Biodegradation of nitroaromatics and other nitrogen-containing xenobiotics

Nitroaromatic compounds constitute a major class of widely distributed environmental contaminants. Compounds like nitrobenzene, nitrotoluenes, nitrophenols, nitrobenzoates and nitrate esters are of considerable industrial importance. They are frequently used as pesticides, explosives, dyes, and in the manufacture of polymers and pharmaceuticals. Many nitroaromatic compounds and their conversion products have been shown to have toxic or mutagenic properties. Most of them are biodegradable in nature by various microorganisms. However, most contaminated environments have combinations of nitroaromatic compounds present, which complicates the bioremediation efforts. During the last 10 years, research on the biodegradation of nitroaromatic compounds has yielded a wealth of information on the microbiological, biochemical and genetic aspects of the process. New metabolic pathways have been discovered and genes and enzymes responsible for key transformation reactions have been identified and characterized. Knowledge and advances in pathway engineering have helped further understanding of the nature of nitroaromatic biodegradation and the development of bioremediation solutions. In this paper, an overview of recent developments on the biodegradation of nitrogen-containing xenobiotics is presented.     

Degradation of nitroaromatic compounds by microorganisms

Nitroaromatic compounds are abundantly present in nature, but are in most cases highly toxic to living organisms. Several microorganisms, however, are capable of mineralizing or converting these compounds. Until now four pathways for the complete degradation of nitroaromatics have been described, which start with either the oxygenolytic or reductive removal of the nitro group from the aromatic ring or with this removal by means of replacement reactions. Besides these conversions many organisms are able to reduce nitroaromatics. The degradation of nitroaromatic compounds does not only occur in pure cultures but also in situ, for example in soil, water and sewage. However, several problems are associated with the application of microorganisms in the bioremediation of contaminated sites, as nitroaromatics or their conversion products may chemically interact with soil particles and cells. Besides the possibilities of applying microorganisms in the cleaning of sites contaminated with nitroaromatics, the use of microorganisms or enzymes in the biocatalytic production of industrially valuable products from nitroaromatics is also discussed.     

Reduction of polynitroaromatic compounds: the bacterial nitroreductases

Most nitroaromatic compounds are toxic and mutagenic for living organisms, but some microorganisms have developed oxidative or reductive pathways to degrade or transform these compounds. Reductive pathways are based either on the reduction of the aromatic ring by hydride additions or on the reduction of the nitro groups to hydroxylamino and/or amino derivatives. Bacterial nitroreductases are flavoenzymes that catalyze the NAD(P)H-dependent reduction of the nitro groups on nitroaromatic and nitroheterocyclic compounds. Nitroreductases have raised a great interest due to their potential applications in bioremediation, biocatalysis, and biomedicine, especially in prodrug activation for chemotherapeutic cancer treatments. Different bacterial nitroreductases have been purified and their biochemical and kinetic parameters have been determined. The crystal structure of some nitroreductases have also been solved. However, the physiological role(s) of these enzymes remains unclear. Nitroreductase genes are widely spread within bacterial genomes, but are also found in archaea and some eukaryotic species. Although studies on regulation of nitroreductase gene expression are scarce, it seems that nitroreductase genes may be controlled by the MarRA and SoxRS regulatory systems that are involved in responses to several antibiotics and environmental chemical hazards and to specific oxidative stress conditions. This review covers the microbial distribution, types, biochemical properties, structure and regulation of the bacterial nitroreductases. The possible physiological functions and the biotechnological applications of these enzymes are also discussed.     

微生物降解硝基芳烃及其卤代衍生物的研究进展

硝基芳烃化合物作为一种重要的化工原料,广泛应用于医药、染料、农药等化工产品的合成。在给人类社会带来空前的物质繁荣的同时,其造成的环境污染问题也成为人类社会面临的重要挑战之一。微生物在这些环境污染物的降解中起着重要的作用。近几十年,环境微生物工作者对微生物降解硝基芳香污染物的各个步骤,包括趋化感应、分解代谢及生物修复进行了大量的研究工作,获得了丰富的知识。本文综述了硝基芳烃及其卤代衍生物的微生物代谢途径、代谢机理、趋化及修复研究进展,并对本领域的研究进行了展望,有助于全面认知硝基芳烃污染物的微生物降解过程,为污染环境修复提供理论基础。     

Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase

Nitroaromatic compounds are used extensively in many industrial processes and have been released into the environment where they are considered environmental pollutants. Nitroaromatic compounds, in general, are resistant to oxidative attack due to the electron-withdrawing nature of the nitro groups and the stability of the benzene ring. However, the bacterium Comamonas sp. strain JS765 can grow with nitrobenzene as a sole source of carbon, nitrogen and energy. Biodegradation is initiated by the nitrobenzene dioxygenase (NBDO) system. We have determined the structure of NBDO, which has a hetero-hexameric structure similar to that of several other Rieske non-heme iron dioxygenases. The catalytic subunit contains a Rieske iron-sulfur center and an active-site mononuclear iron atom. The structures of complexes with substrates nitrobenzene and 3-nitrotoluene reveal the structural basis for its activity with nitroarenes. The substrate pocket contains an asparagine residue that forms a hydrogen bond to the nitro-group of the substrate, and orients the substrate in relation to the active-site mononuclear iron atom, positioning the molecule for oxidation at the nitro-substituted carbon.     

Biodegradation of 5-Nitroanthranilic Acid by Bradyrhizobium sp. Strain JS329

Biodegradation of synthetic compounds has been studied extensively, but the metabolic diversity required for catabolism of many natural compounds has not been addressed. 5-Nitroanthranilic acid (5NAA), produced in soil by Streptomyces scabies, is also the starting material for synthetic dyes and other nitroaromatic compounds. Bradyrhizobium JS329 was isolated from soil by selective enrichment with 5NAA. When grown on 5NAA, the isolate released stoichiometric amounts of nitrite and half of the stoichiometric amounts of ammonia. Enzyme assays indicate that the initial step in 5NAA degradation is an unusual hydrolytic deamination for formation of 5-nitrosalicylic acid (5NSA). Cloning and heterologous expression revealed the genes that encode 5NAA deaminase (naaA) and the 5NSA dioxygenase (naaB) that cleaves the aromatic ring of 5NSA without prior removal of the nitro group. The results provide the first clear evidence for the initial steps in biodegradation of amino-nitroaromatic compounds and reveal a novel deamination reaction for aromatic amines.The research on biodegradation/biotransformation of nitro compounds has focused on synthetic chemicals, but there are a substantial number of natural nitro-substituted compounds whose metabolism has not been explored. The biodegradation pathways for natural nitro compounds probably provided the metabolic diversity that enabled the rapid and recent evolution of pathways for degradation of synthetic nitro compounds.5-Nitroanthranilic acid (5-NAA), a natural nitroaromatic compound, is produced by Streptomyces scabies, but its physiological role is unclear (15). Synthetic 5NAA is used as the starting material for various nitroaromatic compounds and dyes (3). Substitution of the aromatic ring with amino, nitro, and carboxyl functional groups creates an interesting challenge for catabolic enzymes because any of the three groups could serve as a point of attack for dioxygenase enzymes prior to ring cleavage.Synthetic nitroanilines are toxic and used for the synthesis of pharmaceuticals, dyes, and pigments (27). In sewage, nitroanilines can be formed from the corresponding dinitroaromatic compounds under aerobic or anaerobic conditions (11). Early reports indicated that nitroanilines were resistant to biodegradation (1, 9, 11), but 4-nitroaniline was degraded by Pseudomonas sp. strain P6 (32) and Stenotrophomonas strain HPC 135 (26). Saupe reported that 3-nitroaniline could be degraded aerobically (27). The biodegradation pathways of nitroanilines are unknown, and they are typically classified as nondegradable or poorly degradable compounds (27).As part of a search for novel metabolic diversity and an effort to study the degradation pathway for recalcitrant nitroanilines, we report here the biodegradation of 5NAA as the sole carbon, nitrogen, and energy source by Bradyrhizobium JS329. The degradation pathway involves an unusual hydrolytic removal of the amino group and subsequent ring fission without prior removal of the nitro group.(A preliminary report of this work was presented at the 109th General Meeting of the American Society for Microbiology, 2009 [25].)     

Mutagenicity and genotoxicity of nitroarenes. All nitro-containing chemicals were not created equal

The nitrated polycyclic aromatic hydrocarbons constitute a group of chemicals of environmental concern which display a broad spectrum of mutagenic, genotoxic and carcinogenic properties. Some members of the group are the most potent direct-acting bacterial mutagens while others exhibit low levels of potencies which require metabolic activation mixtures. Bacterial mutagenicity is dependent upon reduction of the nitro function. In mammalian cell systems the genetic and genotoxic effects of these nitrated chemicals include the induction of unscheduled DNA synthesis, sister-chromatid exchanges, chromosomal aberrations, gene mutations and cell transformation. The qualitative as well as quantitative expression of these effects is dependent upon the species and tissue of origin as well as culture history of the cell which in turn determine their enzymic capabilities and the conversion of these nitroarenes to ultimate mutagens and genotoxicants. In eukaryotic cells the following bioactivation pathways have been recognized: (a) reduction of the nitro moiety, (b) ring oxidation (the nature of which is influenced by the nitro function) followed by reduction of the nitro group, and (c) ring oxidation without concomitant reduction of the nitro moiety.     

Biodegradation of 2,4-dinitrotoluene by a Pseudomonas sp.

Previous studies of the biodegradation of nonpolar nitroaromatic compounds have suggested that microorganisms can reduce the nitro groups but cannot cleave the aromatic ring. We report here the initial steps in a pathway for complete biodegradation of 2,4-dinitrotoluene (DNT) by a Pseudomonas sp. isolated from a four-member consortium enriched with DNT. The Pseudomonas sp. degraded DNT as the sole source of carbon and energy under aerobic conditions with stoichiometric release of nitrite. During induction of the enzymes required for growth on DNT, 4-methyl-5-nitrocatechol (MNC) accumulated transiently in the culture fluid when cells grown on acetate were transferred to medium containing DNT as the sole carbon and energy source. Conversion of DNT to MNC in the presence of 18O2 revealed the simultaneous incorporation of two atoms of molecular oxygen, which demonstrated that the reaction was catalyzed by a dioxygenase. Fully induced cells degraded MNC rapidly with stoichiometric release of nitrite. The results indicate an initial dioxygenase attack at the 4,5 position of DNT with the concomitant release of nitrite. Subsequent reactions lead to complete biodegradation and removal of the second nitro group as nitrite.     

Biodegradation of 2,4-dinitrotoluene by a Pseudomonas sp.

Previous studies of the biodegradation of nonpolar nitroaromatic compounds have suggested that microorganisms can reduce the nitro groups but cannot cleave the aromatic ring. We report here the initial steps in a pathway for complete biodegradation of 2,4-dinitrotoluene (DNT) by a Pseudomonas sp. isolated from a four-member consortium enriched with DNT. The Pseudomonas sp. degraded DNT as the sole source of carbon and energy under aerobic conditions with stoichiometric release of nitrite. During induction of the enzymes required for growth on DNT, 4-methyl-5-nitrocatechol (MNC) accumulated transiently in the culture fluid when cells grown on acetate were transferred to medium containing DNT as the sole carbon and energy source. Conversion of DNT to MNC in the presence of 18O2 revealed the simultaneous incorporation of two atoms of molecular oxygen, which demonstrated that the reaction was catalyzed by a dioxygenase. Fully induced cells degraded MNC rapidly with stoichiometric release of nitrite. The results indicate an initial dioxygenase attack at the 4,5 position of DNT with the concomitant release of nitrite. Subsequent reactions lead to complete biodegradation and removal of the second nitro group as nitrite.     

Molecular and biochemical characterization of the 5-nitroanthranilic acid degradation pathway in Bradyrhizobium sp. strain JS329

Biodegradation pathways of synthetic nitroaromatic compounds and anilines are well documented, but little is known about those of nitroanilines. We previously reported that the initial step in 5-nitroanthranilic acid (5NAA) degradation by Bradyrhizobium sp. strain JS329 is a hydrolytic deamination to form 5-nitrosalicylic acid (5NSA), followed by ring fission catalyzed by 5NSA dioxygenase. The mechanism of release of the nitro group was unknown. In this study, we subcloned, sequenced, and expressed the genes encoding 5NAA deaminase (5NAA aminohydrolase, NaaA), 5NSA dioxygenase (NaaB) and lactonase (NaaC), the key genes responsible for 5NAA degradation. Sequence analysis and enzyme characterization revealed that NaaA is a hydrolytic metalloenzyme with a narrow substrate range. The nitro group is spontaneously eliminated as nitrite concomitant with the formation of a lactone from the ring fission product of 5NSA dioxygenation. The elimination of the nitro group during lactone formation is a previously unreported mechanism for denitration of nitro aliphatic compounds.     

Cytotoxicity of nitroaromatic explosives and their biodegradation products in mice splenocytes: implications for their immunotoxicity

Nitroaromatic explosives like 2,4,6-trinitrotoluene (TNT) and 2,4,6-trinitrophenyl-N-methyl-nitramine (tetryl) comprise an important group of toxic environmental pollutants, whose toxicity is mainly attributed to the flavoenzyme electrontransferase-catalyzed redox cycling of their free radicals (oxidative stress) and DT-diaphorase [NAD(P)H:quinone oxidoreductase, NQO1, EC 1. 6.99.2]-catalyzed formation of alkylating nitroso and/or hydroxylamine metabolites. Because of the incomprehensive data on the immunotoxic effects of nitroaromatic explosives, we have studied the structure-cytotoxicity relationships in the action of tetryl, TNT as well as its amino and hydroxylamino metabolites, and related nitroaromatic compounds towards mouse splenocyte cells. The protective effects of desferrioxamine and the antioxidant N,N'-diphenyl-p-phenylene diamine against the cytotoxicity of TNT and other nitroaromatics showed that the oxidative stress-type cytotoxicity mechanism takes place. In addition, the cytotoxicity of nitroaromatics is also partly prevented by an inhibitor of NQO1, dicumarol. The cytotoxicity of the amino metabolites of TNT is also partly prevented by alpha-naphthoflavone and isoniazide, which points to the involvement of cytochromes P-450 in their activation. In general the cytotoxicity of nitroaromatics in splenocytes increases with an increase in their single-electron reduction potential, E1(7). This points to the prevailing mechanism of the oxidative stress-type cytotoxicity. The obtained structure-activity relationship and the studies of other mammalian cell lines showed that the immunotoxic potential of nitroaromatic explosives may decrease in the order tetryl > or = TNT > or = hydroxylamino metabolites of TNT > amino and diamino metabolites of TNT.     

有机磷酸酯阻燃剂/增塑剂的生物降解及其机制研究进展

有机磷酸酯(Organophosphate Esters,OPEs)阻燃剂/塑化剂对人类有潜在的健康风险并且广泛分布在各种环境介质中,为应对OPEs带来的挑战,绿色、高效的生物降解方式成为了当前的研究热点。文章目的是叙述目前已知的OPEs的生物降解过程及机制,主要围绕TBP、TPHP这2种热点OPEs来描述生物降解途径及其中间产物。综合来看,生物降解OPEs的主要途径是通过水解作用、羟基化作用或者甲氧基化作用来实现的,在降解过程中细胞色素P450起关键作用,最终多数降解菌能够将OPEs矿化为无机磷酸盐及其他小分子化合物,能够实现对环境的无害化。     

Synthesis of substituted catechols using nitroarene dioxygenases

The nitroarene dioxygenases are in the class of Rieske iron-containing oxygenases that incorporate atmospheric oxygen into substrates via electrophilic attack on the substrate. In their native role, the nitroarene dioxygenases start degradative pathways by hydroxylating nitro-substituted, and adjacent unsubstituted carbons of nitroaromatic compounds. The reaction yields the corresponding nitro-cis-cyclohexadienediol, which is unstable and spontaneously re-aromatizes to form a catechol and nitrite. In bacterial metabolism, the specificity of the hydroxylation determines subsequent steps in degradation pathways. Experiments were done to find whether the specificity could be exploited to direct the hydroxylation of multiply substituted aromatic substrates and thereby produce novel catechols. Recombinant strains carrying genes for nitroarene dioxygenases were used for transformation of various substituted nitroaromatic compounds. The reactions were analyzed using HPLC to track substrate consumption and product formation, then GC–MS and NMR to identify the reaction products. A number of substituted catechols were obtained using the recombinant biocatalysts. The nitro-substituted carbon was the primary site for dioxygenase hydroxylation. When substrates included nitro and halogen substituents, the halogen-substituted positions were also targeted, but less frequently than the nitro-substituted site. The production of catechols was limited in batch fermentations, likely due to toxicity of the quinones that result from air oxidation of catechols. The nitroarene dioxygenases will serve as catalysts for direct synthesis of highly substituted catechols, however, the reaction conditions must be engineered to overcome product toxicity and allow sustained accumulation of catecholic products.     

药物类新污染物的微生物降解机制研究进展

环境微生物作为自然界中主要的分解者蕴含着丰富的遗传和代谢多样性,在有机污染物降解中发挥着重要作用。药物被持续不断地释放到环境中,其环境暴露、环境风险和对人体健康的潜在影响已得到广泛关注。研究药物在环境中的微生物降解过程对于药物的环境命运、药物的环境风险评估和药物污染去除技术的开发等具有重要价值。本文重点综述了目前环境中常检出药物的微生物降解途径及其分子机理,总结了目前药物微生物降解研究领域的进展,最后探讨了药物的微生物降解领域未来的研究趋势。     

Microbial transformation of 2,4,6-trinitrotoluene and other nitroaromatic compounds.

A variety of nitroaromatic compounds, including 2,4,6-trinitrotoluene (TNT), were reduced by hydrogen in the presence of enzyme preparations from Veillonella alkalescens. Consistent with the proposed reduction pathway, R-NO2 H2 leads to R-NO H2 leads to R-NHOH H2 leads to R-NH2, 3 mol of H2 was utilized per mol of nitro group. The rates of reduction of 40 mono-, di-, and trinitroaromatic compounds by V. alkalescens extract were determined. The reactivity of the nitro groups depended on other substituents and on the position of the nitro groups relative to these substituents. In the case of the nitrotoluenes, the para-nitro group was the most readily reduced, the 4-nitro position of 2,4-dinitrotulene being reduced first. The pattern of reduction of TNT (disappearance of TNT and reduction products formed) depended on the type of preparation (cell-free extract, resting cells, or growing culture), on the species, and on the atmosphere (air or H2). The "nitro-reductase" activity of V. alkalescens extracts was associated with protein fractions, one having some ferredoxin-like properties and the other possessing hydrogenase activity. Efforts to eliminate hydrogenase from the reaction have thus far been unsuccessful. The question of whether ferredoxin acts as a nonspecific reductase for nitroaromatic compounds remains unresolved.     

Biological Degradation of 2,4,6-Trinitrotoluene

Nitroaromatic compounds are xenobiotics that have found multiple applications in the synthesis of foams, pharmaceuticals, pesticides, and explosives. These compounds are toxic and recalcitrant and are degraded relatively slowly in the environment by microorganisms. 2,4,6-Trinitrotoluene (TNT) is the most widely used nitroaromatic compound. Certain strains of Pseudomonas and fungi can use TNT as a nitrogen source through the removal of nitrogen as nitrite from TNT under aerobic conditions and the further reduction of the released nitrite to ammonium, which is incorporated into carbon skeletons. Phanerochaete chrysosporium and other fungi mineralize TNT under ligninolytic conditions by converting it into reduced TNT intermediates, which are excreted to the external milieu, where they are substrates for ligninolytic enzymes. Most if not all aerobic microorganisms reduce TNT to the corresponding amino derivatives via the formation of nitroso and hydroxylamine intermediates. Condensation of the latter compounds yields highly recalcitrant azoxytetranitrotoluenes. Anaerobic microorganisms can also degrade TNT through different pathways. One pathway, found in Desulfovibrio and Clostridium, involves reduction of TNT to triaminotoluene; subsequent steps are still not known. Some Clostridium species may reduce TNT to hydroxylaminodinitrotoluenes, which are then further metabolized. Another pathway has been described in Pseudomonas sp. strain JLR11 and involves nitrite release and further reduction to ammonium, with almost 85% of the N-TNT incorporated as organic N in the cells. It was recently reported that in this strain TNT can serve as a final electron acceptor in respiratory chains and that the reduction of TNT is coupled to ATP synthesis. In this review we also discuss a number of biotechnological applications of bacteria and fungi, including slurry reactors, composting, and land farming, to remove TNT from polluted soils. These treatments have been designed to achieve mineralization or reduction of TNT and immobilization of its amino derivatives on humic material. These approaches are highly efficient in removing TNT, and increasing amounts of research into the potential usefulness of phytoremediation, rhizophytoremediation, and transgenic plants with bacterial genes for TNT removal are being done.     

Metabolism of compounds with nitro-functions by Klebsiella pnuemoniae isolated from a regional wetland

Metabolism of nitroaromatic compounds by a Klebsiella pneumoniae isolated from a regional wetland was studied. When it was grown with nitrophenol as the sole nitrogen source, the isolate had the metabolic capability of transforming nitrophenol to phenol; however, it did not use nitrophenol as the sole carbon source. The metabolic pathway showed that the K. pneumoniae reduced the nitro group to an amino group forming aminophenol as a major metabolite. This aminophenol was oxidatively deaminated to phenol. For every mole of nitrophenol metabolized, 1 mol of phenol was produced and the phenol did not undergo further metabolism. The isolate also used several other nitroaromatic compounds including nitrotoluenes and nitrobenzenes as its nitrogen source. Even though this organism did not degrade the nitroaromatics completely, it may be useful in degrading nitroaromatics in contaminated soil and water containing other aromatic degraders in a syntrophic condition in nature.     

Biodegradation of the cyclic nitramine explosives RDX, HMX, and CL-20

Cyclic nitramine explosives are synthesized globally mainly as military munitions, and their use has resulted in environmental contamination. Several biodegradation pathways have been proposed, and these are based mainly on end-product characterization because many of the metabolic intermediates are hypothetical and unstable in water. Biodegradation mechanisms for cyclic nitramines include (a) formation of a nitramine free radical and loss of nitro functional groups, (b) reduction of nitro functional groups, (c) direct enzymatic cleavage, (d) α-hydroxylation, or (e) hydride ion transfer. Pathway intermediates spontaneously decompose in water producing nitrite, nitrous oxide, formaldehyde, or formic acid as common end-products. In vitro enzyme and functional gene expression studies have implicated a limited number of enzymes/genes involved in cyclic nitramine catabolism. Advances in molecular biology methods such as high-throughput DNA sequencing, microarray analysis, and nucleic acid sample preparation are providing access to biochemical and genetic information on cultivable and uncultivable microorganisms. This information can provide the knowledge base for rational engineering of bioremediation strategies, biosensor development, environmental monitoring, and green biosynthesis of explosives. This paper reviews recent developments on the biodegradation of cyclic nitramines and the potential of genomics to identify novel functional genes of explosive metabolism.