Hydroxylation of biphenyl by the yeast Trichosporon mucoides

Moniliella spathulata, an oil-degrading yeast, which promotes growth of barley in oil-polluted soil

The yeast strain Moniliella spathulata SBUG-Y 2180 was isolated from oil-contaminated soil at the Tengiz oil field in the Atyrau region of Kazakhstan on the basis of its unique ability to use crude oil and its components as the sole carbon and energy source. This yeast used a large number of hydrocarbons as substrates (more than 150), including n-alkanes with chain lengths ranging from C10 to C32, monomethyl- and monoethyl-substituted alkanes (C9-C23), and n-alkylcyclo alkanes with alkyl chain lengths from 3 to 24 carbon atoms as well as substituted monoaromatic and diaromatic hydrocarbons. Metabolism of this huge range of hydrocarbon substrates produced a very large number of aliphatic, alicyclic, and aromatic acids. Fifty-one of these were identified by GC/MS analyses. This is the first report of the degradation and formation of such a large number of compounds by a yeast. Inoculation of barley seeds with M. spathulata SBUG-Y 2180 had a positive effect on shoot and root development of plants grown in oil-contaminated sand, pointing toward potential applications of the yeast in bioremediation of polluted soils. KEY POINTS: • Moniliella spathulata an oil-degrading yeast • Increase of the growth of barley.

Diversity and degradative capabilities of bacteria and fungi isolated from oil-contaminated and hydrocarbon-polluted soils in Kazakhstan

Bacteria and fungi were isolated from eight different soil samples from different regions in Kazakhstan contaminated with oil or salt or aromatic compounds. For the isolation of the organisms, we used, on the one hand, typical hydrocarbons such as the well utilizable aliphatic alkane tetradecane, the hardly degradable multiple-branched alkane pristane, and the biaromatic compound biphenyl as enrichment substrates. On the other hand, we also used oxygenated derivatives of alicyclic and monoaromatic hydrocarbons, such as cyclohexanone and p-tert-amylphenol, which are known as problematic pollutants. Seventy-nine bacterial and fungal strains were isolated, and 32 of them that were clearly able to metabolize some of these substrates, as tested by HPLC-UV/Vis and GC-MS analyses, were characterized taxonomically by DNA sequencing. Sixty-two percent of the 32 isolated strains from 14 different genera belong to well-described hydrocarbon degraders like some Rhodococci as well as Acinetobacter, Pseudomonas, Fusarium, Candida, and Yarrowia species. However, species of the bacterial genus Curtobacterium, the yeast genera Lodderomyces and Pseudozyma, as well as the filamentous fungal genera Purpureocillium and Sarocladium, which have rarely been described as hydrocarbon degrading, were isolated and shown to be efficient tetradecane degraders, mostly via monoterminal oxidation. Pristane was exclusively degraded by Rhodococcus isolates. Candida parapsilosis, Fusarium oxysporum, Fusarium solani, and Rhodotorula mucilaginosa degraded cyclohexanone, and in doing so accumulate ε-caprolactone or hexanedioic acid as metabolites. Biphenyl was transformed by Pseudomonas/Stenotrophomonas isolates. When p-tert-amylphenol was used as growth substrate, none of the isolated strains were able to use it.

Fungal biotransformation of short-chain n-alkylcycloalkanes

The cycloalkanes, comprising up to 45% of the hydrocarbon fraction, occur in crude oil or refined oil products (e.g., gasoline) mainly as alkylated cyclohexane derivatives and have been increasingly found in environmental samples of soil and water. Furthermore, short-chain alkylated cycloalkanes are components of the so-called volatile organic compounds (VOCs). This study highlights the biotransformation of methyl- and ethylcyclohexane by the alkane-assimilating yeast Candida maltosa and the phenol- and benzoate-utilizing yeast Trichosporon mucoides under laboratory conditions. In the course of this biotransformation, we detected 25 different metabolites, which were analyzed by HPLC and GC-MS. The biotransformation process of methylcyclohexane in both yeasts involve (A) ring hydroxylation at different positions (C2, C3, and C4) and subsequent oxidation to ketones as well as (B) oxidation of the alkyl side chain to hydroxylated and acid products. The yeast T. mucoides additionally performs ring hydroxylation at the C1-position and (C) oxidative decarboxylation and (D) aromatization of cyclohexanecarboxylic acid. Both yeasts also oxidized the saturated ring system and the side chain of ethylcyclohexane. However, the cyclohexylacetic acid, which was formed, seemed not to be substrate for aromatization. This is the first report of several new transformation reactions of alkylated cycloalkanes for eukaryotic microorganisms.

Novel insights into the fungal oxidation of monoaromatic and biarylic environmental pollutants by characterization of two new ring cleavage enzymes

The phenol-degrading yeast Trichosporon mucoides can oxidize and detoxify biarylic environmental pollutants such as dibenzofuran, diphenyl ether and biphenyl by ring cleavage. The degradation pathways are well investigated, but the enzymes involved are not. The high similarity of hydroxylated biphenyl derivatives and phenol raised the question if the enzymes of the phenol degradation are involved in ring cleavage or whether specific enzymes are necessary. Purification of enzymes from T. mucoides with catechol cleavage activity demonstrated the existence of three different enzymes: a classical catechol-1,2-dioxygenase (CDO), not able to cleave the aromatic ring system of 3,4-dihydroxybiphenyl, and two novel enzymes with a high affinity towards 3,4-dihydroxybiphenyl. The comparison of the biochemical characteristics and mass spectrometric sequence data of these three enzymes demonstrated that they have different substrate specificities. CDO catalyzes the ortho-cleavage of dihydroxylated monoaromatic compounds, while the two novel enzymes carry out a similar reaction on biphenyl derivatives. The ring fission of 3,4-dihydroxybiphenyl by the purified enzymes results in the formation of (5-oxo-3-phenyl-2,5-dihydrofuran-2-yl)acetic acid. These results suggest that the ring cleavage enzymes catalyzing phenol degradation are not involved in the ring cleavage of biarylic compounds by this yeast, although some intermediates of the phenol metabolism may function as inducers.

Cytochrome P450 enzymes in the fungal kingdom

Cytochrome P450 monooxygenases of fungi are involved in many essential cellular processes and play diverse roles. The enzymes catalyze the conversion of hydrophobic intermediates of primary and secondary metabolic pathways, detoxify natural and environmental pollutants and allow fungi to grow under different conditions. Fungal genome sequencing projects have enabled the annotation of several thousand novel cytochromes P450, many of which constitute new families. This review presents the characteristics of fungal cytochrome P450 systems and updates information on the functions of characterized fungal P450 monooxygenases as well as outlines the currently used strategies for determining the function of the many putative P450 enzymes.

Hydroxy-PCBs, methoxy-PCBs and hydroxy-methoxy-PCBs: metabolites of polychlorinated biphenyls formed in vitro by tobacco cells

While the metabolism of polychlorinated biphenyls (PCBs) in plant cells is a rarely studied field, hydroxy-PCBs have been detected in several studies involving the use of various plant species. The ability of the tobacco (Nicotiana tabacum) callus culture WSC-38 to metabolize six dichlorobiphenyls under aseptic conditions was studied, and the resulting PCB metabolites were analyzed. WSC-38 cultures were cultivated with individual dichlorinated PCB congeners. The metabolites were identified based on mass spectra characteristics after gas chromatography separation. In addition, metabolites of PCB 9 (2,5-dichlorobiphenyl) were identified by comparing their retention characteristics with the available standards. In most cases at least two hydroxy-PCBs were produced from each parent PCB. Methoxy-PCBs and hydroxy-methoxy-PCBs were other groups of metabolites produced. To the best of our knowledge, ours is the first report to determine the presence of methoxy- and hydroxy-methoxy-metabolites of PCBs in plants. The role of the O-methyltransferases (OMTs) in the methylation of hydroxy-PCBs is discussed. As methoxy-metabolites of acetophenone were found among our samples, we posit that the OMTs responsible for the methylation of these compounds are also involved in the metabolism of PCBs in cultures of WSC-38.

Oxidative ring cleavage of low chlorinated biphenyl derivatives by fungi leads to the formation of chlorinated lactone derivatives

The yeast Trichosporon mucoides and the filamentous fungus Paecilomyces lilacinus as biphenyl oxidizing organisms are able to oxidize chlorinated biphenyl derivatives. Initial oxidation of derivatives chlorinated at C4 position started at the non-halogenated ring and went on up to ring cleavage. The products formed were mono- and dihydroxylated 4-chlorobiphenyls, muconic acid derivatives 2-hydroxy-4-(4-chlorophenyl)-muconic acid and 2-hydroxy-5-(4-chlorophenyl)-muconic acid as well as the corresponding lactones 4-(4-chlorophenyl)-2-pyrone-6-carboxylic acid and 3-(4-chlorophenyl)-2-pyrone-6-carboxylic acid. Altogether T. mucoides formed 12 products and P. lilacinus accumulated five products. Whereas the rate of the first oxidation step at 4-chlorobiphenyl seems to be diminished by the decreased bioavailability of the compound, no considerable differences were observed between the degradation of 4-chloro-4'-hydroxybiphenyl and 4-hydroxybiphenyl. Twofold chlorinated biphenyl derivatives did not serve as substrates for oxidation by either organism with the exception of 2,2'-dichlorobiphenyl, transformed by the yeast Trichosporon mucoides to two monohydroxylated derivatives. The results show, that soil fungi may contribute to the aerobic degradation of low chlorinated biphenyls accumulating from anaerobic dehalogenation of PCB by bacteria.

Metabolism of aromatic hydrocarbons by the filamentous fungus Cyclothyrium sp

The metabolism of biphenyl, naphthalene, anthracene, phenanthrene, pyrene and benzo[a]pyrene by Cyclothyrium sp. CBS 109850, a coelomycete isolated for the first time in Brazil from industrially polluted estuarine sediment, was studied. The metabolites were extracted and separated by high performance liquid chromatography (HPLC) and characterized by UV spectral analyses and mass, and proton nuclear magnetic resonance ((1)H NMR) spectrometry. Cyclothyrium sp. transformed biphenyl to 4-hydroxybiphenyl and anthracene to anthracene trans-1,2-dihydrodiol. This isolate metabolized 90% of [9-(14)C]phenanthrene, producing phenanthrene trans-9,10-dihydrodiol as a major metabolite, phenanthrene trans-3,4-dihydrodiol, 1-hydroxyphenanthrene, 3-hydroxyphenanthrene, 4-hydroxyphenanthrene, and a novel metabolite, 2-hydroxy-7-methoxyphenanthrene. Circular dichroism spectra analyses indicated that the major enantiomers of phenanthrene trans-9, 10-dihydrodiol, phenanthrene trans-3,4-dihydrodiol and pyrene trans-4,5-dihydrodiol, a pyrene metabolite produced previously by Cyclothyrium sp. CBS 109850, were predominantly in the (R,R) configuration, revealing a high stereoselectivity for initial monooxygenation and enzymatic hydration of phenanthrene and pyrene by Cyclothyrium sp. CBS109850. The results also show a high regioselectivity since the K-regions of phenanthrene and pyrene were the major sites of metabolism.

Oxidation and ring cleavage of dibenzofuran by the filamentous fungus Paecilomyces lilacinus

The ability of the imperfect soil fungus Paecilomyces lilacinus to transform the environmental pollutant dibenzofuran was investigated. Transformation of dibenzofuran and related derivatives lead to 14 products, which were identified by UV spectroscopy, mass spectrometry, and proton nuclear magnetic resonance spectroscopy. Biotransformation was initiated by two separate hydroxylation steps, leading to the accumulation of 4-monohydroxylated and 4-dihydroxylateddibenzofurans. Hydroxylation at both aromatic rings produced 2,7-dihydroxydibenzofuran, 3,7-dihydroxydibenzofuran, and 2,8-dihydroxydibenzofuran. Further oxidation yields ring cleavage of dibenzofuran, which has not been described before for filamentous fungi. The ring fission products were identified as benzo[ b]furo[3,2-d]-2-pyrone-6-carboxylic acid and [2-(1-carboxy-methylidene)-benzofuran-3-ylidene]-hydroxy-acetic acid and its derivatives hydroxylated at carbon 7 and 8 at the non-cleaved ring. Other metabolites were riboside-conjugates of 2-hydroxydibenzofuran and 3-hydroxydibenzofuran. The results showed that P. lilacinus transforms the hydrophobic compound dibenzofuran by phase I/phase II reactions to produce hydroxylated products and excretable sugar conjugates.

Biotransformation of biarylic compounds by yeasts of the genus trichosporon

The biotransformation of biphenyl, dibenzofuran, and diphenyl ether by 24 strains belonging to 18 species of the genus Trichosporon was investigated to assess the taxonomic relevance of this property at species and genus level. With the exceptions of T. brassicae and T. porosum CBS 2040, all other strains were able to transform the parent compounds to monohydroxylated intermediates. A second hydroxylation on the same aromatic ring was carried out by fewer strains and depended on the substrate. It appears that this step is the rate-limiting one in the biotransformation of the biarylic compounds tested. Ring fission of dihydroxylated derivatives of biphenyl was observed within 12 species. The aromatic ring system of dihydroxylated dibenzofuran was cleaved by strains of 5 species, while strains of 13 species were able to cleave the aromatic ring system of dihydroxylated diphenyl ether. Only 4 strains out of 18 species were able to cleave the aromatic ring system of all three parent compounds. These most active yeasts belong to the species T. coremiiforme, T. montevideense, T. mucoides, and T. sporotrichoides. In addition, strains of the species Cryptococcus curvatus and Cryptococcus humicola, closely related to the genus Trichosporon, were tested in parallel.

Novel ring cleavage products in the biotransformation of biphenyl by the yeast Trichosporon mucoides

The yeast Trichosporon mucoides, grown on either glucose or phenol, was able to transform biphenyl into a variety of mono-, di-, and trihydroxylated derivatives hydroxylated on one or both aromatic rings. While some of these products accumulated in the supernatant as dead end products, the ortho-substituted dihydroxylated biphenyls were substrates for further oxidation and ring fission. These ring fission products were identified by high-performance liquid chromatography, gas chromatography-mass spectrometry, and nuclear magnetic resonance analyses as phenyl derivatives of hydroxymuconic acids and the corresponding pyrones. Seven novel products out of eight resulted from the oxidation and ring fission of 3,4-dihydroxybiphenyl. Using this compound as a substrate, 2-hydroxy-4-phenylmuconic acid, (5-oxo-3-phenyl-2,5-dihydrofuran-2-yl)acetic acid, and 3-phenyl-2-pyrone-6-carboxylic acid were identified. Ring cleavage of 3,4,4'-trihydroxybiphenyl resulted in the formation of [5-oxo-3-(4'-hydroxyphenyl)-2,5-dihydrofuran-2-yl]acetic acid, 4-(4'-hydroxyphenyl)-2-pyrone-6-carboxylic acid, and 3-(4'-hydroxyphenyl)-2-pyrone-6-carboxylic acid. 2,3,4-trihydroxybiphenyl was oxidized to 2-hydroxy-5-phenylmuconic acid, and 4-phenyl-2-pyrone-6-carboxylic acid was the transformation product of 3,4,5-trihydroxybiphenyl. All these ring fission products were considerably less toxic than the hydroxylated derivatives.