Preliminary examinations for applying a carbazole-degrader, Pseudomonas sp. strain CA10, to dioxin-contaminated soil remediation

Soil washing for the remediation of dioxin-contaminated soil: A review

Dioxin-contaminated soil has attracted worldwide attention due to its potential negative impacts on human health and the ecosystem. Thus, technological development aiming at high treatment efficiency and low cost for dioxin-contaminated soil is largely needed. In this review, approximately 200 documents were involved to summarize up-to-date scientific achievements of soil washing technology for the remediation of dioxin-contaminated soil. The mechanisms, advantages, and limitations of physical separation techniques (e.g. mechanical stirring, mechanical shaking, ultrasonication, and froth flotation) and washing solutions (e.g. organic solvents, edible oils, and surfactants) used for chemical extraction were comprehensively reviewed. Froth flotation is very promising for field-scale soil washing, whereas organic solvents show high removal efficiencies (up to 99%) of dioxins from contaminated soil. Further, the combination of physical separation and chemical extraction can help enhance dioxin removal efficiency (from 1.5 to 2 times), reducing energy consumption and cost (about 2 times). Among available remediation technologies for dioxin-contaminated soil, soil washing is truly promising since it has shown high removal efficiency (66-99% different remediation scales) with reasonable cost (46 - 250 USD per metric ton). However, the washed solution and volatile organic compounds generated during the process remain a concern and should be addressed in future research.

Indole Derivatives Maintain the Status Quo Between Beneficial Biofilms and Their Plant Hosts

Biofilms formed by bacteria on plant roots play an important role in maintaining an optimal rhizosphere environment that supports plant growth and fitness. Bacillus subtilis is a potent plant growth promoter, forming biofilms that play a key role in protecting the host from fungal and bacterial infections. In this work, we demonstrate that the development of B. subtilis biofilms is antagonized by specific indole derivatives that accumulate during symbiotic interactions with plant hosts. Indole derivatives are more potent signals when the plant polysaccharide xylan serves as a carbon source, a mechanism to sustain beneficial biofilms at a biomass that can be supported by the plant. Moreover, B. subtilis biofilms formed by mutants resistant to indole derivatives become deleterious to the plants due to their capacity to consume and recycle plant polysaccharides. These results demonstrate how a dynamic metabolite-based dialogue can promote homeostasis between plant hosts and their beneficial biofilm communities.

The use of ultrasound-assisted anaerobic compost tea washing to remove poly-chlorinated dibenzo-p-dioxins (PCDDs), dibenzo-furans (PCDFs) from highly contaminated field soils

The remediation of dioxin-contaminated soil of a specific coastal area previously employed for the manufacture of pentachlorophenol (PCP) in southern Taiwan's Tainan City has attracted much attention of researchers there. This work addresses the possibility of providing an effective and environmentally friendly option for removing PCDD/Fs from soil in that field. Soil screening/sieving was first conducted to assess particle distribution. Fine sand was observed to be the major component of the soil, accounting for more than 60% of the total mass. A combination of ultrasonification and mechanical double-blade agitation was used to facilitate the washing of the soil using the biosurfactant anaerobic compost tea. More than 85 and 95% of total removal efficiencies were achieved for moderately and highly contaminated soils after 6 and 10 washing cycles, respectively, under ambient temperature, a soil/liquid ratio 1:2.5, 700 rpm, and over a relatively short duration. These results were achieved through the collision and penetration effects of this combined treatment as well as PCDD/F partitioning between the particles and anaerobic compost tea. This study represents the first to report the use of anaerobic compost tea solvent to wash soil highly contaminated by dioxin. It was concluded that anaerobic compost tea, rich in non-toxic bio-surfactants (e.g., alcohols, humic acids), can be used to improve bioavailability and bioactivity of the soil making bio-attenuation and full remediation more efficient.

Sequential anaerobic-aerobic biodegradation of 2,3,7,8-TCDD contaminated soil in the presence of CMC-coated nZVI and surfactant

Enriched microorganisms in sediment collected from a dioxin-contaminated site in Vietnam (Bien Hoa airbase) were used for examining the effectiveness in biological treatment of 2,3,7,8-Tetrachlorodibenzo-p-dioxin in soil. Four bio-treatments were investigated using a sequential anaerobic (17 weeks) followed by an aerobic (6 weeks) incubation. The maximum removal efficiency was approximately 60% even at an extremely low pH (approx. 3.6) condition. Surfactant Tween-80 was added to enhance the bioavailability of dioxin in two treatments, but it appeared to biostimulate methanogens rather than dechlorinators. As a result, methane production was the highest while the dioxin removal efficiency was the lowest, as compared with the other bio-treatments. Carboxymethylcellulose (CMC) coated on nanoscale zero valent iron (nZVI) surface used in two treatments could prevent the direct contact between bacterial cell surface and nZVI which prevented cell death and lysis, hence enhancing dioxin removal. The presence of CMC--_nZVI in bio-treatments gradually released H2 required for microbiological processes, but the amount used in the experiments were likely too high to maintain optimum H2 levels for biostimulating dechlorinators rather than methanogens.

Traceability of polychlorinated dibenzo-dioxins/furans pollutants in soil and their ecotoxicological effects on genetics, functions and composition of bacterial community

Dioxins (PCDD/Fs) are persistent organic pollutants. Their accumulation in soil is a crucial step in their transmission through the ecosystem. Traceability of dioxin in soil was evaluated in four sites A, B, C and D considered as potential industrial PCDD/Fs sources in Syria. Our results showed that the highest pollution with dioxin (⩾50 ppt) was found in site C (vicinity of Homs refinery). In parallel, analysis of physicochemical proprieties and bacterial density of soil samples were carried out. Bacterial density differed significantly among samples between 68×10(4) and 64×10(6) CFU g(-1)DW. Analysis of 16S rRNA encoding sequences showed that the genus Bacillus was the most abundant (74.7%) in all samples, followed by the genera Arthrobacter and Klebsiella with 5.2% and 4.7%, respectively. The genera Microbacterium, Pantoea, Pseudomonas, Enterobacter and Exiguobacterium formed between 2.1% and 2.6%. Cellulomonas, Kocuria, Lysinibacillus, Staphylococcus and Streptomyces were in a minority (0.5-1%). The bacterial richness and biodiversity, estimated by DMg and H' index, were highest in the heavily polluted site. Molecular screening for angular dioxygenase (AD α-subunit) and the cytochrome P450 (CYPBM3) genes, led to identification of 41 strains as AD-positive and 31 strains as CYPBM3-positive. RT-real-time PCR analysis showed a significant abundance of AD α-subunit transcript in the heavily dioxin-polluted soils, while the expression of CYPBM3 was highest in the moderately polluted soils. Our results illustrate the microbial diversity and functionality in soil exposed to dioxin pollution. Identification of dioxin-degrading bacteria from polluted sites should allow bioremediation to be carried out.

Photodegradation of dioxin in contaminated soil in the presence of solvents and nanoscale TiO2 particles

Decomposition of 2,3,7,8-Tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD) present in soil under ultraviolet (UV) illumination (350-400nm) was investigated using a combination of nontoxic solvents mixed in soil and nanoscale anatase TiO2 (nTiO2) distributed on 2mm top soil surface. Three types of UV-exposure experiments were conducted: intermittent exposure (8 h/day) for 90 days and 120 days, sequential intermittent (120 days) and continuous (24 h/day) for the next 55 days, and continuous exposure for 55 days. The influence of several factors on dioxin photodegradation efficiency was investigated, including the UV absorption by the targeted dioxin, presence of catalytic nTiO2 on soil surface, solvent evaporation rate, as well as vertical gradients of solvents added into the soil columns. Results of dioxin analysis for the soil samples collected at the end of every experiment condition show that the photodegradation enhanced by the nTiO2 presence on the soil surface considerably increased the dioxin removal. Higher removal efficiencies were found for treatments with 15%wt of nTiO2 mixed in the 2-mm surface soil as compared to the 5%wt nTiO2 treatments. The highest removal efficiency (79.6%) was for the sequential intermittent-continuous UV-exposure experiment with nTiO2. Dechlorinated products of 2,3,7,8-TCDD were generally not detected which suggests degradation of targeted dioxin by C-Cl cleavage was negligible. Further modifications to improve removal efficiencies were proposed. Large-scale engineered systems may employ this integrated treatment approach which can also incorporate the reuse of the top soil containing nTiO2 and solvent vapours. With the utilization of natural sunlight such systems would be promisingly suitable for tropical conditions.

Substrate-baited nanoparticles: a catch and release strategy for enzyme recognition and harvesting

The isolation of a single type of protein from a complex mixture is vital for the characterization of the function, structure, and interactions of the protein of interest and is typically the most laborious aspect of the protein purification process. In this work, a model system is utilized to show the efficacy of synthesizing a "baited" nanoparticle to capture and recycle enzymes (proteins that catalyze chemical reactions) from crude cell lysate. Enzyme trapping and recycling is illustrated with the carbazole 1,9a-dioxygenase (CARDO) system, an enzyme important in bioremediation and natural product synthesis. The enzymes are baited with azide-modified carbazolyl moieties attached to poly(propargyl acrylate) nanoparticles through a click transformation. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis indicates the single-step procedure to immobilize the enzymes on the particles is capable of significantly concentrating the protein from raw lysate and sequestering all required components of the protein to maintain bioactivity. These results establish a universal model applicable to concentrating and extracting known substrate-protein pairs, but it can be an invaluable tool in recognizing unknown protein-ligand affinities.

Manipulation of Förster energy transfer of coupled fluorophores through biotransformation by Pseudomonas resinovorans CA10

An alkyne-terminated anthracene and azide-terminated carbazole were joined through a copper-catalyzed cycloaddition to form a joined donor/acceptor pair. The photonic pair exhibited energy transfer when excited at the peak absorbance of carbazole and fluoresced with an anthracene spectral response. The fluorescent behavior was confirmed as Förster energy transfer (FRET). The lysate of Pseudomonas resinovorans CA10, a member of a predominant group of soil microorganisms that can metabolize a host of substrates, was employed to degrade the pair and alter the luminance spectral characteristics. The FRET was diminished and the corresponding, individual fluorescence of carbazole and anthracene returned. This general approach may find applications in single-cell metabolic studies and bioactivity assays.

Novel marine carbazole-degrading bacteria

Eleven carbazole (CAR)-degrading bacterial strains were isolated from seawater collected off the coast of Japan using two different media. Seven isolates were shown to be most closely related to the genera Erythrobacter, Hyphomonas, Sphingosinicella, Caulobacter, and Lysobacter. Meanwhile, strains OC3, OC6S, OC9, and OC11S showed low similarity to known bacteria, the closest relative being Kordiimonas gwangyangensis GW14-5 (90% similarity). Southern hybridization analysis revealed that only five isolates carried car genes similar to those reported in Pseudomonas resinovorans CA10 (car(CA10)) or Sphingomonas sp. strain KA1 (car(KA1)). The isolates were subjected to GC-MS and the results indicated that these strains degrade CAR to anthranilic acid.

Thermal treatment of polychlorinated dibenzo-p-dioxins and dibenzofurans from contaminated soils

Thermal treatment technology was used to remove polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) from heavily contaminated soil. For a soil with an original PCDD/F content of 35,970ng International Toxic Equivalents (I-TEQ)/kg, >99.99% PCDD/F removal efficiency was obtained with a primary furnace at two different treatment temperatures (750 degrees C and 850 degrees C), while a secondary furnace at 1200 degrees C gave >98% decomposition efficiency. The total PCDD/F I-TEQ contents in treated soils at 750 degrees C and 850 degrees C were 1.56ngI-TEQ/kg and 2.15ngI-TEQ/kg, respectively, which were far below the soil pollution standard of Taiwan (1000ngI-TEQ/kg soil). Although air pollution control devices had significant effects on the removal of PCDD/Fs, the total I-TEQ concentrations in the upstream flue gas of PUF cartridge at 750 degrees C and 850 degrees C (2.61ngI-TEQ/Nm(3) and 2.38ngI-TEQ/Nm(3), respectively) were still higher than the stationary emission limit of the Taiwan EPA (0.5ngI-TEQ/Nm(3)). The above results also suggested that additional APCDs, such as activated carbon injection in front of the filter are needed to enhance PCDD/F removal efficiency.

Microbial degradation of chlorinated dioxins

Polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) were introduced into the biosphere on a large scale as by-products from the manufacture of chlorinated phenols and the incineration of wastes. Due to their high toxicity they have been the subject of great public and scientific scrutiny. The evidence in the literature suggests that PCDD/F compounds are subject to biodegradation in the environment as part of the natural chlorine cycle. Lower chlorinated dioxins can be degraded by aerobic bacteria from the genera of Sphingomonas, Pseudomonas and Burkholderia. Most studies have evaluated the cometabolism of monochlorinated dioxins with unsubstituted dioxin as the primary substrate. The degradation is usually initiated by unique angular dioxygenases that attack the ring adjacent to the ether oxygen. Chlorinated dioxins can also be attacked cometabolically under aerobic conditions by white-rot fungi that utilize extracellular lignin degrading peroxidases. Recently, bacteria that can grow on monochlorinated dibenzo-p-dioxins as a sole source of carbon and energy have also been characterized (Pseudomonas veronii). Higher chlorinated dioxins are known to be reductively dechlorinated in anaerobic sediments. Similar to PCB and chlorinated benzenes, halorespiring bacteria from the genus Dehalococcoides are implicated in the dechlorination reactions. Anaerobic sediments have been shown to convert tetrachloro- to octachlorodibenzo-p-dioxins to lower chlorinated dioxins including monochlorinated congeners. Taken as a whole, these findings indicate that biodegradation is likely to contribute to the natural attenuation processes affecting PCDD/F compounds.

Methods for treating soils contaminated with polychlorinated dibenzo-p-dioxins, dibenzofurans, and other polychlorinated aromatic compounds

This review provides a summary of methods for treating soils contaminated with polychlorinated aromatic compounds, especially polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs). Unlike many other soil pollutants, PCDD/Fs bind tightly to the soil, which severely reduces the efficiency of most aqueous treatment procedures and leaves few realistic alternatives besides the traditional containment techniques (landfill, solidification/stabilization, and in situ vitrification). Incineration has long been, and still is, the most efficient destruction technique, with a removal efficiency of >99.9999%. However, supercritical water oxidation, base-catalyzed decomposition, steam distillation, and various extraction techniques, such as solvent and liquefied gas and subcritical water extraction, may provide removal efficiencies of >95%. Many of the alternative techniques are expected to be cheaper than incineration and may therefore be attractive for moderately polluted soils. However, some of them are at an early stage of development and need to be further tested before their true potential can be assessed.

Microbial degradation of sulfur, nitrogen and oxygen heterocycles

Sulfur (S), nitrogen (N) and oxygen (O) heterocycles are among the most potent environmental pollutants. Microbial degradation of these pollutants is attracting more and more attention because such bioprocesses are environmentally friendly. The biotechnological potential of these processes is being investigated, for example, to achieve better sulfur removal by immobilized biocatalysts with magnetite nanoparticles or by solvent-tolerant bacteria, and to obtain valuable intermediates from these heterocycles. Other recent advances have demonstrated the mechanisms of angular dioxygenation of nitrogen heterocycles by microbes. However, these technologies are not yet available for large-scale applications so future research must investigate proper modifications for industrial applications of these processes. This review focuses on recent progress in understanding how microbes degrade S, N and O heterocycles.

Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system

The carbazole 1,9a-dioxygenase (CARDO) system of Pseudomonas resinovorans strain CA10 catalyzes the dioxygenation of carbazole; the 9aC carbon bonds to a nitrogen atom and its adjacent 1C carbon as the initial reaction in the mineralization pathway. The CARDO system is composed of ferredoxin reductase (CarAd), ferredoxin (CarAc), and terminal oxygenase (CarAa). CarAc acts as a mediator in the electron transfer from CarAd to CarAa. To understand the structural basis of the protein-protein interactions during electron transport in the CARDO system, the crystal structure of CarAc was determined at 1.9 A resolution by molecular replacement using the structure of BphF, the biphenyl 2,3-dioxygenase ferredoxin from Burkholderia cepacia strain LB400 as a search model. CarAc is composed of three beta-sheets, and the structure can be divided into two domains, a cluster-binding domain and a basal domain. The Rieske [2Fe-2S] cluster is located at the tip of the cluster-binding domain, where it is exposed to solvent. While the overall folding of CarAc and BphF is strongly conserved, the properties of their surfaces are very different from each other. The structure of the cluster-binding domain of CarAc is more compact and protruding than that of BphF, and the distribution of electric charge on its molecular surface is very different. Such differences are thought to explain why these ferredoxins can act as electron mediators in respective electron transport chains composed of different-featured components.

Biodegradation of Dibenzofuran by Janibacter terrae Strain XJ-1

The dibenzofuran (DF)-degrading bacterium, Janibacter terrae strain XJ-1, was isolated from sediment from East Lake in Wuhan, China. This strain grows aerobically on DF as the sole source of carbon and energy; it has a doubling time of 12 hours at 30 degrees C; and it almost completely degraded 100 mg/L(-1) DF in 5 days, producing 2,2',3-trihydroxybiphenyl, salicylic acid, gentisic acid, and other metabolites. The dbdA (DF dioxygenase) gene cluster in the strain is almost identical to that on a large plasmid in Terrabacter sp. YK3. Unlike Janibacter sp. strain YY-1, XJ-1 accumulates gentisic acid rather than catechol as a final product of DF degradation.

Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676

The car and ant operons originally isolated from Pseudomonas resinovorans strain CA10 contain the genes encoding the carbazole/dioxin-degrading enzymes and anthranilate 1,2-dioxygenase, respectively, and are located on the plasmid pCAR1. The entire nucleotide sequence of pCAR1 was determined to elucidate the mechanism by which the car operon may have been assembled and distributed in nature. pCAR1 is a 199,035-bp circular plasmid, and carries 190 open reading frames. Although the incompatibility group of pCAR1 is unclear, its potential origin for replication, OriP, and Rep and Par proteins appeared to be closely related to those of plasmid pL6.5 isolated from Pseudomonas fluorescens. The potential tellurite-resistance klaABC genes identified in the neighboring region of repA gene were also related to those in IncP plasmid originally identified from pseudomonads. On the other hand, we found genes encoding proteins that showed low but significant homology (20-45% identity) with Trh and Tra proteins from Enterobacteriaceae, which are potentially involved in conjugative transfer of plasmids or genomic island, suggesting that pCAR1 is also a conjugative plasmid. In pCAR1, we found tnpAcCST genes that encoded the proteins showing >70% length-wise identities with those are encoded by the toluene/xylene-degrading transposon Tn4651 of TOL plasmid pWW0. Both car and ant degradative operons were found within a 72.8-kb Tn4676 sequence defined by flanking tnpAcC and tnpST genes and bordered by a 46-bp inverted repeat (IR). Within Tn4676 and its flanking region, we found the remnants of numerous mobile genetic elements, such as the duplicated transposase genes that are highly homologous to tnpR of Tn4653 and the multiple candidates of IRs for Tn4676 and Tn4653-like element. We also found distinct regions with high and low G+C contents within Tn4676, which contain an ant operon and car operon, respectively. These results suggested that multiple step assembly could have taken place before the current structure of Tn4676 had been captured.

Purification and characterization of carbazole 1,9a-dioxygenase, a three-component dioxygenase system of Pseudomonas resinovorans strain CA10

The carbazole 1,9a-dioxygenase (CARDO) system of Pseudomonas resinovorans strain CA10 consists of terminal oxygenase (CarAa), ferredoxin (CarAc), and ferredoxin reductase (CarAd). Each component of CARDO was expressed in Escherichia coli strain BL21(DE3) as a native form (CarAa) or a His-tagged form (CarAc and CarAd) and was purified to apparent homogeneity. CarAa was found to be trimeric and to have one Rieske type [2Fe-2S] cluster and one mononuclear iron center in each monomer. Both His-tagged proteins were found to be monomeric and to contain the prosthetic groups predicted from the deduced amino acid sequence (His-tagged CarAd, one FAD and one [2Fe-2S] cluster per monomer protein; His-tagged CarAc, one Rieske type [2Fe-2S] cluster per monomer protein). Both NADH and NADPH were effective as electron donors for His-tagged CarAd. However, since the k(cat)/K(m) for NADH is 22.3-fold higher than that for NADPH in the 2,6-dichlorophenolindophenol reductase assay, NADH was supposed to be the physiological electron donor of CarAd. In the presence of NADH, His-tagged CarAc was reduced by His-tagged CarAd. Similarly, CarAa was reduced by His-tagged CarAc, His-tagged CarAd, and NADH. The three purified proteins could reconstitute the CARDO activity in vitro. In the reconstituted CARDO system, His-tagged CarAc seemed to be indispensable for electron transport, while His-tagged CarAd could be replaced by some unrelated reductases.

Degradation characteristics of a dibenzofuran-degrader Terrabacter sp. strain DBF63 toward chlorinated dioxins in soil

To obtain basic information towards applying a dibenzofuran (DF)-degrader Terrabacter sp. strain DBF63 to bioremediate dioxin-contaminated soil, we investigated the degradative potential of strain DBF63 for either chlorinated or polychlorinated dibenzo-p-dioxins and dibenzofurans (ClxDD/ClxDF) in soil. In the soil slurry system with a soil to water ratio of 1:5 (w/v), the DF-grown DBF63 cells degraded 90% of 1 ppm 2,8-Cl2DF, whereas only 40% of 1 ppm 2,3-Cl2DD during the 7-day incubation. The degradation rates of 2-CIDF, 2-ClDD, 2,8-Cl2DF and 2,3-Cl2DF by strain DBF63 in the soil slurry system (5-day incubation) were approximately 89%, 65%, 78% and 32%, respectively. These results suggest that strain DBF63 was able to degrade mono- to dichlorinated dibenzofurans more effectively than mono- to dichlorinated dibenzo-p-dioxins. Using the same soil slurry system, we performed a preliminary bioremediation experiment using the actual dioxin-contaminated soil at an incineration site. We found that approximately 10% of tetra- to hexa-chlorinated congeners was decreased by a single inoculation with DBF63 cells within a 7-day incubation.

Sphingomonas sp. strain KA1, carrying a carbazole dioxygenase gene homologue, degrades chlorinated dibenzo-p-dioxins in soil

Hybridization analysis showed that a newly isolated carbazole (CAR)-degrading bacterium Sphingomonas sp. strain KA1 did not possess the gene encoding the terminal oxygenase component (carAa) of CAR 1,9a-dioxygenase at high homology (more than 90% identity) to that of another CAR-degrader, Pseudomonas resinovorans strain CA10. However, PCR experiments using the primers for amplifying the internal fragment of the carAa gene (810 bp for strain CA10) showed that a PCR product of unexpected size (1100 bp) was amplified. Sequence analysis revealed that this DNA region contained the portion of two possible ORFs, which showed moderate homology to CarAa and CarBa from strain CA10 (61% and 40% identities at the amino acid level, respectively). Inoculation of strain KA1 into dioxin-contaminated model soil resulted in 96% and 70% degradation of 2-mono- and 2,3-dichlorinated dibenzo-p-dioxin, respectively, after 7-day incubation.

Bacterial degradation of aromatic compounds via angular dioxygenation

Dioxygenation is one of the important initial reactions of the bacterial degradation of various aromatic compounds. Aromatic compounds, such as biphenyl, toluene, and naphthalene, are dioxygenated at lateral positions of the aromatic ring resulting in the formation of cis-dihydrodiol. This "normal" type of dioxygenation is termed lateral dioxygenation. On the other hand, the analysis of the bacterial degradation of fluorene (FN) analogues, such as 9-fluorenone, dibenzofuran (DF), carbazole (CAR), and dibenzothiophene (DBT)-sulfone, and DF-related diaryl ether compounds, dibenzo-p-dioxin (DD) and diphenyl ether (DE), revealed the presence of the novel mode of dioxygenation reaction for aromatic nucleus, generally termed angular dioxygenation. In this atypical dioxygenation, the carbon bonded to the carbonyl group in 9-fluorenone or to heteroatoms in the other compounds, and the adjacent carbon in the aromatic ring are both oxidized. Angular dioxygenation of DF, CAR, DBT-sulfone, DD, and DE produces the chemically unstable hemiacetal-like intermediates, which are spontaneously converted to 2,2',3-trihydroxybiphenyl, 2'-aminobiphenyl-2,3-diol, 2',3'-dihydroxybiphenyl-2-sulfinate, 2,2',3-trihydroxydiphenyl ether, and phenol and catechol, respectively. Thus, angular dioxygenation for these compounds results in the cleavage of the three-ring structure or DE structure. The angular dioxygenation product of 9-fluorenone, 1-hydro-1,1a-dihydroxy-9-fluorenone is a chemically stable cis-diol, and is enzymatically transformed to 2'-carboxy-2,3-dihydroxybiphenyl. 2'-Substituted 2,3-dihydroxybiphenyls formed by angular dioxygenation of FN analogues are degraded to monocyclic aromatic compounds by meta cleavage and hydrolysis. Thus, after the novel angular dioxygenation, subsequent degradation pathways are homologous to the corresponding part of that of biphenyl. Compared to the bacterial strains capable of catalyzing lateral dioxygenation, few bacteria having angular dioxygenase have been reported. Only a few degradation pathways, CAR-degradation pathway of Pseudomonas resinovorans strain CA10, DF/DD-degradation pathway of Sphingomonas wittichii strain RW1, DF/DD/FN-degradation pathway of Terrabacter sp. strain DBF63, and carboxylated DE-degradation pathway of P. pseudoalcaligenes strain POB310, have been investigated at the gene level. As a result of the phylogenetic analysis and the comparison of substrate specificity of angular dioxygenase, it is suggested that this atypical mode of dioxygenation is one of the oxygenation reactions originating from the relaxed substrate specificity of the Rieske nonheme iron oxygenase superfamily. Genetic characterization of the degradation pathways of these compounds suggests the possibility that the respective genetic elements constituting the entire catabolic pathway have been recruited from various other bacteria and/or other genetic loci, and that these pathways have not evolutionary matured.

Degradation of chlorinated dibenzofurans and dibenzo-p-dioxins by two types of bacteria having angular dioxygenases with different features

Two kinds of bacteria having different-structured angular dioxygenases-a dibenzofuran (DF)-utilizing bacterium, Terrabacter sp. strain DBF63, and a carbazole (CAR)-utilizing bacterium, Pseudomonas sp. strain CA10-were investigated for their ability to degrade some chlorinated dibenzofurans (CDFs) and chlorinated dibenzo-p-dioxins (CDDs) (or, together, CDF/Ds) using either wild-type strains or recombinant Escherichia coli strains. First, it was shown that CAR 1,9a-dioxygenase (CARDO) catalyzed angular dioxygenation of all mono- to triCDF/Ds investigated in this study, but DF 4,4a-dioxygenase (DFDO) did not degrade 2,7-diCDD. Secondly, degradation of CDF/Ds by the sets of three enzymes (angular dioxygenase, extradiol dioxygenase, and meta-cleavage compound hydrolase) was examined, showing that these enzymes in both strains were able to convert 2-CDF to 5-chlorosalicylic acid but not other tested substrates to the corresponding chlorosalicylic acid (CSA) or chlorocatechol (CC). Finally, we tested the potential of both wild-type strains for cooxidation of CDF/Ds and demonstrated that both strains degraded 2-CDF, 2-CDD, and 2,3-diCDD to the corresponding CSA and CC. We investigated the sites for the attack of angular dioxygenases in each CDF/D congener, suggesting the possibility that the angular dioxygenation of 2-CDF, 2-CDD, 2,3-diCDD, and 1,2,3-triCDD (10 ppm each) by both DFDO and CARDO occurred mainly on the nonsubstituted aromatic nuclei.