Use of 13C nuclear magnetic resonance to assess fossil fuel biodegradation: fate of [1-13C]acenaphthene in creosote polycyclic aromatic compound mixtures degraded by bacteria.

[1-13C]acenaphthene, a tracer compound with a nuclear magnetic resonance (NMR)-active nucleus at the C-1 position, has been employed in conjunction with a standard broad-band-decoupled 13C-NMR spectroscopy technique to study the biodegradation of acenaphthene by various bacterial cultures degrading aromatic hydrocarbons of creosote. Site-specific labeling at the benzylic position of acenaphthene allows 13C-NMR detection of chemical changes due to initial oxidations catalyzed by bacterial enzymes of aromatic hydrocarbon catabolism. Biodegradation of [1-13C]acenaphthene in the presence of naphthalene or creosote polycyclic aromatic compounds (PACs) was examined with an undefined mixed bacterial culture (established by enrichment on creosote PACs) and with isolates of individual naphthalene- and phenanthrene-degrading strains from this culture. From 13C-NMR spectra of extractable materials obtained in time course biodegradation experiments under optimized conditions, a number of signals were assigned to accumulated products such as 1-acenaphthenol, 1-acenaphthenone, acenaphthene-1,2-diol and naphthalene 1,8-dicarboxylic acid, formed by benzylic oxidation of acenaphthene and subsequent reactions. Limited degradation of acenaphthene could be attributed to its oxidation by naphthalene 1,2-dioxygenase or related dioxygenases, indicative of certain limitations of the undefined mixed culture with respect to acenaphthene catabolism. Coinoculation of the mixed culture with cells of acenaphthene-grown strain Pseudomonas sp. strain A2279 mitigated the accumulation of partial transformation products and resulted in more complete degradation of acenaphthene. This study demonstrates the value of the stable isotope labeling approach and its ability to reveal incomplete mineralization even when as little as 2 to 3% of the substrate is incompletely oxidized, yielding products of partial transformation. The approach outlined may prove useful in assessing bioremediation performance.

Biotransformation of 6,6-Dimethylfulvene by Pseudomonas putida RE213.

The biotransformation of 6,6-dimethylfulvene [5-(1-methylethylidene)-1,3-cyclopentadiene], a nonaromatic C(inf5) carbocyclic analog of isopropylbenzene, was examined by using Pseudomonas putida RE213, a Tn5-generated dihydrodiol-accumulating mutant of the isopropylbenzene-degrading strain P. putida RE204. 6,6-Dimethylfulvene was converted to a single chiral product identified as (+)-(1R,2S)-cis-1,2-dihydroxy-5-(1-methylethylidene)-3-cyclopentene. This isopropylbenzene 2,3-dioxygenase-catalyzed transformation demonstrates the potential of bacterial arene dioxygenases for the direct conversion of cyclopentadienylidene compounds to homochiral C(inf5) carbocyclic cis-diols for use in enantiocontrolled organic syntheses.

Oxidation of naphthenoaromatic and methyl-substituted aromatic compounds by naphthalene 1,2-dioxygenase.

Oxidation of acenaphthene, acenaphthylene, and fluorene was examined with recombinant strain Pseudomonas aeruginosa PAO1(pRE695) expressing naphthalene dioxygenase genes cloned from plasmid NAH7. Acenaphthene underwent monooxygenation to 1-acenaphthenol with subsequent conversion to 1-acenaphthenone and cis- and trans-acenaphthene-1,2-diols, while acenaphthylene was dioxygenated to give cis-acenaphthene-1,2-diol. Nonspecific dehydrogenase activities present in the host strain led to the conversion of both of the acenaphthene-1,2-diols to 1,2-acenaphthoquinone. The latter was oxidized spontaneously to naphthalene-1,8-dicarboxylic acid. No aromatic ring dioxygenation products were detected from acenaphthene and acenaphthylene. Mixed monooxygenase and dioxygenase actions of naphthalene dioxygenase on fluorene yielded products of benzylic 9-monooxygenation, aromatic ring dioxygenation, or both. The action of naphthalene dioxygenase on a variety of methyl-substituted aromatic compounds, including 1,2,4-trimethylbenzene and isomers of dimethylnaphthalene, resulted in the formation of benzylic alcohols, i.e., methyl group monooxygenation products, which were subsequently converted to the corresponding carboxylic acids by dehydrogenase(s) in the host strain. Benzylic monooxygenation of methyl groups was strongly predominant over aromatic ring dioxygenation and essentially nonspecific with respect to the substitution pattern of the aromatic substrates. In addition to monooxygenating benzylic methyl and methylene groups, naphthalene dioxygenase behaved as a sulfoxygenase, catalyzing monooxygenation of the sulfur heteroatom of 3-methylbenzothiophene.

Actions of a versatile fluorene-degrading bacterial isolate on polycyclic aromatic compounds.

Pseudomonas cepacia F297 grew with fluorene as a sole source of carbon and energy; its growth yield corresponded to an assimilation of about 40% of fluorene carbon. The accumulation of a ring meta-cleavage product during growth and the identification of 1-indanone in growth media and washed-cell suspensions suggest that strain F297 metabolizes fluorene by mechanisms analogous to those of naphthalene degradation. In addition to fluorene, strain F297 utilized for growth a wide variety of polycyclic aromatic compounds (PACs), including naphthalene, 2,3-dimethylnaphthalene, phenanthrene, anthracene, and dibenzothiophene. Fluorene-induced cells of the strain also transformed 2,6-dimethylnaphthalene, biphenyl, dibenzofuran, acenaphthene, and acenaphthylene. The identification of products formed from those substrates (by gas chromatography-mass spectrometry) in washed-cell suspensions indicates that P. cepacia F297 carries out the following reactions: (i) aromatic ring oxidation and cleavage, apparently using the pyruvate released for growth, (ii) methyl group oxidations, (iii) methylenic oxidations, and (iv) S oxidations of aromatic sulfur heterocycles. Strain F297 grew with a creosote-PAC mixture, producing an almost complete removal of all aromatic compounds containing 2 to 3 rings in 14 days, as demonstrated by gas chromatography analysis of the remaining PACs recovered from cultures. The identification of key chemicals confirmed that not only are certain compounds depleted but also the anticipated reaction products are found.

Transformation of Substituted Fluorenes and Fluorene Analogs by Pseudomonas sp. Strain F274.

Pseudomonas sp. strain F274, previously shown to catabolize fluorene via fluorenone and its angular dioxygenation, 2(prm1),3(prm1)-dihydroxy-2-carboxybiphenyl, phthalate, and protocatechuate, was examined for its ability to transform substituted fluorenes and S- and N-heterocyclic analogs. Halogen- and methyl-substituted fluorenes were metabolized to correspondingly substituted phthalates via attack on the unsubstituted ring. In the case of 1-methylfluorene, initial oxidation of the methyl group to carboxyl prevented all other transformations but 9-monooxygenation. This strain also oxidized the S-heteroatoms and benzylic methylenic groups of fluorene analogs. No angular dioxygenation of S- and N-heterocycles was observed.

Regioselective dioxygenation of ortho-trifluoromethylbenzoate by Pseudomonas aeruginosa 142: evidence for 1,2-dioxygenation as a mechanism in ortho-halobenzoate dehalogenation.

Pseudomonas aeruginosa strain 142 oxidizes 2-halobenzoates via a multicomponent oxygenase (V. Romanov and R.P. Hausinger, J. Bacteriol., 1994, 176(11), 3368-3374). The intermediacy of a highly unstable cis-diol in the reaction has been proposed. Direct evidence for this is currently lacking and the stereochemical course of the reaction cannot be inferred from previous studies. In this study, 2-trifluoromethylbenzoate was stoichiometrically oxidized by P. aeruginosa 142 to a chiral product identified as (-)2-trifluoromethyl-cis-1,2-dihydroxy-3,5-cyclohexadiene-1-carboxylic acid. These data rigorously establish a dioxygenative mechanism for 2-halobenzoate metabolism.

Evidence for a novel pathway in the degradation of fluorene by Pseudomonas sp. strain F274.

A fluorene-utilizing microorganism, identified as a species of Pseudomonas, was isolated from soil severely contaminated from creosote use and was shown to accumulate six major metabolites from fluorene in washed-cell incubations. Five of these products were identified as 9-fluorenol, 9-fluorenone, (+)-1,1a-dihydroxy-1-hydro-9-fluorenone, 8-hydroxy-3,4-benzocoumarin, and phthalic acid. This last compound was also identified in growing cultures supported by fluorene. Fluorene assimilation into cell biomass was estimated to be approximately 50%. The structures of accumulated products indicate that a previously undescribed pathway of fluorene catabolism is employed by Pseudomonas sp. strain F274. This pathway involves oxygenation of fluorene at C-9 to give 9-fluorenol, which is then dehydrogenated to the corresponding ketone, 9-fluorenone. Dioxygenase attack on 9-fluorenone adjacent to the carbonyl group gives an angular diol, 1,1a-dihydroxy-1-hydro-9-fluorenone. Identification of 8-hydroxy-3,4-benzocoumarin and phthalic acid suggests that the five-membered ring of the angular diol is opened first and that the resulting 2'-carboxy derivative of 2,3-dihydroxy-biphenyl is catabolized by reactions analogous to those of biphenyl degradation, leading to the formation of phthalic acid. Cell extracts of fluorene-grown cells possessed high levels of an enzyme characteristic of phthalate catabolism, 4,5-dihydroxyphthalate decarboxylase, together with protocatechuate 4,5-dioxygenase. On the basis of these findings, a pathway of fluorene degradation is proposed to account for its conversion to intermediary metabolites. A range of compounds with structures similar to that of fluorene was acted on by fluorene-grown cells to give products consistent with the initial reactions proposed.

Isolation and characterization of (+)-1,1a-dihydroxy-1-hydrofluoren-9-one formed by angular dioxygenation in the bacterial catabolism of fluorene.

Transformation of fluorene by washed cells of fluorene-grown Pseudomonas sp. F274 yielded 1,la-dihydroxy-1-hydrofluoren-9-one (up to 100 mg/l) as the stable product of angular dioxygenation of 9-fluorenone. Structural identity of the angular keto-diol was established by 13C- and 1H-NMR, gas chromatography- and direct probe-mass spectrometry. Definitive assignment of 1,1a-dioxygenation, but not 4,4a-, was based on the isolation and rigorous identification of 1-hydroxyfluoren-9-one as the exclusive product of acidic dehydration. Chiral 1H-NMR analysis and optical rotation of isolated 1,1a-dihydroxy-1-hydrofluoren-9-one ([alpha]D = + 132.1 degrees) are indicative of a single enantiomer with an inferred cis-stereochemistry of the hydroxyl groups. This compound is evidently an intermediate of fluorene catabolism by this strain and not a dead-end product because its formation is transient in washed cell incubations and ultimately it is completely consumed with the formation of acidic metabolites.

Microbial oxidation of adamantanone by Pseudomonas putida carrying the camphor catabolic plasmid.

Intact cells of (+/-)camphor-grown Pseudomonas putida, ATCC17453(CAM), have been shown to oxidize readily the monoketone derivative of cage hydrocarbon adamantane, forming oxygenated products indicative of both biological Baeyer-Villiger and hydroxylation reactions. Formed products were identified as 4-oxahomoadamantan-5-one, 5-hydroxyadamantan-2-one and 1-hydroxy-4-oxahomoadamantan-5-one. Minor products formed as a result of secondary reactions were tentatively identified as syn- and anti-1,4-dihydroxyadamantanes and bicyclo[3.3.1]nonan-3-ol. Adamantanone initial concentrations determined whether 1-hydroxy-4-oxahomoadamantan-5-one was the sole product (below 120 mg/l) or 4-oxahomoadamantan-5-one was the principle (up to 92%) product (240-600 mg/l). Formation of 1-hydroxy-4-oxahomoadamantan-5-one appears to occur by two routes determined by the sequence of lactonization and hydroxylation.

[Oxidation of dibenzofuran by Pseudomonas strains harboring plasmids of naphthalene degradation]. / Okislenie dibenzofurana shtammami Pseudomonas, nesushchimi plazmidy biodegradatsii naftalina.

Pseudomonas strains harboring plasmids pBS3, pBS4, NAH7 were shown to carry out initial transformation of dibenzofurane to 4-[2'-(3'-hydroxy)-benzofuranyl]-2-keto-3-butenic acid due to broad substrate specificity of the enzymes of naphthalene catabolism nahA, nahB, nahC and nahD. These strains did not grow on dibenzofurane because of the inability of the enzyme nahE to split pyruvate of 4-[2'-(3' hydroxy)-benzofuranyl]-2-keto-3-butenic acid, which leads to accumulation of the latter. The strains harboring plasmids pBS2 and NPL-1 are not capable of any transformation of dibenzofurane.

[Comparative study of aromatic ring meta-cleavage enzymes in Pseudomonas strains with plasmid and chromosomal genetic control of the catabolism of biphenyl and m-toluate]. / Sravnitel'noe izuchenie fermentov meta-rasshchepleniia aromaticheskogo kol'tsa u shtammov bakterii Pseudomonas s plazmidnym i khromosomnym geneticheskim kontrolem katabolizm bifenila i m-toluilate.

It was shown that two different enzymes of aromatic ring oxidative meta-cleavage (2,3-dihydroxybiphenyl-1,2-dioxygenase), DBO and catechol-2,3-dioxygenase, C230) function in Pseudomonas strains with a plasmid and chromosomal genetic control of biphenyl and toluate catabolism. A comparative analysis of DBO's and C230's expressed by the pBS241 biphenyl degradative plasmid in P. putida BS893, pBS311 in P. putida U83, chromosomal genes in P. putida BF and C230 from P. putida PaW160 (pWWO) was carried out. It was found that the DBO's of all strains under study are highly specialized enzymes in respect of 2,3-dihydroxybiphenyl cleavage and are also able to cleave 3-methyl-catechol and catechol (but not 4-methylcatechol) at low rates. In contrast with DBO's, in Pseudomonas strains the substrate specificities of all C230's are variable. The C230's expressed by the D-plasmids pBS241 and pBC311 have a moderate affinity for catechol, 3-methyl- and 4-methylcatechol, but are unable to cleave 2,3-dihydroxybiphenyl. The C230 which is encoded by the chromosomal structure gene from P. putida BF is very similar to C230 which codes for the TOL-plasmid pWWO. These plasmid differ from C230's expressed by biphenyl D-plasmids due to their capability to cleave 2,3-dihydroxybiphenyl in addition to catechol cleavage. All DBO's and C230's under study possess a number of properties that are typical for the enzymes having an oxidative meta-cleaving effect. The different roles of these enzymes in biphenyl and toluate catabolism in Pseudomonas strains are discussed.

[Plasmids for biphenyl, chlorobiphenyl and metatoluylate degradation from Pseudomonas putida]. / Plazmida degradatsii bifenila, khlorbifenilov, meta-toluilata Pseudomonas putida.

Pseudomonas putida strain SU83, harbors the pBS311 plasmid coding for the degradation of biphenyl, 2- and 4-chlorbiphenyl, meta- and paratoluylate. The insertional mutants of the plasmid obtained by the transposon Tn5 insertion were isolated. One of the mutants was used for cloning of the biphenyl degradation genes. The plasmid pBS311:: Tn5 DNA was inserted into the BamHI site of the plasmid pBR322 and cloned. 11 recombinants of 354 tested were treated with 0.1% solution of 2,3-dioxybiphenyl. One of them has acquired the yellow colour testifying to conversion of 2,3-dioxyphenyl to "2-hydroxy-6-keto-6-phenylhexa-2,4-diene acid. The recombinant plasmid pBS312 from this clone is 10.5 kb in size, the size of the insert being 6.2 kb. Escherichia coli SU185 cells harbouring pBS312 are able to support metacleavage of 2,3-dioxybiphenyl, 3-methylcatechol and catechol, but not of 4-methylcatechol. The results suggest the cloned fragment to contain a gene for 2,3-dioxybiphenyl-1,2-dioxygenase, the third enzyme for biphenyl catabolism.

[Cloning and expression of Pseudomonas putida gene controlling the catechol-2,3-oxygenase activity in Escherichia coli cells]. / Klonirovanie i ékspressiia gena Pseudomonas putida, kontroliruiushchego katekhol-2,3-oksigenaznuiu aktivnost' v kletkakh Escherichia coli.

The genes nahC and nahD from Pseudomonas putida naphthalene degradation plasmid pBS286 were cloned on the vector pUC19 in Escherichia coli cells. The catechol-2,3-oxygenase activity observed in E. coli cells containing recombinant plasmid pBS955 demands the participation of 32 kD polypeptide which is apparently the product of the nahC gene. Second polypeptide of molecular weight 34.5 kD is synthesized in pBS955 containing E. coli minicells and perhaps it is a nahD gene product. The data obtained indicate that 1,2-dihydroxynaphthalene dioxygenase possesses a relaxed substrate specificity, at least, when cloned on a multicopy vector. The cloned DNA insert of pBS955 is not likely to contain its own promoter, so that expression of nahC and nahD genes from the nah1 operon is controlled by the vector lac promoter. The direction of transcription and localization of both polypeptides on the pBS955 map are determined.

[Purification and properties of two enzymes of meta-cleaving the aromatic ring controlled by the biphenyl biodegradation plasmid pBS 241 from Pseudomonas putida]. / Ochistka i svoistva dvukh fermentov meta-rasshchepleniia aromaticheskogo kol'tsa, kontroliruemykh plazmidoi biodegradatsii bifenila pBS 241, iz bakterii Pseudomonas putida]

It was shown that two metapyrocatechases (EC 1.13.11.2) function in Pseudomonas putida BS893. Biphenyl degradative plasmid pBS241 carries the genes of these enzymes. The basic properties of the both enzymes, i. e., MPC1 and MPC2, were investigated. It was found that MPC1 is an enzyme with a molecular mass of 135 kD and has a heterotetrameric subunit structure (alpha 2 beta 2), being made up of two non-identical polypeptides with Mr of 34 and 22.5 kD; pI is 5.15, the pH optimum is at 8.0, a temperature optimum is at 54 degrees C. MPC2 has a molecular mass of 154 kD and possesses a homotetrameric subunit structure (alpha 4); it consists of identical polypeptides with Mr of 41 kD and has a pI of 4.95, a pH optimum at 7.5 and a temperature optimum at 60 degrees C. The substrate specificity of the enzymes was studied, and the Km and Vmax values for substituted catechols were determined. MPC1 shows a high affinity for 2.3-dihydroxybiphenyl and hydrolyzes 3-methylcatechol and catechol (but not 4-methylcatechol) at a low rate. MPC2 has a moderate affinity for catechol, 3- and 4-methylcatechols, but is incapable of cleaving 2.3-dihydroxybiphenyl. Both enzymes share in common some typical properties of metapyrocatechases. The different role of MPC1 and MPC2 in biphenyl catabolism is discussed.

[Mutations of plasmid pBS286 blocking the initial stages of naphthalene oxidation induced by Tn5]. / Mutatsii plazmidy pBS286, blokiruiushchie pervichnye étapy okisleniia naftalina, indutsirovannye Tn5.

A collection of Tn5 transposon Nah- mutants of the plasmid pBS286 was obtained. The insertion sites were localized and orientation of Tn5 determined. The mutants obtained were biochemically analyzed, the nah-region map of the plasmid being elaborated. Structural genes of the nah operon were shown to be organized similarly to those of the nah1 operon of the NAH7 plasmid discussed in the literature. The data obtained are in favour of the previously published information on the presence of elements operating the pBS286 plasmid. The results are given indicating a possibility of regulating the expression of catechol splitting meta-pathway genes with participation of products on early stages of naphthalene oxidation.

[Catabolism of biphenyl by Pseudomonas putida BS 893 strain containing the biodegradation plasmid pBS241]. / Katabolizm bifenila shtammom Pseudomonas putida BS 893, soderzhashchim plazmidu biodegradatsii pBS241.

The isolation and identification of biphenyl catabolism products in Pseudomonas putida BS 893 (pBS241) showed the presence of benzoic, m-hydroxybenzoic and cinnamic acids. The two latter compounds were not found in biphenyl degradation by other bacterial strains. P. putida BS 893 (pBS241) differed from other biphenyl-positive Pseudomonas strains in the enzyme activity. These differences may stem from peculiarities in the pathway of biphenyl catabolism controlled by plasmid pBS241.