Bacterial metabolism of side chain fluorinated aromatics: cometabolism of 4-trifluoromethyl(TFM)-benzoate by 4-isopropylbenzoate grown Pseudomonas putida JT strains

Enzymes of the p-cymene pathway in Pseudomonas putida strains cometabolized the intermediate analogue 4-trifluoromethyl(TFM)benzoate. Three products, 4-TFM-2,3-dihydro-2,3-dihydroxybenzoate, 4-TFM-2,3-dihydroxy-benzoate and 2-hydroxy-6-oxo-7,7,7-trifluorohepta-2,4-dienoate (7-TFHOD) were identified chemically and by spectroscopic proterties.Certain TFM-substituted analogue metabolites of the p-cymene pathway were transformed at drastically reduced rates.Hammett type analysis of ring cleavage reactions of 4-substituted 2,3-dihydroxybenzoates revealed the negative inductive and especially mesomeric effect of substituents to be rate determining. Whereas decarboxylation of 3-carboxy-7-TFHOD was not affected by fluorine substitution the subsequent hydrolysis of 7-TFHOD proceeded very slowly. The negative inductive effect of the TFM-group probably inhibited heterolysis of the carbon bond between C₅ and C₆ of 7-TFHOD.Abbreviations DHB 1,2-Dihydroxy-2-hydrobenzoate - DHC 2,3-Dihydro-2,3-dihydroxybenzoate, this compound was termed DHC simply to distinguish it from the similar 1,2-dihydroxy-2-hydrobenzoate (DHB) as described in the preceeding paper (Engesser et al. 1988) - HMS 2-Hydroxymuconic semialdehyde - HOD 2-Hydroxy-6-oxohepta-2,4-dienoate - 7-TFHOD 2-Hydroxy-6-oxo-7,7,7-trifluorohepta-2,4-dienoate - TFM Trifluoromethyl This work was supported, in part, by the Gesellschaft für Strahlen- und Umweltforschung, Neuherberg/München, FRG     

Naphthalene degradation and incorporation of naphthalene-derived carbon into biomass by the thermophile Bacillus thermoleovorans

The thermophilic aerobic bacterium Bacillus thermoleovorans Hamburg 2 grows at 60 degrees C on naphthalene as the sole source of carbon and energy. In batch cultures, an effective substrate degradation was observed. The carbon balance, including naphthalene, metabolites, biomass, and CO(2), was determined by the application of [1-(13)C]naphthalene. The incorporation of naphthalene-derived carbon into the bulk biomass as well as into specified biomass fractions such as fatty acids and amino acids was confirmed by coupled gas chromatography-mass spectrometry (GC-MS) and isotope analyses. Metabolites were characterized by GC-MS; the established structures allow tracing the degradation pathway under thermophilic conditions. Apart from typical metabolites of naphthalene degradation known from mesophiles, intermediates such as 2, 3-dihydroxynaphthalene, 2-carboxycinnamic acid, and phthalic and benzoic acid were identified for the pathway of this bacterium. These compounds indicate that naphthalene degradation by the thermophilic B. thermoleovorans differs from the known pathways found for mesophilic bacteria.     

Determination of the kinetic parameters of the phenol-degrading thermophile Bacillus themoleovorans sp. A2

Phenolic compounds are pollutants in many wastewaters, e.g. from crude oil refineries, coal gasification plants or olive oil mills. Phenol removal is a key process for the biodegradation of pollutants at high temperatures because even low concentrations of phenol can inhibit microorganisms severely. Bacillus thermoleovorans sp. A2, a recently isolated thermophilic strain (temperature optimum 65 degrees C), was investigated for its capacity to degrade phenol. The experiments revealed that growth rates were about four times higher than those of mesophilic microorganisms such as Pseudomonas putida. Very high specific growth rates of 2.8 h(-1) were measured at phenol concentrations of 15 mg/l, while at phenol concentrations of 100-500 mg/l growth rates were still in the range of 1 h(-1). The growth kinetics of the thermophilic Bacillus thermoleovorans sp. A2 on phenol as sole carbon and energy source can be described using a three-parameter model developed in enzyme kinetics. The yield coefficient Yx/s of 0.8-1 g cell dry weight/g phenol was considerably higher than cell yields of mesophilic bacteria (Yx/s 0.40-0.52 g cell dry weight/g phenol). The highest growth rate was found at pH 6. Bacillus thermoleovorans sp. A2 was found to be insensitive to hydrodynamic shear stress in stirred bioreactor experiments (despite possible membrane damage caused by phenol) and flourished at an ionic strength of the medium of 0.25(-1) mol/l (equivalent to about 15-60 g NaCl/l). These exceptional properties make Bacillus thermoleovorans sp. A2 an excellent candidate for technical applications.     

Cloning, sequencing and expression in Escherichia coli of a thermophilic lipase from Bacillus thermoleovorans ID-1

A thermophilic lipase of Bacillus thermoleovorans ID-1 was cloned and sequenced. The lipase gene codes 416 amino acid residues and contains the conserved pentapeptide Ala-X-Ser-X-Gly as other Bacillus lipase genes. The optimum temperature of the lipase is 75 degrees C, which is higher than other known Bacillus lipases. For expression in Escherichia coli, the lipase gene was subcloned in pET-22b(+) vector with a strong T7 promoter. Lipase activity was approximately 1.4-fold greater than under the native promoter.     

Characterization of bacteriocins from two strains of Bacillus thermoleovorans, a thermophilic hydrocarbon-utilizing species.

Bacillus thermoleovorans S-II and B. thermoleovorans NR-9 produce bacteriocins, and these bacteriocins are designated thermoleovorin-S2 and thermoleovorin-N9, respectively. The bacteriocins are effective against all but the producing strain of B. thermoleovorans, as well as being effective against Salmonella typhimurium, Branhamella catarrhalis, Streptococcus faecalis, and Thermus aquaticus. Thermoleovorins are produced during log-phase growth and are inhibitory to actively growing cells. The bacteriocins are proteinaceous in nature, being sensitive to selected proteases (protease type XI and pepsin). They are stable at pHs of 3 to 10. Thermoleovorin-S2 was more thermostable than thermoleovorin-N9 at 70 and 80 degrees C. Thermoleovorins-S2 and -N9 apparently act by binding to the susceptible organisms, resulting in lysis of the cell. Thermoleovorins-S2 has an estimated M(r) of 42,000, while thermoleovorin-N9 has a M(r) of 36,000.     

Characterization of bacteriocins from two strains of Bacillus thermoleovorans, a thermophilic hydrocarbon-utilizing species.

Bacillus thermoleovorans S-II and B. thermoleovorans NR-9 produce bacteriocins, and these bacteriocins are designated thermoleovorin-S2 and thermoleovorin-N9, respectively. The bacteriocins are effective against all but the producing strain of B. thermoleovorans, as well as being effective against Salmonella typhimurium, Branhamella catarrhalis, Streptococcus faecalis, and Thermus aquaticus. Thermoleovorins are produced during log-phase growth and are inhibitory to actively growing cells. The bacteriocins are proteinaceous in nature, being sensitive to selected proteases (protease type XI and pepsin). They are stable at pHs of 3 to 10. Thermoleovorin-S2 was more thermostable than thermoleovorin-N9 at 70 and 80 degrees C. Thermoleovorins-S2 and -N9 apparently act by binding to the susceptible organisms, resulting in lysis of the cell. Thermoleovorins-S2 has an estimated M(r) of 42,000, while thermoleovorin-N9 has a M(r) of 36,000.     

The degradation of α-quaternary nonylphenol isomers by Sphingomonas sp. strain TTNP3 involves a type II ipso-substitution mechanism

The degradation of radiolabeled 4(3′,5′-dimethyl-3′-heptyl)-phenol [nonylphenol (NP)] was tested with resting cells of Sphingomonas sp. strain TTNP3. Concomitantly to the degradation of NP, a metabolite identified as hydroquinone transiently accumulated and short-chain organic acids were then produced at the expense of hydroquinone. Two other radiolabeled isomers of NP, 4(2′,6′-dimethyl-2′-heptyl)-phenol and 4(3′,6′-dimethyl-3′-heptyl)-phenol, were synthesized. In parallel experiments, the 4(2′,6′-dimethyl-2′-heptyl)-phenol was degraded more slowly than the other isomers of NP by strain TTNP3, possibly because of effects of the side-chain structure on the kinetics of degradation. Alkylbenzenediol and alkoxyphenol derivatives identified as metabolites during previous studies were synthesized and tested as substrates. The derivatives were not degraded, which indicated that the mineralization of NP does not proceed via alkoxyphenol as the principal intermediate. The results obtained led to the elucidation of the degradation pathway of NP isomers with a quaternary α-carbon. The proposed mechanism is a type II ipso substitution, leading to hydroquinone and nonanol as the main metabolites and to the dead-end metabolites alkylbenzenediol or alkoxyphenol, depending on the substitution at the α-carbon of the carbocationic intermediate formed.     

Bacterial metabolism of side chain fluorinated aromatics: cometabolism of 3-trifluoromethyl(TFM)-benzoate by Pseudomonas putida (arvilla) mt-2 and Rhodococcus rubropertinctus n657

The TOL plasmid-encoded enzymes of the methyl-benzoate pathway in Pseudomonas putida mt-2 cometabolized 3-trifluoromethyl (TFM)-benzoate. Two products, 3-TFM-1,2-dihydroxy-2-hydrobenzoate (3-TFM-DHB) and 2-hydroxy-6-oxo-7,7,7-trifluoro-hepta-2,4-dienoate (7-TFHOD) were identified chemically and by spectroscopic properties. TFM-substituted analogues of the metabolites of the methylbenzoate pathway were generally converted at drastically reduced rates. The catechol-2,3-dioxygenase from Pseudomonas putida showed moderate turnover rates with 3-TFM-catechol. The catechol-1,2-dioxygenase of Rhodococcus rubropertinctus N657 was totally inhibited by 3-TFM-catechol and did not cleave this substrate. Hammett-type analysis showed the catechol-1,2-dioxygenase reaction to be strongly dependent on the electronic nature of the substituents. Electronegative substituents strongly inhibited catechol cleavage. The catechol-2,3-dioxygenase reaction, however, was only moderately sensitive to electronegative substituents.     

Synthesis and biological activities of 4-trifluoromethylindole-3-acetic acid: a new fluorinated indole auxin

In our studies on the development of new promoters for the root formation of tree cuttings, 4-trifluoromethylindole-3-acetic acid (4-CF(3)-IAA), a new fluorinated auxin, was synthesized via 4-trifluoromethylindole and 4-trifluoromethylindole-3-acetonitrile by using 2-methyl-3-nitrobenzotrifluoride as the starting material. As a control compound for comparing biological activities, 4-methylindole-3-acetic acid (4-CH(3)-IAA) was also synthesized by using 2,3-dimethylnitrobenzene as the starting material. The biological activities of these compounds were compared by three bioassays with those of indole-3-acetic acid and 4-chloroindole-3-acetic acid (4-Cl-IAA), which, like 4-CF(3)-IAA and 4-CH(3)-IAA, has a substituent at the 4-position of the indole nucleus. 4-CF(3)-IAA showed strong root formation-promoting activity with black gram cuttings which was 1.5 times higher than that of 4-(3-indole)butyric acid at 1x10(-4) M. 4-CH(3)-IAA, however, only weakly promoted root formation in spite of its strong inhibition of hypocotyl growth in Chinese cabbage and promotion of hypocotyl swelling and lateral root formation in black gram. On the other hand, 4-CF(3)-IAA demonstrated weaker activities than 4-CH(3)-IAA and 4-Cl-IAA in these two bioassays.     

Isolation and characterization of a Geobacillus thermoleovorans strain from an ultra-deep South African gold mine

A thermophilic facultative bacterial isolate was recovered from 3.2km depth in a gold mine in South Africa. This isolate, designated GE-7, was cultivated from pH 8.0, 50 degrees C water from a dripping fracture near the top of an exploration tunnel. GE-7 grows optimally at 65 degrees C and pH 6.5 on a wide range of carbon substrates including cellobiose, hydrocarbons and lactate. In addition to O(2), GE-7 also utilizes nitrate as an electron acceptor. GE-7 is a long rod-shaped bacterium (4-6microm longx0.5microm wide) with terminal endospores and flagella. Phylogenetic analysis of GE-7 16S rDNA sequence revealed high sequence similarity with G. thermoleovorans DSM 5366(T) (99.6%), however, certain phenotypic characteristics of GE-7 were distinct from this and other previously described strains of G. thermoleovorans.     

Reaction pathways for biodehalogenation of fluorinated anilines

Pathways for biodehalogenation of fluorinated aniline derivatives were investigated. Microsomal NADPH-dependent dehalogenation of fluoroanilines was shown to proceed by three different reaction pathways. The first route appeared to result in monooxygenation at a fluorinated position and release of the fluorine atom as a fluoride anion. The primary additional reaction product formed is the reactive quinoneimine, not the 4-hydroxyaniline. In NADPH-containing microsomal systems with 4-fluoro-substituted anilines, formation of the 4-hydroxyaniline derivative is observed because NADPH chemically reduces this quinoneimine metabolite. A second pathway for dehalogenation proceeds by protein binding of a fluoro-containing (semi)quinoneimine metabolite, the formation of which may result from the mono-oxygenase reaction (pathway 1) and/or from (re)oxidation of a hydroxyaniline metabolite by superoxide anion radicals produced by the microsomal system. This latter reaction pathway becomes more important with increasing number of fluoro-substituents in the fluoroaniline derivative. The higher ratio of fluoride anion formed to 4-hydroxyaniline derivative detected in incubations with liver microsomes from dexamethasone-treated rats, as compared to incubations with liver microsomes from control rats, can in part be explained by the higher production of superoxide anion radicals observed in the dexamethasone systems. The third mechanism was shown to proceed by formation of a hydroxylated metabolite that loses fluoride anion upon exposure to oxygen. The reactive intermediate formed upon oxygen exposure might be the semiquinoneimine which loses its fluorine atom as a fluoride anion upon dimerization or polymerization and/or protein binding. The fluorohydroxyanilines, in which the hydroxyl group is ortho or para with respect to the fluoro substituent, appear especially to be highly unstable and lose fluoride anion in the presence of oxygen. Finally, it is concluded that all three pathways for dehalogenation of fluorinated aniline derivatives are bioactivation pathways. The reactivity of the (semi)quinoneimines formed in these reactions is dependent on their substitution pattern and increases with increasing number of fluoro-substituents. Therefore, bioactivation for a series of fluorinated aniline derivatives, can be expected to vary with the substitution pattern and to increase with increasing number of halogen substituents.     

New approaches to augment fungal biotransformation

The possibility of using solid supports and intermittent substrate feeding to manipulate biotransformation by fungi was examined, with amoxapine as a model compound. Cunninghamella elegans ATCC 8688a grown as free cells in six-well plates showed 7-hydroxyamoxapine as the major metabolite of amoxapine biotransformation. However, when cells were grown in the presence of activated carbon, N-formyl-7-hydroxyamoxapine was formed as the major metabolite. Intermittent feeding of amoxapine also favored the formation of N-formyl-7-hydroxyamoxapine.     

Characterization of a newly isolated strain Rhodococcus erythropolis ZJB-09149 transforming 2-chloro-3-cyanopyridine to 2-chloronicotinic acid

2-Chloronicotinic acid is receiving much attention for its effective applications as a key precursor in the synthesis of pesticides and medicines. In this study, a strain ZJB-09149 converting 2-chloro-3-cyanopyridine to 2-chloronicotinic acid was newly isolated and identified as Rhodococcus erythropolis, based on its physiological and biological tests, and 16S rDNA sequence analysis. In addition, the effects of inducer, carbon source and nitrogen source were examined. Maximum activity was achieved when the above parameters were set as 8 g/l ?-caprolactam, 7 g/l yeast extract and 5 g/l maltose. Moreover, the biotransformation pathway of 2-chloro-3-cyanopyridine to 2-chloronicotinic acid in strain ZJB-09149 was investigated as well. This study revealed that the nitrile hydratase (NHase) and amidase expressed in R. erythropolis ZJB-09149 are responsible for the conversion of 2-chloro-3-cyanopyridine. This is the first time to report on the biotransformation preparation of 2-chloronicotinic acid.     

Biotransformation of benzo[a]pyrene by the thermophilic bacterium <Emphasis Type="Italic">Bacillus licheniformis</Emphasis> M2-7

Benzo[a]pyrene (BaP) is recognized as a potentially carcinogenic and mutagenic hydrocarbon, and thus, its removal from the environment is a priority. The use of thermophilic bacteria capable of biodegrading or biotransforming this compound to less toxic forms has been explored in recent decades, since it provides advantages compared to mesophilic organisms. This study assessed the biotransformation of BaP by the thermophilic bacterium Bacillus licheniformis M2-7. Our analysis of the biotransformation process mediated by strain M2-7 on BaP shows that it begins during the first 3 h of culture. The gas chromatogram of the compound produced shows a peak with a retention time of 17.38 min, and the mass spectra shows an approximate molecular ion of m/z 167, which coincides with the molecular weight of the chemical formula C₆H₄(COOH)₂, confirming a chemical structure corresponding to phthalic acid. Catechol 2,3-dioxygenase (C23O) enzyme activity was detected in minimal saline medium supplemented with BaP (0.33 U mg^?1 of protein). This finding suggests that B. licheniformis M2-7 uses the meta pathway for biodegrading BaP using the enzyme C23O, thereby generating phthalic acid as an intermediate.     

Preparation of enantiopure (R)-hydroxy metabolite of denbufylline using immobilized Lactobacillus kefiri DSM 20587 as a catalyst

Lactobacillus kefiri DSM 20587 cells were immobilized in calcium alginate and carrageenan. The immobilized cells were used as biocatalysts for the enantioselective reduction of the methyl ketone group of denbufylline to synthesize the enantiopure (R)-hydroxy metabolite: (-)-1,3-dibutyl-7-((2'R)-hydroxypropyl)-1H-purine-2,6(3H,7H)-dione (1). The experimental conditions for the biotransformation were optimized. As denbufylline is insoluble in aqueous media, the influence of cosolvents (dimethylsulfoxide (DMSO), acetonitrile) and different concentrations of each solvent in the reaction mixture on the yield and enantiomeric excess of the final biotransformation product was studied. The maximum biotransformation yield (96-98%) and highest enantioselectivity (96% ee) for the obtained metabolite were reached using DMSO as a cosolvent at a concentration of 7.5% (v/v) in the presence of L. kefiri immobilized either in calcium alginate or in carrageenan. The absolute configuration of the stereogenic center of 1 was determined by applying Mosher's method.     

Identification of intermediate and branch metabolites resulting from biotransformation of 2-benzoxazolinone by Fusarium verticillioides

Detoxification of the maize (Zea mays) antimicrobial compound 2-benzoxazolinone by the fungal endophyte Fusarium verticillioides involves two genetic loci, FDB1 and FDB2, and results in the formation of N-(2-hydroxyphenyl)malonamic acid. Intermediate and branch metabolites were previously suggested to be part of the biotransformation pathway. Evidence is presented here in support of 2-aminophenol as the intermediate metabolite and 2-acetamidophenol as the branch metabolite, which was previously designated as BOA-X. Overall, 2-benzoxazolinone metabolism involves hydrolysis (FDB1) to produce 2-aminophenol, which is then modified (FDB2) by addition of a malonyl group to produce N-(2-hydroxyphenyl)malonamic acid. If the modification is prevented due to genetic mutation (fbd2), then 2-acetamidophenol may accumulate as a result of addition of an acetyl group to 2-aminophenol. This study resolves the overall chemistry of the 2-benzoxazolinone detoxification pathway, and we hypothesize that biotransformation of the related antimicrobial 6-methoxy-2-benzoxazolinone to produce N-(2-hydroxy-4-methoxyphenyl)malonamic acid also occurs via the same enzymatic modifications. Detoxification of these antimicrobials by F. verticillioides apparently is not a major virulence factor but may enhance the ecological fitness of the fungus during colonization of maize stubble and field debris.     

Induction of carbofuran oxidation to 4-hydroxycarbofuran by Pseudomonas sp. 50432

Pseudomonas sp. 50432 biotransformed a highly toxic pesticide, carbofuran (2,3-dihydro-2,2-dimethylbenzofuran-7-yl methylcarbamate) to 7-phenol (2,3-dihydro-2,2-dimethyl-7-hydroxy benzofuran) and several unknown metabolites. One of the unknown metabolites identified by gas chromatography/mass spectroscopy was 4-hydroxycarbofuran (2,3-dihydro-2,2-dimethyl-4-hydroxybenzofuran-7-yl methylcarbamate). It had a mass (237) similar to 3-hydroxycarbofuran and 5-hydroxycarbofuran but different fragmentation patterns. This is the first report in which an inducible oxidative enzyme, hydroxylase, mediated the conversion of carbofuran to 4-hydroxycarbofuran. A second constitutively synthesized enzyme hyrolase transformed carbofuran to 7-phenol.     

Microbiological degradation of bile acids. Ring a cleavage and 7α,12α-dehydroxylation of cholic acid by Arthrobacter simplex

The metabolism of cholic acid by Arthrobacter simplex was investigated. This organism effected both ring a cleavage and elimination of the hydroxyl groups at C-7 and C-12 and gave a new metabolite, (4R)-4-[4alpha-(2-carboxyethyl)-3aalpha-hexahydro-7abeta-methyl-5-oxoindan-1beta-yl]valeric acid, which was isolated and identified through its partial synthesis. A degradative pathway of cholic acid into this metabolite is tentatively proposed, and the possibility that the proposed pathway could be extended to the cholic acid degradation by other microorganisms besides A. simplex is discussed. The possibility that the observed reactions in vitro could occur during the metabolism of bile acids in vivo is considered.     

Rapid oxidation of ring methyl groups is the primary mechanism of biotransformation of gemfibrozil by the fungus <Emphasis Type="Italic">Cunninghamella elegans</Emphasis>

The hypolipidemic agent gemfibrozil (GEM), which has been studied for its metabolism in humans and animals, was investigated to elucidate its primary metabolism by Cunninghamella elegans. The fungus produced ten metabolites (FM1–FM9 and FM6′) from the biotransformation of GEM. Based on LC/MS/MS and NMR analyses, a major metabolite, FM7, was identified as 2′-hydroxymethyl GEM. FM6 was considered to be 5′-hydroxymethyl GEM, after comparison of results LC/MS, LC/MS/MS, and UV absorption spectra to FM7. The combined concentration of FM6 and FM7 was found to increase up to 0.83 mM by day 2, and then decreased gradually with incubation time, followed by a noticeable increase in the biotransformation product, FM1, up to 0.86 mM by day 15. NMR analyses confirmed that FM1 was 2′,5′-dihydroxymethyl GEM. Further minor oxidations of the aromatic ring and carboxylic acid intermediates were also detected. Based upon these findings, the major fungal metabolic pathway for GEM is likely to occur via production of 2′,5′-dihydroxymethyl GEM from 2′-hydroxymethyl GEM. These relatively rapid and diverse biotransformations of GEM by C. elegans suggest that depending upon conditions, it may also follow a similar biodegradation fate when released into the natural environment.