The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs)

Many members of the sphingomonad genus isolated from different geological areas can degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs) and related compounds. These sphingomonads such as Sphingobium yanoikuyae strain B1, Novosphingobium aromaticivorans strain F199, and Sphingobium sp. strain P2 have been found to possess a unique group of genes for aromatic degradation, which are distantly related with those in pseudomonads and other genera reported so far both in sequence homology and gene organization. Genes for aromatics degradation in these sphingomonads are complexly arranged; the genes necessary for one degradation pathway are scattered through several clusters. These aromatic catabolic gene clusters seem to be conserved among many other sphingomonads such as Sphingobium yanoikuyae strain Q1, Sphingomonas paucimobilis strain TNE12, S. paucimobilis strain EPA505, Sphingobium agrestis strain HV3, and Sphingomonas chungbukensis strain DJ77. Furthermore, some genes for naphthalenesulfonate degradation found in Sphingomonas xenophaga strain BN6 also share a high sequence homology with their homologues found in these sphingomonads. On the other hand, protocatechuic catabolic gene clusters found in fluorene-degrading Sphingomonas sp. strain LB126 appear to be more closely related with those previously found in lignin-degrading S. paucimobilis SYK-6 than the genes in this group of sphingomonads. This review summarizes the information on the distribution of these strains and relationships among their aromatic catabolic genes.     

Fate of polycyclic aromatic hydrocarbons (PAH) in the rhizosphere and mycorrhizosphere of ryegrass

Polycyclic aromatic hydrocarbons (PAH) can be degraded in the rhizosphere but may also interact with vegetation by accumulation in plant tissues or adsorption on root surface. Previous studies have shown that arbuscular mycorrhizal (AM) fungi contribute to the establishment and maintenance of plants in a PAH contaminated soil. We investigated the fate of PAH in the rhizosphere and mycorrhizosphere including biodegradation, uptake and adsorption. Experiments were conducted with ryegrass inoculated or not with Glomus mosseae P2 (BEG 69) and cultivated in pots filled with soil spiked with 5 g kg⁻¹ of anthracene or with 1 g kg⁻¹ of a mixture of 8 PAH in a growth chamber. PAH were extracted from root surfaces, root and shoot tissue and rhizosphere soil and were analysed by GC-MS. In both experiments, 0.006 – 0.11‰ of the initial extractable PAH concentration were adsorbed to roots, 0.003 – 0.16‰ were found in root tissue, 0.001‰ in shoot tissue and 36 – 66% were dissipated, suggesting that the major part of PAH dissipation in rhizosphere soil was due to biodegradation or biotransformation. With mycorrhizal plants, anthracene and PAH were less adsorbed to roots and shoot tissue concentrations were lower than with non mycorrhizal plants, which could contribute to explain the beneficial effect of AM fungi on plant survival in PAH contaminated soils. This revised version was published online in June 2006 with corrections to the Cover Date.     

Biodegradation of polycyclic aromatic hydrocarbons

The intent of this review is to provide an outline of the microbial degradation of polycyclic aromatic hydrocarbons. A catabolically diverse microbial community, consisting of bacteria, fungi and algae, metabolizes aromatic compounds. Molecular oxygen is essential for the initial hydroxylation of polycyclic aromatic hydrocarbons by microorganisms. In contrast to bacteria, filamentous fungi use hydroxylation as a prelude to detoxification rather than to catabolism and assimilation. The biochemical principles underlying the degradation of polycyclic aromatic hydrocarbons are examined in some detail. The pathways of polycyclic aromatic hydrocarbon catabolism are discussed. Studies are presented on the relationship between the chemical structure of the polycyclic aromatic hydrocarbon and the rate of polycyclic aromatic hydrocarbon biodegradation in aquatic and terrestrial ecosystems.     

The development and evaluation of monoclonal antibodies for the detection of polycyclic aromatic hydrocarbons

A highly sensitive enzyme-linked immunosorbent assay (ELISA) for the detection of 3- to 5-ring polycyclic aromatic hydrocarbons (PAHs) has been developed. A functional derivative of dibenzothiophene was synthesized and covalently linked to carrier proteins that were used to produce monoclonal antibodies (mAbs). During the conjugation step, the conjugation efficiency was improved by the presence of 25% N,N-dimethylformamide (DMF). Antibodies were selected based on a competitive inhibition assay to isolate those with the highest sensitivity for free PAHs. When using the mAb in an ELISA format, free PAHs were detected at a concentration as low as 0.1 μg/L (0.1 ppb) in aqueous samples.     

An enzyme-linked immunosorbent assay for detection of pyrene and related polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) can form DNA-binding compounds that show genotoxicity and carcinogenicity. Pyrene, as a PAH, was covalently linked to carrier protein bovine serum albumin and ovalbumin. A monoclonal antibody (McAb) was produced that showed high cross-reactivity values with chrysene (169.73%), benzo[a]pyrene (693.34%), benzo[a]anthracene (16.36%), and indeno[1,2,3-cd]pyrene (40.96%) and showed no significant cross-reactivity values with other homologues (<0.1%). A competitive enzyme-linked immunosorbent assay (ELISA) was developed for detection of pyrene and some homologues in water samples. The detection limit of the assay was 65.08 pg ml⁻¹. The average recoveries of PAHs from tap water, lake water, and mineral water were 99.13, 99.74, and 99.19%, respectively, indicating that matrices of water samples do not interfere with the assay. The results demonstrated that the developed ELISA seems to be a potential method for monitoring of pyrene and some homologous PAHs in water samples.     

Molecular biology approaches for understanding microbial polycyclic aromatic hydrocarbons (PAHs) degradation

The known or suspected hazards of polycyclic aromatic hydrocarbons (PAHs) have provoked enormous concentration and endeavours to relieve or eliminate these precarious compounds from miscellaneous environments including soil, water and air. Among various interventions, biodegradation is an appealing approach for its comparative high efficiency and preferable safety. Microorganisms played crucial role in biodegradation of PAHs. Traditional access mainly including culture-dependent procedures has discovered and isolated PAHs-degrading microorganisms which could be subsequently applied to specific contaminated locus. Although certain progress has been achieved owing to traditional methods, much details in PAHs bioremedation leave pending because of the complexity nature of this process. As the rapid development of biology, molecular techniques such as PCR, fingerprinting technique (mainly DGGE), DNA hybridization technique and gene reporters technique have been intensively applied to gain further insight into the mechanism of PAHs degradation. These techniques not only proved the existence and role of uncultivable microorganisms in the whole population of PAHs degrading related microbials, but also made it possible to revealed the otherwise undetectable complex relationships between multi-microorganism concerned in PAHs biodegradation. Application of such techniques in the field of PAHs biodegradation were reviewed in this article.     

Molecular biology approaches for understanding microbial polycyclic aromatic hydrocarbons (PAHs) degradation

The known or suspected hazards of polycyclic aromatic hydrocarbons (PAHs) have provoked enormous concentration and endeavours to relieve or eliminate these precarious compounds from miscellaneous environments including soil, water and air. Among various interventions, biodegradation is an appealing approach for its comparative high efficiency and preferable safety. Microorganisms played crucial role in biodegradation of PAHs. Traditional access mainly including culture-dependent procedures has discovered and isolated PAHs-degrading microorganisms which could be subsequently applied to specific contaminated locus. Although certain progress has been achieved owing to traditional methods, much details in PAHs bioremedation leave pending because of the complexity nature of this process. As the rapid development of biology, molecular techniques such as PCR, fingerprinting technique (mainly DGGE), DNA hybridization technique and gene reporters technique have been intensively applied to gain further insight into the mechanism of PAHs degradation. These techniques not only proved the existence and role of uncultivable microorganisms in the whole population of PAHs degrading related microbials, but also made it possible to revealed the otherwise undetectable complex relationships between multi-microorganism concerned in PAHs biodegradation. Application of such techniques in the field of PAHs biodegradation were reviewed in this article.     

Porphinatoiron-mediated oxidation of polycyclic aromatic hydrocarbons

Although porphinatoiron complexes have been used extensively as biomimetic catalysts for oxidation of aliphatic and olefinic hydrocarbons, few oxidations of polycyclic aromatic hydrocarbons (PAH) have been reported. In all cases, heterogeneous iodosobenzene/tetraphenylporphinatoiron(III) systems were employed, oxidations were inefficient and control experiments demonstrating the requirement for catalyst were not described. The current study investigates the oxidation of pyrene, benzo[a]pyrene and benzanthracene in a homogeneous m-chloroperoxybenzoic acid/bifacially hindered porphinatoiron system in which the peroxyacid was shown to be unreactive in the absence of catalyst. Pyrene and benzo[a]pyrene were oxidized efficiently, with pyrene yielding mixtures of 1.6- and 1.8-quinones and benzo[a]pyrene yielding mixtures of phenols and quinones. Benzanthracene was oxidized less efficiently, primarily at the meso positions, to give 7.12-quinone. Initial oxidation of meso carbons of benzo[a]pyrene (confirmed by the presence of the 6-hydroxy derivative as a product) and benzanthracene indicates that PAH-to-catalyst charge transfer may be an important oxidation pathway. Oxidation of pyrene was performed by addition of pyrene to observable oxo iron(V) species as well as in a catalytic reaction where excess peroxyacid was added to a solution of pyrene and catalyst and oxo iron(V) is not generated as an observable intermediate. Yields (based on oxidant consumed), were identical under both conditions, strongly supporting oxo iron(V) as a common intermediate.     

Impact of microbial/plant interactions on the transformation of polycyclic aromatic hydrocarbons in rhizosphere of Festuca arundinacea

The promotion of polycyclic aromatic hydrocarbon (PAH) degradation was demonstrated in the rhizosphere of Festuca arundinacea with Pseudomonas fluorescens. P. fluorescens 5RL more significantly interacted with salicylate and dextrose in the agar containing tall fescue than agar without plant roots. Although the presence of tall fescue did not promote catabolic enzyme induction in the absence of salicylate, an increase in dioxygenase activity relative to no plant controls implies that this plant may enhance the degradation of PAHs or facilitate the genotypes that are capable of transforming PAH in the rhizosphere.     

The origin of the polycyclic aromatic hydrocarbons in meteorites

Polycyclic aromatic hydrocarbons (PAHs) in C1 and C2 Carbonaceous Chondrites appear to be the product of a high-temperature synthesis. This observation counters a prevailing view that PAHs in meteorites are a thermal alternation product of preexisting aliphatic compounds, which in turn required the presence of low-temperature mineral phases such as magnetite and hydrated phyllosilicates for their formation. Such a process would necessarily lead to a more low-temperature assemblage of PAHs, as many low-temperature minerals and compounds are extant in meteorites.Ivuna, a C1 carbonaceous chondrite, has been shown to contain abundant amounts of the three-ring PAHs phenanthrene/anthracene, but no detectable levels of the two- and four-ring PAHs naphthalene and pyrene/fluoranthene. Ivuna and other C1 carbonaceous chondrites are known to have been extensively altered by water. The aqueous solubities of PAHs indicate that some PAHs would have been mobilized during the aqueous alteration phase in meteorite parent bodies. Model geochromatography experiments using crushed serpentine or beach sand as the solid phase and water for elution suggest that the complete separation of two, three, and four-ring PAHs could be expected to occur in the parent body of C1 carbonaceous chondrites. It is proposed that aqueous fluids driven by heat in the parent body of Ivuna migrated from the interior to the surface, in the process transporting, separating and concentrating PAHs at various zones in the parent body.The presence of indigenous PAHs and absence of indigenous amino acids in the H4 ordinary chondrite Forest Vale provides support for the contention that different processes and environments contributed to the synthesis of the organic matter in the solar system.     

Tissue-specific expression of hormonal carcinogenesis target genes in rats treated with polycyclic aromatic hydrocarbons

We have investigated the effect of polycyclic aromatic hydrocarbons (PAHs) on expression of the estrogen-metabolizing genes CYP1A1, CYP1B1, CYP19 and also ERα, and cyclinD1 genes, regulating cell division in estrogen-depended tissues. Treatment of rats with benzo(a)pyrene (BP) or 3-methylcholantrene (MCA) significantly up-regulated CYP1A1, CYP1B1 gene expression in liver, uterus and ovary, whereas α-naphthoflavone (α-NF) did not have any effect. The high level of aromatase gene (CYP19) expression was detected in ovary only. Treatment of rats with BP or MCA significantly down-regulated expression of this gene (15- and 5,5-fold, respectively), whereas α-NF was ineffective. Administration of BP but not MCA or α-NF increased ERα and cyclinD1 gene expression in rat liver. The levels of ERα and cyclinD1 mRNA levels remained unchanged in uterus of after treatment of rats with these PAHs. BP administration increased ERα and cyclinD1 mRNA levels (3,5- and 2,5-fold, respectively) in ovary, while MCA and α-NF were ineffective. Thus, our results give evidence for tissue-specific effects of PAHs on expression of genes, which participate in hormonal carcinogenesis. On the other hand, the fact that BP and MCA treatments influenced the expression of estrogen-metabolizing genes and genes, which control cell division, supports the viewpoint that PAHs may be one of the causes of endocrine disorders and subsequent hormonal carcinogenesis.     

Methanogenic biodegradation of two-ringed polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAH) are widespread in methane-rich subsurface environments, such as oil reservoirs and fuel-contaminated aquifers; however, little is known about the biodegradation of these compounds under methanogenic conditions. To assess the metabolism of PAH in the absence of electron acceptors, a crude oil-degrading methanogenic enrichment culture was tested for the ability to biodegrade naphthalene, 1-methylnaphthalene (1-MN), 2-methylnaphthalene (2-MN), and 2, 6-dimethylnaphthalene (2, 6-diMN). When methane was measured as an indicator of metabolism, nearly 400 μmol of methane was produced in the 2-MN- and 2, 6-diMN-amended cultures relative to substrate-unamended controls, which is close to the amount of methane stoichiometrically predicted based on the amount of substrate added (51-56 μmol). In contrast, no substantial methane was produced in the naphthalene- and 1-MN-amended enrichments. In time course experiments, metabolite analysis of enrichments containing 2-MN and 2, 6-diMN revealed the formation of 2-naphthoic acid and 6-methyl-2-naphthoic acid, respectively. Microbial community analysis by 454 pyrosequencing revealed that these PAH-utilizing enrichments were dominated by archaeal members most closely affiliated with Methanosaeta and Methanoculleus species and bacterial members most closely related to the Clostridiaceae, suggesting that these organisms play an important role in the methanogenic metabolism of the substituted naphthalenes in these cultures.     

Biomonitoring of polycyclic aromatic hydrocarbons in human urine

Measurement of polycyclic aromatic hydrocarbons (PAH) metabolites in human urine is the method of choice to determine occupational and/or environmental exposure of an individual to PAH, in particular, when multiple routes of exposure have to be taken into account. Requirements for methods of biomonitoring PAH metabolites in urine are presented. Studies using 1-hydroxypyrene or phenanthrene metabolites including its phenols and dihydrodiols are summarized. The role of these PAH metabolites as established biomarkers and also more recent developments of PAH biomonitoring are discussed.     

多环芳烃类化合物在土壤上的吸附

研究了几种多环芳烃化合物在土壤上的吸附行为．通过一个连续投药－取样试验装置,在没有任何其它有机试剂干扰的情况下,测定了荧蒽与菲在土壤上的吸附量．研究表明,这两种多环芳烃化合物在土壤上的吸附量与土壤有机质含量之间呈显著相关．对多环芳烃化合物的分子结构及理化特性,如辛醇－水分配系数、溶解度等参数与ＬｏｇＫｏｃ关系的研究发现多环芳烃化合物的ＬｏｇＫｏｃ与化合物的水溶性、辛酸－水分配系数以及分子结构中的苯环数线性相关．     

Mutational spectra for polycyclic aromatic hydrocarbons in the supF target gene

An SV40-based shuttle vector system was used to identify the types of mutational changes and the sites of mutation within the supF DNA sequence generated by the four stereoisomers of benzo[c]phenanthrene 3,4-dihydrodiol 1,2-epoxide (B[c]PhDE), by racemic mixtures of bay or fjord region dihydrodiol epoxides (DE) of 5-methylchrysene, of 5,6-dimethylchrysene, of benzo[g]chrysene and of 7-methylbenz[a]anthracene and by two direct acting polycyclic aromatic hydrocarbon carcinogens, 7-bromomethylbenz[a]anthracene (7-BrMeBA) and 7-bromomethyl-12-methylbenz[a]anthracene (7-BrMe-12-MeBA). The results of these studies demonstrated that the predominant type of mutation induced by these compounds is the base substitution. The chemical preference for reaction at deoxyadenosine (dAdo) or deoxyguanosine (dGuo) residues in DNA, which is in general correlated with the spatial structure (planar or non-planar) of the reactive polycyclic aromatic hydrocarbon, is reflected in the preference for mutation at AT or GC pairs. In addition, if the ability to react with DNA in vivo is taken into account, the relative mutagenic potencies of the B[c]PhDE stereoisomers are consistent with the higher tumorigenic activity associated with non-planar polycyclic aromatic hydrocarbons and their extensive reaction with dAdo residues in DNA. Comparison of the types of mutations generated by polycyclic aromatic hydrocarbons and other bulky carcinogens in this shuttle vector system suggests that all bulky lesions may be processed by a similar mechanism related to that involved in replication past apurinic sites. However, inspection of the distribution of mutations over the target gene induced by the different compounds demonstrated that individual polycyclic aromatic hydrocarbons induce unique patterns of mutational hotspots within the target gene. A polymerase arrest assay was used to determine the sequence specificity of the interaction of reactive polycyclic aromatic hydrocarbons with the shuttle vector DNA. The results of these assays revealed a divergence between mutational hotspots and polymerase arrest sites for all compounds investigated, i.e., sites of mutational hotspots do not correspond to sites where high levels of adduct formation occur, and suggested that some association between specific adducts and sequence context may be required to constitute a premutagenic lesion. A site-specific mutagenesis system employing a single-stranded vector (M13mp7L2) was used to investigate the mutational events a single benzo[a]pyrene or benzo[c]phenanthrene dihydrodiol epoxide–DNA adduct elicits within specific sequence contexts. These studies showed that sequence context can cause striking differences in mutagenic frequencies for given adducts. In addition, these sequence context effects do not originate only from nucleotides immediately adjacent to the adduct, but are also modulated by more distal nucleotides. The implications of these results for mechanisms of polycyclic aromatic hydrocarbon-induced mutagenesis and carcinogenesis are discussed.     

Detoxification of polycyclic aromatic hydrocarbons by fungi

Summary The polycyclic aromatic hydrocarbons (PAHs) are a group of hazardous environmental pollutants, many of which are acutely toxic, mutagenic, or carcinogenic. A diverse group of fungi, includingAspergillus ochraceus, Cunninghamella elegans, Phanerochaete chrysosporium, Saccharomyces cerevisiae, andSyncephalastrum racemosum, have the ability to oxidize PAHs. The PAHs anthracene, benz[a]anthracene, benzo[a]pyrene, fluoranthene, fluorene, naphthalene, phenanthrene, and pyrene, as well as several methyl-, nitro-, and fluoro-substituted PAHs, are metabolized by one or more of these fungi. Unsubstituted PAHs are oxidized initially to arene oxides,trans-dihydrodiols, phenols, quinones, and tetralones. Phenols andtrans-dihydrodiols may be further metabolized, and thus detoxified, by conjugation with sulfate, glucuronic acid, glucose, or xylose. Although dihydrodiol epoxides and other mutagenic and carcinogenic compounds have been detected as minor fungal metabolites of a few PAHs, most transformations performed by fungi reduce the mutagenicity and thus detoxify the PAHs.