesis of indole-3-acetic acid involves indole-3-acetamide-hydrolysis by AtAMI1.

Amidohydrolases↗

PubMed2003

Pentacyclic triterpenoids from Embelia schimperi.

Five oleanane-type pentacyclic triterpenoids were isolated by chromatographic separation of a chloroform extract of the stem bark of Embelia schimperi. Three of these compounds have a methyleneoxy bridge. Two compounds, embelinone and schimperinone, are reported here for the first time from a natural source (they have been synthesized previously during chemical transformations). Their structures were determined by spectroscopic techniques, among which 2-D NMR was useful for complete characterization. Three of the triterpenoids exhibited mild antibacterial properties against the gram-positive bacterial strain Rhodococcus sp.

Anti-Bacterial Agents↗

PubMed1997

Preparation of 3-ketodesogestrel metabolites by microbial transformation and chemical synthesis.

Specific microbial reactions were used for the preparation of metabolites of 3-ketodesogestrel (13-ethyl-17 beta-hydroxy-11-methylene-18,19-dinor-17 alpha-pregn-4-en-20-yn-3-one, the active from of the progestagen desogestrel. Clostridium paraputrificum transformed 3-ketodesogestrel (KDG) to the 5 beta-dihydro and tetrahydro metabolites 13-ethyl-17 beta-hydroxy-11-methylene-18,19-dinor-5 beta, 17 alpha-pregnan-20-yn-3-one and 13-ethyl-11-methylene-18,19-dinor-5 beta, 17 alpha-pregnan-20-yne-3 alpha, 17 beta-diol, respectively. The epimeric compound 13-ethyl-11-methylene-18,19-dinor-5 beta, 17 alpha-pregnan-20-yne-3 beta, 17 beta-diol was obtained by chemical reduction of the 3-oxo compound. Mycobacterium smegmatis converted KDG to metabolites of the 5 alpha H-series: 13-ethyl-17 beta-hydroxy-11-methylene-18,19-dinor-5 alpha, 17 alpha-pregnan-20-yn-3-one, 13-ethyl-11-methylene-18,19-dinor-5 alpha, 17 alpha-pregnan-20-yne-3 alpha, 17 beta-diol and 13-ethyl-11-methylene-18,19-dinor-5 alpha, 17 alpha-pregnan-20-yne-3 beta, 17 beta-diol. The ring A-aromatized analog of KDG 13-ethyl-11-methylene-18,19-dinor-17 alpha-pregna-1,3,5(10)-trien-20-yne-3,17 beta-diol was obtained by microbial 1-dehydrogenation with Rhodococcus rhodochrous. Additionally, chemical syntheses of the microbially obtained KDG metabolites listed above were carried out. These included Birch reduction, reduction of KDG with sodium borohydride in aqueous pyridine and in methanol, reduction of KDG with potassium selectride in tetrahydrofuran, and dehydrogenation of KDG with cupric-II bromide in acetonitrile. The problems encountered in chemical syntheses favor the microbial procedures. The compounds were characterized by mass spectra (MS), IR, and circular dichroism (CD). Complete assignments of 1H and 13C chemical shifts were made using homo- and heteronuclear 2-DN-NMR spectroscopy. Chromatographic [gas-liquid chromatography (GLC), high-performance liquid chromatography (HPLC), thin-layer chromatography (TLC)] data of all the prepared KDG metabolites are presented.

Clostridium↗

PubMed2001

Degradation of aroclor 1242 in a single-stage coupled anaerobic/aerobic bioreactor.

Degradation of Aroclor 1242 was studied in granular biofilm reactors with limited aeration. An aerobic biphenyl degrader, Rhodococcus sp. M5, was used to supplement a natural bacterial population present in a "bioaugmented" reactor, while the "non-bioaugmented" reactor only contained natural granular sludge. The bioaugmentation, however appeared to have no effect on the reactor performance. Aroclor measurements showed its disappearance in both reactors with only 16-19% of Aroclor recovered from the reactor biomass and effluent. Simultaneously, a chlorine balance indicated that dechlorination occurred at a specific rate of 1.43 mg PCB (g volatile suspended solids)(-1) d(-1), which was comparable to the observed rate of Aroclor disappearance. Intermediates detected in both reactors were biphenyl, benzoic acid, and mono-hydroxybiphenyls. This suggests that a near-complete mineralization of Aroclor can be achieved in a single-stage anaerobic/aerobic system due to a combination of reductive and oxidative degradation mechanisms.

Aroclors↗

PubMed2001

Fe-type nitrile hydratase.

The characteristic features of Fe-type nitrile hydratase (NHase) from Rhodococcus sp. N-771 are described. Through the biochemical analyses, we have found that nitric oxide (NO) regulates the photoreactivity of this enzyme by association with the non-heme iron center and photoinduced dissociation from it. The regulation is realized by a unique structure of the catalytic non-heme iron center composed of post-translationally modified cysteine-sulfinic (Cys-SO2H) and -sulfenic acids (Cys-SOH). To understand the biogenic mechanism and the functional role of these modifications, we constructed an over-expression system of whole NHase and individual subunits in Escherichia coli. The results of the studies on several recombinant NHases have shown that the Cys-SO2H oxidation of alphaC112 is indispensable for the catalytic activity of Fe-type NHase.

Binding Sites↗

PubMed2002

Site-directed mutagenesis for cysteine residues of cobalt-containing nitrile hydratase.

Three cysteine residues, which are completely conserved among alpha-subunits in all nitrile hydratases, are thought to be the ligands of a metal ion in the catalytic center of this enzyme. These cysteine residues (i.e. alpha C102, alpha C105 and alpha C107) in the high-molecular-mass nitrile hydratase (H-NHase) of Rhodococcus rhodochrous J1 were replaced with alanine by site-directed mutagenesis using the R. rhodochrous ATCC12674 host-vector system, and the resultant transformants were investigated. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for the cell-free extracts of each mutant transformant revealed that four mutant transformants (i.e. alpha C105A, alpha C107A, alpha C102A/C105A and alpha C105A/C107A) showed predominant alpha- and beta-subunit protein bands with a mobility identical to those of the native H-NHase, while three mutant transformants (i.e. alpha C102A, alpha C102A/C107A and alpha C102A/C105A/C107A) did not produce the corresponding proteins. The purified former four mutant enzymes showed neither enzymatic activity nor the maximum absorption at 410 nm which was detected in the wild type H-NHase. They also did not contain cobalt ions. Based upon these findings, these three cysteine residues were found to be essential for the active expression of H-NHase.

Amino Acid Sequence↗

PubMed2000

Real-time monitoring of nitrile biotransformations by mid-infrared spectroscopy.

In this study mid-infrared spectroscopy was used to follow the enzyme kinetics involved in nitrile biocatalysis using whole cell suspensions of the bacterium Rhodococcus rhodochrous LL100-21. The bacteria were grown on acetonitrile to induce a two-step enzymatic pathway. Acetonitrile was biotransformed to acetamide by a nitrile hydratase enzyme and subsequently to acetic acid (carboxylate ion) by an amidase enzyme. The bacteria were also grown on benzonitrile to induce a one-step enzymatic pathway. Benzonitrile was biotransformed directly to benzoic acid (carboxylate ion) by a nitrilase enzyme. These reactions were followed by React IR using a silicon probe and gave excellent quantitative and qualitative real-time data of both nitrile biocatalytic reactions. This study has shown that this novel technique has potentially useful applications in biocatalysis.

Acetonitriles↗

PubMed1999

An enzyme controlled by light: the molecular mechanism of photoreactivity in nitrile hydratase.

Extensive studies have revealed the molecular mechanism of the photoreactivity of nitrile hydratase from Rhodococcus sp. N-771. In the inactive enzyme, nitric oxide is bound to the non-heme ferric iron at the catalytic center, stabilized by a claw-like structure formed by two post-translationally modified cysteines and a serine. The inactive nitrile hydratase is activated by the photoinduced release of the nitric oxide. This result might provide a means of designing novel photoreactive chemical compounds or proteins that would be applicable to biochips and light-controlled metabolic systems.

Crystallography, X-Ray↗

PubMed2002

Population analysis of a binary bacterial culture by multi-parametric flow cytometry.

To study the degradation of a xenobiotic that requires a mixed culture it is essential to monitor the proportions and to control the population dynamics of the component strains. For these purposes fluorochromising techniques and multi-parametric flow cytometry were used to follow Rhodococcus erythropolis K2-3 and Ochrobactrum anthropi K2-14, both of which are needed to degrade 4-(2,4-dichlorophenoxy)butyric acid (2,4-DB). Although the two strains can grow in constant proportions in mixed cultures on other substrates, 2,4-DB could not be degraded as a sole substrate in a continuous process and R. erythropolis K2-3 was clearly impaired in the binary mixture. Addition of a second, easily assimilable substrate (xylitol) in appropriate concentrations (empirically determined) helped this strain survive, and thus facilitated complete degradation of the xenobiotic. This combination of substrates was found to stabilise the growth of R. erythropolis K2-3 and, consequently promoted the action of O. anthropi K2-14. Thus, the two organisms became established in constant proportions in a continuous process until reaching steady state. Consequently, multiplication and cell division activities of the two components of the binary culture were high and reached similar values to those attained when they are grown in pure culture.

2,4-Dichlorophenoxyacetic Acid↗

PubMed2003

Evolution of the soluble diiron monooxygenases.

Based on structural, biochemical, and genetic data, the soluble diiron monooxygenases can be divided into four groups: the soluble methane monooxygenases, the Amo alkene monooxygenase of Rhodococcus corallinus B-276, the phenol hydroxylases, and the four-component alkene/aromatic monooxygenases. The limited phylogenetic distribution of these enzymes among bacteria, together with available genetic evidence, indicates that they have been spread largely through horizontal gene transfer. Phylogenetic analyses reveal that the alpha- and beta-oxygenase subunits are paralogous proteins and were derived from an ancient gene duplication of a carboxylate-bridged diiron protein, with subsequent divergence yielding a catalytic alpha-oxygenase subunit and a structural beta-oxygenase subunit. The oxidoreductase and ferredoxin components of these enzymes are likely to have been acquired by horizontal transfer from ancestors common to unrelated diiron and Rieske center oxygenases and other enzymes. The cumulative results of phylogenetic reconstructions suggest that the alkene/aromatic monooxygenases diverged first from the last common ancestor for these enzymes, followed by the phenol hydroxylases, Amo alkene monooxygenase, and methane monooxygenases.

Amino Acid Sequence↗

PubMed2001

Factors affecting mass transfer limited biodegradation in saturated porous media.

Microbial degradation rates in the subsurface are not only limited by the physiological capacity of the organisms, but also by inefficient supply of nutrients to the microbes. Although mass transfer limitation of biodegradation in the subsurface has been postulated for years, experimental evidence is still scarce. In the column experiments described here, diffusive transport of 4-nitroanisole from the bulk solution to cells of Rhodococcus opacus strain AS2 immobilized on glass beads or sand appeared to be responsible for the slow transformation rates observed. Assuming steady state, we applied a coupled transformation/transport equation to these data (Best equation) and apparent bead-related mass transfer coefficients were found to increase in proportion to the surface area covered with bacteria. This implies that mass transfer coefficients for individual cells remained constant. In an idealized oligotrophic environment where cells are only loosely clustered and do not shield each other, we would therefore expect biodegradation rates to be independent from the longitudinal distribution of the total biomass along a given flow path. Moreover, apparent mass transfer coefficients increased with the grain size of the column fillings, but did not change upon varying the flow rate. With a limiting external transport step, overall transformation fluxes do not become saturated at concentrations as low as predicted for Michaelis-Menten-type kinetics. Mass transfer limitation thus offers a justification for the common assumption that biodegradation rates in the subsurface follow first order kinetics in a wide concentration range.

Anisoles↗

PubMed2004

Bioremediation of chlorobenzene-contaminated ground water in an in situ reactor mediated by hydrogen peroxide.

New in situ reactive barrier technologies were tested nearby a local aquifer in Bitterfeld, Saxonia-Anhalt, Germany, which is polluted mainly by chlorobenzene (CB), in concentrations up to 450 microM. A reactor filled with original aquifer sediment was designed for the microbiological remediation of the ground water by indigenous bacterial communities. Two remediation variants were examined: (a) the degradation of CB under anoxic conditions in the presence of nitrate; (b) the degradation of CB under mixed electron acceptor conditions (oxygen+nitrate) using hydrogen peroxide as the oxygen-releasing compound. Under anoxic conditions, no definite degradation of CB was observed. Adding hydrogen peroxide (2.94 mM) and nitrate (2 mM) led to the disappearance of CB (ca. 150 microM) in the lower part of the reactor, accompanied by a strong increase of the number of cultivable aerobic CB degrading bacteria in reactor water and sediment samples, indicating that CB was degraded mainly by productive bacterial metabolism. Several aerobic CB degrading bacteria, mostly belonging to the genera Pseudomonas and Rhodococcus, were isolated from reactor water and sediments. In laboratory experiments with reactor water, oxygen was rapidly released by hydrogen peroxide, whereas biotic-induced decomposition reactions of hydrogen peroxide were almost four times faster than abiotic-induced decomposition reactions. A clear chemical degradation of CB mediated by hydrogen peroxide was not observed. CB was also completely degraded in the reactor after reducing the hydrogen peroxide concentration to 880 microM. The CB degradation completely collapsed after reducing the hydrogen peroxide concentration to 440 microM. In the following, the hydrogen peroxide concentrations were increased again (to 880 microM, 2.94 mM, and 880 microM, respectively), but the oxygen demand for CB degradation was higher than observed before, indicating a shift in the bacterial population. During the whole experiment, nitrate was uniformly reduced during the flow path in the reactor.

Biodegradation, Environmental↗

PubMed2001

High-density sampling of a bacterial operon using mRNA differential display.

We have implemented a simplified high throughput approach to differential display in order to identify transcriptionally regulated genes in bacteria. In contrast with the few previous applications of differential display to prokaryotes, we use a large number of primers which allows for a high-density sampling of the mRNA population and the identification of many differentially amplified DNA fragments. From the overlap of these short sequences, long contiguous sequences that encode several genes can be assembled. The multiplicity of sampling provides a strong indication that the genes identified are indeed differentially regulated. As a test case, we looked for the genes involved in the degradation of 2,4-dinitrophenol (2,4-DNP) in a Rhodococcus erythropolis strain, HL PM-1. In this experiment a long polycistronic mRNA was sampled repeatedly. The induction of these genes by 2,4-DNP was confirmed by dot blot analysis and two of them were confirmed to be involved in the degradation of 2,4-DNP. This work shows that mRNA differential display is an important tool for the identification of metabolic genes in prokaryotes.

2,4-Dinitrophenol↗

PubMed2001

Vitamin requirements of hydrocarbon-utilizing soil bacteria.

The numbers of oil-utilizing bacteria in several samples of clean and oil-polluted soils counted on vitamin-containing media were severalfold higher than the numbers counted on vitamin-free media. Colonies that grew on a medium containing a vitamin mixture were tested for growth on the same medium lacking any vitamins. More than 90% of the total colonies failed to grow. The remaining 10% grew, yet their growth was enhanced, when vitamins were added. The predominant oil-utilizing bacteria in one of the test desert soil samples were various strains of Cellulomonas flavigena and Rhodococcus erythropolis. Minor organisms belonged to the genera Pseudomonas, Bacillus and Arthrobacter. Two vitamin-requiring biovars of C. flavigena and R. erythropolis were selected for further study. Their growth on n-octadecane and phenanthrene as sole sources of carbon and energy as well as their potential for hydrocarbon consumption were enhanced by added vitamins, e.g. folic acid, pyridoxine, vitamin B12, biotin and others. In a field experiment, it was confirmed that vitamin fertilization of an oil-polluted sand sample enhanced the biodegradation of constituent hydrocarbons of that sample.

Actinomycetales↗

PubMed1998

Screening of xenobiotic compounds degrading microorganisms using biosensor techniques.

A screening device based on microorganisms immobilised onto a Clark-type oxygen electrode was used to monitor the potential of these microorganisms for the degradation and detection of xenobiotic compounds especially their chlorinated derivatives. The sensitivity and specificity of various species of Pseudomonas, Sphinomonas, Ralstonia, Rhodococcus were characterised in relation to xenobiotic compounds by using biosensor techniques. The following groups of xenobiotics were subjects of investigation: chlorophenols, chlorobenzoates, 2,4-D, PCB, dibenzofurane and their putative intermediates. Using this simple setup it proved possible to screen microbial strains for their potential to catabolize aromatic and chloroaromatic compounds under oxygen consumption. In a kinetic regime, a reproducible signal was obtained within minutes. Based on these results the sensor technique was a suitable method for the rapid characterization of microorganisms and allowed to gather information about the substrate spectrum.

2,4-Dichlorophenoxyacetic Acid↗

PubMed1999

Development of an automated microbial sensor system.

An automated whole cell biosensor system was developed by integration of immobilized microbial cells in a flow-through system with screen-printed flow-through electrodes as detectors. The detectors used were thick-film Pt-electrodes in a 3-electrode configuration constructed as sandwich flow-through cells with a volume of about 36 microliters polarized at -900 mV. The measuring principle was the determination of oxygen consumption due to the microbial metabolism. Fructose was used as model analyte. The microorganisms were immobilized on cellulose-acetate membranes and integrated into a newly created reaction chamber (membrane reactor). The microbial cells used were Rhodococcus erythropolis and Issatchenkia orientalis known to be suitable for the determination of biological oxygen demand.

Biosensing Techniques↗

PubMed2002

Versatile persistence pathways for pathogens of animals and plants.

The glyoxylate cycle and the glycine cleavage system are part of conserved metabolic pathways involved in the chronic persistence of microorganisms in animal hosts. In the chromosome of the plant pathogen Rhodococcus fascians, the vic locus has been identified as a region containing genes essential for persistence inside induced leafy galls. Sequence analysis showed that this 18-kb locus is syntenic with chromosomal regions of Mycobacterium species that encompass the 'persistence' loci of these mammalian pathogens. Hence, the ability to switch diet inside the host appears to be governed by 'persistence' enzymes that are conserved between pathogens of animals and plants.

Animals↗