Review TRENDS in Microbiology Vol.14 No.9 Microbial degradation of sulfur, nitrogen and oxygen heterocycles Ping Xu, Bo Yu, Fu Li Li, Xiao Feng Cai and Cui Qing Ma State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People’s Republic of China 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. Hazardous heterocycles in the environment Sulfur (S), nitrogen (N), and oxygen (O) heterocycles are polycyclic aromatic compounds that contain one or more S, N and/or O atoms in five- or six-membered rings (Figure 1). S, N and O heterocycles and their degradation products have been detected in groundwater, seawater, sediments, soil and atmospheric samples. Their unusual toxicity and mutagenicity call for great attention in studying such chemicals [1]. S heterocycles, particularly dibenzothiophene (DBT) and its derivatives, can persist for up to three years in the environment [2]. N heterocycles such as carbazole and its derivatives are used in the production of dyes, medicine and plastics [3] and, moreover, they readily undergo radical chemical changes to generate the more genotoxic hydroxynitrocarbazoles [4]. DBT and carbazole are widely used as model compounds for the study of biodegradation of polycyclic aromatic sulfurand nitrogen-containing hydrocarbons, respectively. Dibenzofuran (DBF), an O heterocycle, has been used as an insecticide and is formed from the photolysis of chlorinated biphenyl ethers [5]. DBF is a model for the biodegradation of chlorinated dibenzofurans and biaryl ethers that are of great environmental concern. Owing to biological weathering processes, the environment is able to handle these pollutants to a certain extent. Among such processes, microbial degradation is a key method for mineralization (the complete conversion of pollutants into biomass or inorganic compounds) of these persistent toxic Corresponding authors: Xu, P. ([email protected]); Yu, B. ([email protected]). Available online 24 July 2006. www.sciencedirect.com substances (PTSs) or persistent organic pollutants (POPs) [6]. Therefore, it is necessary to investigate the fates of the heterocycles that are metabolized by microorganisms. Here, we review recent progress in understanding the microbial metabolism of DBT, carbazole and DBF, and provide a short introduction to the biotechnological potential of these transformations. Mechanisms of heterocyclic biodegradation S heterocycles: dibenzothiophene DBT and its derivatives are the major sulfur-containing aromatic compounds in fuels, accounting for up to 70% of the sulfur content [7]. Many microorganisms such as Rhodococcus [8], Mycobacterium [9] and Pseudomonas species [10] can degrade DBT and the reactions can be classified into three independent categories: sulfur oxidation, carbon–carbon cleavage and sulfur-specific cleavage. The last category is the most extensively studied because a sulfur atom is released from DBT, leaving the carbon skeleton intact, which is useful in petroleum biodesulfurization [11]. Biotransformation of DBT by sulfur oxidation is catalyzed by laccase from white rot fungi [12] and ring dioxygenases from bacteria, which convert DBT into dibenzothiophene sulfone and/or hydroxylated derivatives [13,14]. The carbon–carbon cleavage (Figure 2) by which the carbon skeleton of DBT is broken following the Kodama pathway has been reviewed previously [10]. This enzymatic attack on the carbon atom is undesirable for a process designed to remove organic sulfur compounds selectively without oxidizing other aromatics in petroleum. In the sulfur-specific cleavage of DBT, 2-hydroxybiphenyl (2-HBP) is formed with the loss of sulfite. Until recently, no DBT-desulfurizing microorganisms were known to degrade 2-HBP further. Because there are many publications on selective sulfur removal through the 4S pathway, especially on the genetic and enzymatic mechanisms [10,11], here we focus only on the newly-reported pathway: the extended 4S pathway in the sulfur-specific cleavage category. Li et al. [15] isolated a new thermophilic bacterium that could initially desulfurize DBT to 2-HBP. The isolated bacterium was identified as Mycobacterium goodii X7B [15] and could further convert 2-HBP, the end product of the 4S pathway, to 2-methoxybiphenyl (2-MBP). This extended 4S pathway [9] is shown in Figure 3. The formation of the methoxylated product 2-MBP by Mycobacterium sp. G3 was also detected. Although the substrate in the methoxylation reaction was 2-HBP, there was no correlation between the expression of methoxylation activity and 0966-842X/$ – see front matter ß 2006 Elsevier Ltd. All rights reserved. doi:10.1016/j.tim.2006.07.002 Review TRENDS in Microbiology Vol.14 No.9 399 Figure 1. Examples of sulfur, nitrogen and oxygen heterocycles that are found in environmental pollutants. not yet clear. Recently, a similar strain was isolated that is capable of degrading DBT – Microbacterium sp. ZD-M2 [19]. Besides 2-HBP and a small amount of 2-MBP, trace amounts of biphenyl were also observed. As far as the authors are aware, no other DBT-degrading strains capable of converting 2-HBP to 2-MBP have been reported. Although the mechanism of selective sulfur removal has been studied for >15 years, none of these isolated strains meet the industrial requirements of biodesulfurization, which demand a high sulfur-removal rate, extensive sulfur removal from heavy oils and decreased operation costs. Therefore, a further detailed understanding of the metabolic mechanism is still expected and this will be the focus of the majority of research. Figure 2. Proposed Kodama pathway of DBT degradation through carbon–carbon cleavage by Pseudomonas strains. that of the desulfurization activity [16]. The alkylated derivatives of DBT were also metabolized to their methoxy forms by this pathway, and these results were consistent with those obtained from Mycobacterium goodii X7B [9]. Many O-methyltransferases involved in methyl-transfer reactions have also been reported [17,18] in which S-adenosyl-L-methionine functions as a methyl donor. For example, the conversion of abietic acid (a pesticide) to methyl abietate is performed by the O-methyltransferase of Mycobacterium sp. MB3683 [18]. Okada et al. [16] expected that a similar reaction system could be involved in the methoxylation process in Mycobacterium sp. G3 but the mechanism is N heterocycles Carbazole degradation by carbazole 1,9a-dioxygenase N heterocycles such as carbazole and its derivatives are wellknown environmental pollutants in areas that have been contaminated with wastes from coal gasification plants. Most of the isolated species that degrade carbazole follow a similar metabolic pathway in which the heterocycle undergoes ring-cleavage to produce anthranilic acid as an intermediate, which is then completely mineralized [20–23]. In this pathway, carbazole is first degraded to 20 -aminobiphenyl-2,3-diol by carbazole 1,9a-dioxygenase (CARDO) [24]. The novel catalytic mechanism of CARDO has recently been clarified [25]. CARDO is a multicomponent enzyme and functional analysis revealed that the CARDO of Pseudomonas resinovorans CA10 consists of four parts: two terminal oxygenases (CarAa), a ferredoxin (CarAc), and a ferredoxin reductase (CarAd) (Figure 4). Figure 3. Proposed extended 4S pathway of DBT metabolism by Mycobacterium goodii X7B. DBT is converted to 2-hydroxybiphenyl by the traditional sulfur-specific pathway in the initial steps. A new product, 2-methoxylbiphenyl, appeared in the M. goodii X7B desulfurizing process and was confirmed as the end product of this pathway. www.sciencedirect.com 400 Review TRENDS in Microbiology Vol.14 No.9 Figure 4. The genetic arrangement and enzymatic mechanism of CARDO from Pseudomonas resinovorans CA10 [24]. CARDO is a multicomponent enzyme that catalyzes the angular dioxygenation of carbazole to yield an unstable dihydroxylated intermediate, which is thought to be spontaneously converted to 20 -aminobiphenyl-2,3-diol. Functional analysis revealed that CARDO consists of terminal oxygenase (CarAa), ferredoxin (CarAc) and ferredoxin reductase (CarAd) components (green arrows). Figure reproduced, with permission, from Ref. [24]. Among the many reported aromatic compound dioxygenases, CARDO is the only dioxygenase that can catalyze cis-dihydroxylation, monooxygenation and angular dioxygenation on diverse aromatic compounds [13]. The catalytic component of CARDO, CarAa, has been purified and crystallized and its 3D structure has been determined [25]. CarAa from Janthinobacterium sp. J3 has a homotrimeric structure that governs the substrate specificity of CARDO. The overall a3 trimeric structure of the CarAa molecule approximately corresponds to the partial a3 structure of other terminal oxygenase components of Rieske non-haem iron-oxygenase systems (ROSs) that have the a3b3 configuration. The CarAa structure is the first example of a terminal oxygenase component of a ROS that has the a3 configuration. The shape of the substrate-binding pocket of CarAa is markedly different from those of other oxygenase components that are involved in naphthalene and biphenyl degradation. The results indicate that carbazole binds to the substratebinding pocket in a manner suitable for angular dioxygenation catalysis [25–27]. Although complete mineralization of carbazole is welcome in bioremediation, it is not suitable for the biotreatment of fossil fuels because the carbon value decreases during the nitrogen removal process. However, a microorganism that can selectively cleave C–N bonds in quinoline and remove nitrogen from petroleum has been isolated and characterized [28], and several Pseudomonas cultures are well known for using carbazole as the sole nitrogen source. Nevertheless, these bacteria cannot selectively cleave both C–N bonds in carbazole while leaving the rest of the molecule intact: the first step catalyzed by CARDO converts carbazole to 20 -aminobiphenyl-2,3-diol, which cleaves the first C–N bond, but there are no known deaminases that can metabolize 20 -aminobiphenyl-2,3-diol to achieve cleavage of the final C–N bond. Recently, however, a method for the selective cleavage of both C–N bonds of carbazole was proposed. Genes that encode CARDO were www.sciencedirect.com combined with a genetically manipulated gene encoding an amidase, which is suitable for selective cleavage of the C–N bond in 20 -aminobiphenyl-2,3-diol. This approach formed an operon, which encodes enzymes that catalyze the cleavage of both C–N bonds of carbazole [29]. This conversion of carbazole could be a useful method for the selective removal of recalcitrant organonitrogen compounds from petroleum. A novel attempt to combine two heteroatom-specific degradation pathways in one biocatalyst could reduce the operation costs that are associated with bioremediation of S and N heterocycles. The well-known desulfurization of DBT through the 4S pathway was combined with carbazole conversion by Yu et al. [30], who introduced CARDO into a DBT-degrader, Rhodococcus erythropolis XP. The recombinant could simultaneously degrade DBT and carbazole in crude oil [30]. This study represents a new step towards the development of biorefining processes. Future research might enable the development of biocatalysts that can simultaneously and selectively remove sulfur and nitrogen from petroleum. Carbazole degradation by other dioxygenases Carbazole can also be metabolized by a hydroxylation reaction to form monohydroxylated products. 3-Hydroxycarbazole is detected as a major bioconversion product, whereas 1hydroxy- and 2-hydroxycarbazoles are observed as minor products [31]. Bacterial dioxygenases often catalyze the initial oxidation of aromatic hydrocarbons and related heterocycles including carbazole. Naphthalene 1,2dioxygenase from Pseudomonas sp. NCIB 9816–4 and biphenyl dioxygenase from Beijerinckia sp. B8/36 also oxidize carbazole to 3-hydroxycarbazole but the toluene dioxygenase from Pseudomonas putida F39/D does not [32]. Biotransformation of carbazole to 3-hydroxycarbazole is of great interest because hydroxylated carbazole derivatives have strong antioxidant activity and are value-added substances in the pharmaceutical industry, Review TRENDS in Microbiology with a wide application in therapies for encephalopathy, cardiopathy, hepatopathy and arteriosclerosis [31]. Degraded N heterocycles as pharmaceutical precursors Nicotine is also an N-heterocyclic pollutant and is commonly found in many solid, liquid and airborne wastes that are generated during the tobacco manufacturing process. The intermediates of nicotine degradation, 6-hydroxynicotine and 6-hydroxy-3-succinoyl-pyridine (HSP), are useful precursors in the syntheses of insecticides and pharmaceuticals [33]. An environmentally friendly method of HSP production from nicotine in tobacco waste has been developed [34] and this biotransformation is a good example of how toxic wastes can be converted into valuable compounds. O heterocycles Bacterial degradation of dibenzofuran Microbes that degrade DBF are of increasing interest because of their potential ability to co-metabolize highly toxic polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans [35]. Here, only a brief introduction to the DBF metabolic pathway is given [a comprehensive review on the metabolism of dioxin-like compounds (O heterocycles) by microorganisms is available elsewhere [5]]. The initial steps in the biodegradation of DBF (Figure 5) are categorized into three pathways: angular dioxygenation, lateral dioxygenation and lateral oxygenation. The angular attack (Figure 5a) occurs at carbon atoms 4 and 4a of DBF. Molecular oxygen is incorporated into the angular position of DBF, which creates unstable hemiacetals that break up spontaneously to yield 2,3,20 -trihydroxybiphenyl (THBP). Subsequent ring cleavage of THBP is catalyzed by extradiol dioxygenases to yield 2-hydroxy-6-(2-hydrophenyl)-6-oxo-2,4-hexadienoic acid, which is then hydrolyzed to 3-(chroman-4-on-2-yl)-pyruvate and salicylic acid. Salicylic acid is then converted to catechol or gentisic acid. These compounds are further degraded and channeled into the tricarboxylic acid (TCA) cycle. Following this pathway, which is similar to the carbazole-degradation process carried out by P. resinovorans CA10, DBF is completely mineralized [3]. The initial angular dioxygenase, which can react at the angular position adjacent to the oxygen atom of DBF, is a key determinant of substrate range in the degradation of aromatic compounds including dibenzo-pdioxins and other dibenzofurans [13]. Compared with other initial dioxygenases such as naphthalene dioxygenases, biphenyl dioxygenases and toluene dioxygenases, there is still a lack of knowledge concerning angular dioxygenases [36]. By contrast, lateral dioxygenation, which is carried out mainly by naphthalene- or biphenyl-utilizing bacteria, occurs at the 1,2, the 2,3 and the 3,4 positions to produce DBF-dihydrodiols (Figure 5b) [37,38]. Ring fission of 1,2dihydroxydibenzofuran results in the production of 2hydroxy-4-(30 -oxo-30 H-benzofuran-20 -ylidene)but-2-enoic acid, which is degraded to salicylic acid. Salicylic acid is then metabolized to catechol or gentisic acid followed by incorporation into the TCA cycle, similar to the angular dioxygenation pathway. The lateral dioxygenation www.sciencedirect.com Vol.14 No.9 401 pathway is also used in the co-metabolic degradation of DBF by biphenyl-utilizing bacteria. There are only a few reports of bacteria that transform DBF by both angular and lateral dioxygenation [38–40]. Fungal degradation of dibenzofuran Although fungi constitute the majority of microbial biomass in soil, data on fungal catabolism of biaryl ether compounds are limited and restricted to hydroxylation processes. A fungus that can metabolize DBF (Figure 5c) was identified as Trichosporon mucoides SBUG 801 [41]. The accumulation of a high level of monohydroxylated DBF and the formation of dihydroxylated derivatives from both 2-hydroxydibenzofuran and 3-hydroxydibenzofuran indicate the action of a monooxygenase during the initial degradation steps. T. mucoides SBUG 801 degrades DBF to 2,3-dihydroxydibenzofuran and subsequent ring cleavage leads to the formation of 2-(1-carboxymethylidene)-2,3dihydrobenzo-[b]-furanylidene glycolic acid. Presumably, cleavage of the dihydroxylated ring uses a mechanism similar to that described for the degradation of biphenyl ether by Trichosporon sp. SBUG 752. In both species, a third hydroxyl group must be introduced into the dihydroxylated intermediates before ortho cleavage of the aromatic structure can take place [41]. Bioremediation continues to be an attractive option for degradation of environmentally hazardous compounds. The oxygen heterocyclic biodegradation studies described here represent an important milestone in this field because they demonstrate the possibility of aerobic biotransformation of POP substrates. A clearer understanding of the biodegradation mechanism of wild-type strains or genetically modified bacteria will be beneficial to future bioremediation studies. Environmental validity of heterocyclic biodegradation Exploitation of the biodegradative activities of microorganisms to remove environmental pollutants and recalcitrant xenobiotics is becoming more popular as an alternative to physical and chemical methods because of the relatively low cost and minimal impact on the environment. Many researchers have focused their studies on the isolation and identification of specific strains and some preliminary applications, especially soil remediation, have been performed using bacteria [42]. The use of specific bacteria to remove sulfur pollutants from petroleum will reduce the amount of sulfur oxides released and, therefore, reduce serious environmental pollution [11]. However, genetic modifications to improve the sulfur removal efficiencies of microorganisms are needed before a practical biorefining process for the removal of sulfur compounds from petroleum can be developed. Genetically engineered microorganisms are required to remove the ‘heavier’ sulfur compounds with more complex structures to an acceptable level. Cultures with improved substrate ranges are also needed to address the complicated mixture of chemicals present in petroleum. Unlike biodesulfurization, the biological removal of nitrogen from petroleum (biodenitrogenation), has not received much attention. So far, only a few reports have been published and the reported nitrogen reduction is 402 Review TRENDS in Microbiology Vol.14 No.9 Figure 5. Three pathways of DBF degradation by microorganisms. The pathways are categorized according to initial steps in the biodegradation of DBF and are summarized as angular dioxygenation, lateral dioxygenation and lateral oxygenation, respectively. (a) The angular attack occurs at the 4 and 4a carbon atoms of DBF. (b) Lateral dioxygenation, mainly by naphthalene- or biphenyl-utilizing bacteria, occurs at the 1,2, the 2,3 and the 3,4 positions to produce DBF-dihydrodiols. (c) In lateral oxygenation, monooxygenase catalysis during the initial degradation steps contributes to the accumulation of a high level of monohydroxylated DBF and the formation of dihydroxylated derivatives from both 2-hydroxydibenzofuran and 3-hydroxydibenzofuran. unsatisfactory [20,28]. This might be a result of the highly complex nitrogen compounds and the diverse compound structures present in petroleum, which cannot be degraded by one type of nitrogen heterocycle-degrading strain alone. Currently, no biocatalyst capable of selectively removing www.sciencedirect.com nitrogen is available, which also significantly limits the development of biodenitrogenation processes. Interestingly, the reported carbazole-degrader P. resinovorans CA10 can also detoxify poisonous oxygen compounds and their chloro-derivatives such as PCDDs [35,43,44]. Review TRENDS in Microbiology Similar to the DBF-degrader Sphingomonas wittichii RW1, carbazole-degraders have been used to mineralize these PTSs or POPs, which cause serious environmental problems. Some initial experiments on soil bioremediation have been carried out and good reductions were obtained [6]. Therefore, eradication of these persistent pollutants from the environment has attracted much attention from academia, industry and governmental agencies. Bioremediation by these heterocycle-degraders is likely to become a commercial prospect in the near future [45]. Solvent-tolerant bacteria for heterocyclic biodegradation At present, biotreatments of petroleum (especially biodesulfurization of petroleum-derived fractions such as diesel oil and gasoline) face the problem of a high ratio of water to oil in petroleum, which increases the reaction volume and makes practical operations of biotreatments difficult. The water-flooding techniques used to increase crude oil recovery in oilfields lead to a high ratio of water in crude oils, which, by contrast, is more suitable for bacterial strain survival and petroleum biodesulfurization. Therefore, it would be more practical to incubate microorganisms in this water–oil system before the water is removed [8,30]. Until now, there have been few reports concerning the biodesulfurization of crude oil. R. erythropolis XP was recently used to treat crude oil and gasoline samples and a high level of sulfur removal was achieved [8,46]. However, the bacterium did not maintain a good desulfurization activity under high concentrations of oils. By contrast, a biphasic system containing water-immiscible organic solvents has been exploited for biocatalysis because it can integrate bioconversion and product recovery in a single reactor, overcome the problem of low productivity in conventional media caused by poor substrate solubility and also shift chemical equilibrium to enhance yields and selectivity [33,47]. However, many organic solvents are highly toxic and can kill most microorganisms even at low concentrations (e.g. 0.1% v/ v) [48], which makes the selection of biocompatible solvents with the desired physicochemical properties a difficult task. In addition, biotransformation is always an energetically expensive multistep process. Cell integrity and viability are essential for this type of reaction [49]. It is reasonable to expect cells that maintain high activity in a biphasic system to survive in the presence of toxic organic solvents. Thus, microorganisms with high tolerance to organic solvents are especially important and useful in many biotechnological fields such as biocatalysis [24,47]. Considering the difficulty of isolating strains that have both solvent tolerance and the desired catalytic activity from the environment, it might be preferable to combine solvent-tolerance with unique catalytic characteristics using genetic engineering. Recently, Tao et al. [50] reported the introduction of biodesulfurizing gene clusters into a solvent-tolerant bacterium. The resultant recombinant Pseudomonas putida A4 could function even in the 50% p-xylene that was present. This study is an important step towards exploring novel biocatalysts for developing efficient bioprocesses in biphasic reactions. www.sciencedirect.com Vol.14 No.9 403 Immobilization with magnetite nanoparticles The use of immobilized microorganisms rather than free cells in biotransformation can be advantageous to enhance the stability of the biocatalyst and to facilitate its recovery and re-use. These advantages have encouraged researchers to investigate the use of immobilized cells in bioconversion, biotransformation and biosynthesis processes including oil biodesulfurization [15,51]. However, immobilization of cells using traditional entrapment methods has major drawbacks. The mass-transfer problems of limited diffusion and steric hindrance [47] reduce cell access to the substrate and lead to a reduction in biotransformation activity. As a result, immobilization by adsorption is currently gaining considerable importance because it reduces (and in some cases eliminates) these mass-transfer problems associated with entrapment methods. Techniques that immobilize microorganisms on nanoparticles have emerged as a novel aspect of the industrialization of cell immobilization because such particles have a large specific surface area and high surface energy. Recently, Shan et al. [52,53] reported the use of immobilized cells coated with magnetite (Fe3O4) nanoparticles in biodesulfurization. The nanoparticles were surface-modified using ammonium oleate and then monodispersed in an aqueous solution. Importantly, cells coated with magnetite nanoparticles had the same biocatalytic activity as free cells and could overcome the mass-transfer resistance of traditional immobilization processes. Therefore, the nanoparticle-coated cells had greater desulfurizing activity compared to traditional immobilization methods. This attempt to develop efficient biocatalysts using immobilized cells is a step towards improving biocatalysts for use in many other fields such as biotransformation, biocatalysis and biodegradation [54]. Concluding remarks and future perspectives Although a more detailed understanding of all aspects of the metabolic pathways is still needed, the understanding of how microorganisms metabolize heterocycles is improving rapidly. Because only 0.1–1% of microorganisms can be cultivated using current techniques, new techniques including metagenomic methods have been developed to explore novel genes and metabolic pathways for the biodegradation of recalcitrant and xenobiotic molecules [55]. Initial pilot-scale testing of microbial degradation of some environmental pollutants by the cultures described earlier is under way, which should lead to lower costs for biocatalyst preparation [56] and more efficient bacterial degradation of hazardous compounds. A recent example is the incorporation of a specialized membrane structure termed a ‘superchannel’ into the dioxin-degrading strain Sphingomonas wittichii RW1, which enabled the direct incorporation of macromolecules into the recombinant cell and consequently increased the bioremediation capability [57]. The emergence of new in vitro tools for mutation and genetic rearrangement has enabled the limits of enzymatic systems to be extended. Microorganisms with a wider substrate range and higher substrate affinity in biphasic reactions that contain toxic solvents or complex heterocycles could be engineered if the biocatalysts were to be 404 Review TRENDS in Microbiology Vol.14 No.9 used for environmental remediation, petroleum treatment or the production of bioderived compounds. These possibilities represent a future challenge for both microbiologists and environmental engineers. 23 24 Acknowledgements We gratefully acknowledge the support for our previous research from the National Natural Science Foundation of China (grant numbers 20590368, 20377026, 30400008 and 20577031) and the Chinese National Programs for High Technology Research and Development (grant number 2004AA649160). 25 26 References 1 Jensen, A.M. et al. (2003) Degradation of carbazole, dibenzothiophene, and dibenzofuran at low temperature by Pseudomonas sp. strain C3211. Environ. Toxicol. Chem. 22, 730–735 2 Gundlach, E.R. et al. (1983) The fate of Amoco Cadiz oil. Science 221, 122–129 3 Benedik, M.J. et al. (1998) Microbial denitrogenation of fossil fuels. Trends Biotechnol. 16, 390–395 4 Jha, A.M. and Bharti, M.K. (2002) Mutagenic profiles of carbazole in the male germ cells of Swiss albino mice. Mutat. Res. 500, 97–101 5 Wittich, R.M. (1998) Degradation of dioxin-like compounds by microorganisms. Appl. Microbiol. Biotechnol. 49, 489–499 6 Nam, I. et al. (2006) Biotransformation of 1,2,3-tri- and 1,2,3,4,7,8hexa- chlorodibenzo-p-dioxin by Sphingomonas wittichii strain RW1. Appl. Environ. Microbiol. 72, 112–116 7 Kertesz, M.A. and Wirtek, C. (2001) Desulfurization and desulfonation: application of sulfur-controlled gene expression in bacteria. Appl. Microbiol. Biotechnol. 57, 460–466 8 Yu, B. et al. (2006) Deep desulfurization of diesel oil and crude oils by a newly isolated Rhodococcus erythropolis strain. Appl. Environ. Microbiol. 72, 54–58 9 Li, F.L. et al. (2003) Deep desulfurization of hydrodesulfurizationtreated diesel oil by a facultative thermophilic bacterium Mycobacterium sp. X7B. FEMS Microbiol. Lett. 223, 301–307 10 Gupta, N. et al. (2005) Biotechnology of desulfurization of diesel: prospects and challenges. Appl. Microbiol. Biotechnol. 66, 356–366 11 Monticello, D.J. (2000) Biodesulfurization and the upgrading of petroleum distillates. Curr. Opin. Biotechnol. 11, 540–546 12 Villasenor, F. et al. (2004) Oxidation of dibenzothiophene by laccase or hydrogen peroxide and deep desulfurization of diesel fuel by the latter. Fuel Process. Technol. 86, 49–59 13 Nojiri, H. et al. (1999) Diverse oxygenation catalyzed by carbazole 1,9adioxygenase from Pseudomonas sp. strain CA10. J. Bacteriol. 181, 3105–3113 14 van Herwijnen, R. et al. (2003) Elucidation of the metabolic pathway of fluorene and cometabolic pathways of phenanthrene, fluoranthene, anthracene and dibenzothiophene by Sphingomonas sp. LB126. Res. Microbiol. 154, 199–206 15 Li, F. et al. (2005) Microbial desulfurization of gasoline in a Mycobacterium goodii X7B immobilized-cell system. Appl. Environ. Microbiol. 71, 276–281 16 Okada, H. et al. (2002) Analysis of dibenzothiophene metabolic pathway in Mycobacterium strain G3. J. Biosci. Bioeng. 93, 491–497 17 Dhar, K. and Rosazza, J.P.N. (2000) Purification and characterization of Streptomyces griseus catechol O-methyltransferase. Appl. Environ. Microbiol. 66, 4877–4882 18 Orpiszewski, J. et al. (1991) Multiple forms of O-methyltransferase involved in the microbial conversion of abietic acid into methyl abietate by Mycobacterium sp. FEMS Microbiol. Lett. 66, 233–236 19 Li, W. et al. (2005) Biodesulfurization of dibenzothiophene and other organic sulfur compounds by a newly isolated Microbacterium strain ZD-M2. FEMS Microbiol. Lett. 247, 45–50 20 Kilbane, J.J., II et al. (2002) Isolation and characterization of Sphingomonas sp. GTIN11 capable of carbazole metabolism in petroleum. Biochem. Biophys. Res. Commun. 297, 242–248 21 Schneider, J. et al. (2000) Biodegradation of carbazole by Ralstonia sp. RJGII. 123 isolated from a hydrocarbon contaminated soil. Can. J. Microbiol. 46, 269–277 22 Riddle, R.R. et al. (2003) Purification and properties of 2-hydroxy-6oxo-6-(20 -aminophenyl)hexa-2,4-dienoic acid hydrolase involved in www.sciencedirect.com 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 microbial degradation of carbazole. Protein Expr. Purif. 28, 182– 189 Li, L. et al. (2004) Degradation of carbazole in the presence of nonaqueous phase liquids by Pseudomonas sp. Biotechnol. Lett. 26, 581– 584 Riddle, R.R. et al. (2003) Recombinant carbazole-degrading strains for enhanced petroleum processing. J. Ind. Microbiol. Biotechnol. 30, 6–12 Nojiri, H. et al. (2005) Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase. J. Mol. Biol. 351, 355–370 Nam, J.W. et al. (2002) Crystallization and preliminary crystallographic analysis of the terminal oxygenase component of carbazole 1,9a-dioxygeanase of Pseudomonas resinovorans strain CA10. Acta Crystallogr. D Biol. Crystallogr. 58, 1350–1352 Nam, J.W. et al. (2002) Purification and characterization of carbazole 1,9a-dioxygenase, a three-component dioxygenase system of Pseudomonas resinovorans strain CA10. Appl. Environ. Microbiol. 68, 5882–5890 Kilbane, J.J., II et al. (2000) Selective removal of nitrogen from quinoline and petroleum by Pseudomonas ayucida IGTN9m. Appl. Environ. Microbiol. 66, 688–693 Kayser, K.J. and Kilbane, J.J., II Gas Technology Institute. Method for metabolizing carbazole in petroleum, US Patent No. 6,943,006 B2 Yu, B. et al. (2006) Selective biodegradation of S and N heterocycles by a recombinant Rhodococcus erythropolis strain containing carbazole dioxygenase. Appl. Environ. Microbiol. 72, 2235–2238 Lobastova, T.G. et al. (2004) Hydroxylation of carbazoles by Aspergillus flavus VKM F-1024. FEMS Microbiol. Lett. 235, 51–56 Resnick, S.M. et al. (1993) Oxidation of carbazole to 3-hydroxycarbazole by naphthalene 1,2-dioxygenase and biphenyl 2,3-dioxygenase. FEMS Microbiol. Lett. 113, 297–302 Schmid, A. et al. (2001) Industrial biocatalysis today and tomorrow. Nature 409, 258–268 Wang, S.N. et al. (2005) ‘Green’ route to 6-hydroxy-3-succinoyl-pyridine from (S)-nicotine of tobacco waste by whole cells of a Pseudomonas sp. Environ. Sci. Technol. 39, 6877–6880 Habe, H. et al. (2001) Preliminary examinations for applying a carbazole-degrader, Pseudomonas sp. strain CA10, to dioxincontaminated soil remediation. Appl. Microbiol. Biotechnol. 56, 788– 795 Kasuga, K. et al. (2001) Isolation and characterization of the gene encoding a novel oxygenase component of angular dioxygenase from the Gram-positive dibenzofuran-degrader Terrabacter sp. strain DBF63. Biochem. Biophys. Res. Commun. 283, 195–204 Becher, D. et al. (2000) Cometabolic degradation of dibenzofuran by biphenyl-cultivated Ralstonia sp. strain SBUG 290. Appl. Environ. Microbiol. 66, 4528–4531 Yamazoe, A. et al. (2004) Degradation of polycyclic aromatic hydrocarbons by a newly isolated dibenzofuran-utilizing Janibacter sp. strain YY-1. Appl. Microbiol. Biotechnol. 65, 211–218 Stope, M.B. et al. (2002) Cometabolic ring fission of dibenzofuran by Gram-negative and Gram-positive biphenyl-utilizing bacteria. Appl. Microbiol. Biotechnol. 59, 62–67 Fuse, H. et al. (2003) Degradation of chlorinated biphenyl, dibenzofuran, and dibenzo-p-dioxin by marine bacteria that degrade biphenyl, carbazole, or dibenzofuran. Biosci. Biotechnol. Biochem. 67, 1121–1125 Hammer, E. et al. (1998) Isolation and characterization of a dibenzofuran-degrading yeast: identification of oxidation and ring cleavage products. Appl. Environ. Microbiol. 64, 2215– 2219 Sayler, G.S. and Ripp, S. (2000) Field applications of genetically engineered microorganisms for bioremediation processes. Curr. Opin. Biotechnol. 11, 286–289 Widada, J. et al. (2002) Enhanced degradation of carbazole and 2,3dichlorodibenzo-p-dioxin in soils by Pseudomonas resinovorans strain CA10. Chemosphere 49, 485–491 Saiki, Y. et al. (2003) Rhizoremedation of dioxin-like compounds by a recombinant Rhizobium tropici strain expressing carbazole 1,9a-dioxygenase constitutively. Biosci. Biotechnol. Biochem. 67, 1144–1148 Review TRENDS in Microbiology 45 Furukawa, K. (2003) ‘Super bugs’ for bioremediation. Trends Biotechnol. 21, 187–190 46 Yu, B. et al. (2006) Microbial desulfurization of gasoline by free wholecells of Rhodococcus erythropolis XP. FEMS Microbiol. Lett. 258, 284– 289 47 León, R. et al. (1998) Whole-cell biocatalysis in organic media. Enzyme Microb. Tech. 23, 483–500 48 Inoue, A. and Horikoshi, K. (1989) A Pseudomonas thrives in high concentrations of toluene. Nature 338, 264–266 49 Ishige, T. et al. (2005) Whole organism biocatalysis. Curr. Opin. Chem. Biol. 9, 174–180 50 Tao, F. et al. (2006) Biodesulfurization in biphasic systems containing organic solvents. Appl. Environ. Microbiol. 72, 4604–4609 51 Naito, M. et al. (2001) Long-term repeated biodesulfurization by immobilized Rhodococcus erythropolis KA2-5-1 cells. Appl. Microbiol. Biotechnol. 55, 374–378 Vol.14 No.9 52 Guobin, S. et al. (2005) Improvement of biodesulfurization rate by assembling nanosorbents on the surfaces of microbial cells. Biophys. J. 89, L58–L60 53 Shan, G. et al. (2005) Biodesulfurization of dibenzothiophene by microbial cells coated with magnetite nanoparticles. Appl. Environ. Microbiol. 71, 4497–4502 54 Parales, R.E. et al. (2002) Biodegradation, biotransformation, and biocatalysis (B3). Appl. Environ. Microbiol. 68, 4699–4709 55 Galvão, T.C. et al. (2005) Exploring the microbial biodegradation and biotransformation gene pool. Trends Biotechnol. 23, 497–506 56 Ma, C.Q. et al. Methods for the preparation of a biodesulfurization biocatalyst using Rhodococcus sp. Chemosphere (in press) DOI:10.1016/ j.chemosphere.2006.03.010 (http://www.sciencedirect.com) 57 Aso, Y. et al. (2006) Engineered membrane superchannel improves bioremediation potential of dioxin-degrading bacteria. Nat. Biotechnol. 24, 188–189 Elsevier celebrates two anniversaries with a gift to university libraries in the developing world In 1580, the Elzevir family began their printing and bookselling business in the Netherlands, publishing works by scholars such as John Locke, Galileo Galilei and Hugo Grotius. On 4 March 1880, Jacobus George Robbers founded the modern Elsevier company intending, just like the original Elzevir family, to reproduce fine editions of literary classics for the edification of others who shared his passion, other ‘Elzevirians’. Robbers co-opted the Elzevir family printer’s mark, stamping the new Elsevier products with a classic symbol of the symbiotic relationship between publisher and scholar. Elsevier has since become a leader in the dissemination of scientific, technical and medical (STM) information, building a reputation for excellence in publishing, new product innovation and commitment to its STM communities. In celebration of the House of Elzevir’s 425th anniversary and the 125th anniversary of the modern Elsevier company, Elsevier donated books to ten university libraries in the developing world. Entitled ‘A Book in Your Name’, each of the 6700 Elsevier employees worldwide was invited to select one of the chosen libraries to receive a book donated by Elsevier. The core gift collection contains the company’s most important and widely used STM publications, including Gray’s Anatomy, Dorland’s Illustrated Medical Dictionary, Essential Medical Physiology, Cecil Essentials of Medicine, Mosby’s Medical, Nursing and Allied Health Dictionary, The Vaccine Book, Fundamentals of Neuroscience, and Myles Textbook for Midwives. The ten beneficiary libraries are located in Africa, South America and Asia. They include the Library of the Sciences of the University of Sierra Leone; the library of the Muhimbili University College of Health Sciences of the University of Dar es Salaam, Tanzania; the library of the College of Medicine of the University of Malawi; and the University of Zambia; Universite du Mali; Universidade Eduardo Mondlane, Mozambique; Makerere University, Uganda; Universidad San Francisco de Quito, Ecuador; Universidad Francisco Marroquin, Guatemala; and the National Centre for Scientific and Technological Information (NACESTI), Vietnam. Through ’A Book in Your Name’, these libraries received books with a total retail value of approximately one million US dollars. For more information, visit www.elsevier.com www.sciencedirect.com 405
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