Biodegradation of 2,4,6-trinitrotoluene (TNT): An enzymatic perspective

Enzymatic degradation of TNT by aerobic bacteria is mediated by oxygen insensitive (Type 1) or by oxygen sensitive nitroreductases (Type II nitroreductases). Transformation by Type I nitroreductases proceeds through two successive electron reductions either by hydride addition to the aromatic ring or by direct nitro group reduction following a ping pong kinetic mechanism. TNT is reduced to the level of hydroxylaminodinitrotoluenes and aminodinitrotoluenes by pure enzyme preparations without achieving mineralization. Interestingly, database gene and amino acid sequence comparisons of nitroreductases reveal a close relationship among all enzymes involved in TNT transformation. They are all flavoproteins which use NADPH/NADH as electron donor and reduce a wide range of electrophilic xenobiotics. TNT degradation by fungi is initiated by mycelia bound nitroreductases which reduce TNT to hydroxylaminodinitrotoluenes and aminodinitrotoluenes. Further degradation of these products and mineralization is achieved through the activity of oxidative enzymes especially lignin degrading enzymes (lignin and manganese peroxidases).     

Biodegradation of 2,4,6-trinitrotoluene (TNT): An enzymatic perspective

Enzymatic degradation of TNT by aerobic bacteria is mediated by oxygen insensitive (Type 1) or by oxygen sensitive nitroreductases (Type II nitroreductases). Transformation by Type I nitroreductases proceeds through two successive electron reductions either by hydride addition to the aromatic ring or by direct nitro group reduction following a ping pong kinetic mechanism. TNT is reduced to the level of hydroxylaminodinitrotoluenes and aminodinitrotoluenes by pure enzyme preparations without achieving mineralization. Interestingly, database gene and amino acid sequence comparisons of nitroreductases reveal a close relationship among all enzymes involved in TNT transformation. They are all flavoproteins which use NADPH/NADH as electron donor and reduce a wide range of electrophilic xenobiotics. TNT degradation by fungi is initiated by mycelia bound nitroreductases which reduce TNT to hydroxylaminodinitrotoluenes and aminodinitrotoluenes. Further degradation of these products and mineralization is achieved through the activity of oxidative enzymes especially lignin degrading enzymes (lignin and manganese peroxidases).     

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.     

An unusually cold active nitroreductase for prodrug activations

A set of PCR primers based on the genome sequence were used to clone a gene encoding a hypothetical nitroreductases (named as Ssap-NtrB) from uropathogenic staphylococcus, Staphylococcus saprophyticus strain ATCC 15305, an oxygen insensitive flavoenzyme. Activity studies of the translation product revealed that the nitroreductase catalyses two electron reduction of a nitroaromatic drug of nitrofurazone (NFZ), cancer prodrugs of CB1954 and SN23862 at optimum temperature of 20 °C together with retaining its maximum activity considerably at 3 °C. The required electrons for such reduction could be supplied by either NADH or NADPH with a small preference for the latter. The gene was engineered for heterologous expression in Escherichia coli, and conditions were found in which the enzyme was produced in a mostly soluble form. The recombinant enzyme was purified to homogeneity and physical, spectral and catalytical properties were determined. The findings lead us to propose that Ssap-NtrB represents a novel nitro reductase with an unusual cold active property, which has not been described previously for prodrug activating enzymes of nitroreductases.     

Synthesis and structure-activity relationships of nitrobenzyl phosphoramide mustards as nitroreductase-activated prodrugs

A series of nitrobenzyl phosphoramide mustards and their analogs was designed and synthesized to explore their structure-activity relationships as substrates of nitroreductases from Escherichia coli and trypanosomes and as potential antiproliferative and antiparasitic agents. The position of the nitro group on the phenyl ring was important with the 4-nitrobenzyl phosphoramide mustard (1) offering the best combination of enzyme activity and antiproliferative effect against both mammalian and trypanosomatid cells. A preference was observed for halogen substitutions ortho to benzyl phosphoramide mustard but distinct differences were found in their SAR of substituted 4-nitrobenzyl phosphoramide mustards in E. coli nitroreductase-expressing cells and in trypanosomatids expressing endogenous nitroreductases.     

Nitroreductase II involved in 2,4,6-trinitrotoluene degradation: Purification and characterization from <Emphasis Type="Italic">Klebsiella</Emphasis> sp. Cl

Three 2,4,6-trinitrotoluene (TNT) nitroreductases from Klebsiella sp. CI have different reduction capabilities that can degrade TNT by simultaneous utilization of two initial reduction pathways. Of these, nitroreductase II was purified to homogeneity by sequential chromatographies. Nitroreductase II is an oxygen-insensitive enzyme and reduces both TNT and nitroblue tetrazolium. The N-terminal amino acid sequence of the enzyme did not show any sequence similarity with those of other nitroreductases reported. However, it transformed TNT by the reduction of nitro groups like nitroreductase I. It had a higher substrate affinity and specific activity for TNT reduction than other nitroreductases, and it showed a higher oxidation rate of NADPH with the ortho-substituted isomers of TNT metabolites (2-hydroxylaminodinitrotoluene and 2-aminodinitrotoluene) than with para-substituted compounds (4-hydroxylaminodinitrotoluene and 4-amino-dinitrotoluene).     

The role of catalytic superoxide formation in the O2 inhibition of nitroreductase.

Many nitroreductases are strongly inhibited by oxygen. The first intermediate of nitroreductase activity, the nitroaromatic anion free radical, cannot be detected in aerobic microsomal incubations. Even though the nitro compounds are unchanged, both nitrofurantoin and $\text{p}$-nitrobenzoate profoundly increase the NADPH-supported oxygen uptake. This catalytic oxygen consumption is partially reversed by superoxide dismutase, suggesting that superoxide anion free radical is being formed by the rapid air oxidation of the nitroaromatic anion radical.     

Oxygen-sensitive and -insensitive nitroreduction by Escherichia coli and rat hepatic microsomes.

Nitrofurazone is shown to undergo an initial 1-electron (oxygen-sensitive) or 2- or more electron (oxygen-insensitive) reduction by partially purified nitroreductases from Escherichia coli. Nitrofurazone (50 micronM) is reduced by the oxygen-sensitive reductase to a nitro anion free radical as indicated by ESR and visible spectroscopy. The visible spectrum of the nitro anion free radical is characterized by an increase in absorption at 406 nm. In the presence of the oxygen-sensitive reductase, nitrofurazone stimulates superoxide formation and oxygen consumption. This enzyme gives a steady state radical concentration which is proportional to the square root of the enzyme concentration, suggesting that the nitrofurazone anion radical is an obligate intermediate in the reduction and that the radical decays by a nonenzymatic second order process. The oxygen-insensitive reductase does not form the nitro anion free radical nor in the presence of nitrofurazone does it stimulate oxygen consumption. Visible spectroscopy shows that nitrofurazone is reduced by the oxygen-sensitive reductase to a species with an absorption maximum at 335 nm, which has been previously identified as the amine. The oxygen-insensitive reductase reduces nitrofurazone to a previously identified cyano derivative with an absorption maximum at 280 nm. Rat hepatic microsomes appear to metabolize nitrofurazone in a manner similar to the oxygen-sensitive E. coli reductase.     

Crystal Structure of Reduced MsAcg,a Putative Nitroreductase from Mycobacterium smegmatis and a Close Homologue of Mycobacterium tuberculosis Acg

This paper presents the structure of MsAcg (MSMEG_5246), a Mycobacterium smegmatis homologue of Mycobacterium tuberculosis Acg (Rv2032) in its reduced form at 1.6 Å resolution using x-ray crystallography. Rv2032 is one of the most induced genes under the hypoxic model of tuberculosis dormancy. The Acg family turns out to be unusual flavin mononucleotide (FMN)-binding proteins that have probably arisen by gene duplication and fusion from a classical homodimeric nitroreductase such that the monomeric protein resembles a classical nitroreductase dimer but with one active site deleted and the other active site covered by a unique lid. The FMN cofactor is not reduced by either NADH or NADPH, but the chemically reduced enzyme is capable of reduction of nitro substrates, albeit at no kinetic advantage over free FMN. The reduced enzyme is rapidly oxidized by oxygen but without any evidence for a radical state commonly seen in oxygen-sensitive nitroreductases. The presence of the unique lid domain, the lack of reduction by NAD(P)H, and the slow rate of reaction of the chemically reduced protein raises a possible alternative function of Acg proteins in FMN storage or sequestration from other biochemical pathways as part of the bacteria''s adaptation to a dormancy state.     

Purification and characterization of NAD(P)H-dependent nitroreductase I from Klebsiella sp. C1 and enzymatic transformation of 2,4,6-trinitrotoluene

Three NAD(P)H-dependent nitroreductases that can transform 2,4,6-trinitrotoluene (TNT) by two reduction pathways were detected in Klebsiella sp. C1. Among these enzymes, the protein with the highest reduction activity of TNT (nitroreductase I) was purified to homogeneity using ion-exchange, hydrophobic interaction, and size exclusion chromatographies. Nitroreductase I has a molecular mass of 27 kDa as determined by SDS-PAGE, and exhibits a broad pH optimum between 5.5 and 6.5, with a temperature optimum of 30–40°C. Flavin mononucleotide is most likely the natural flavin cofactor of this enzyme. The N-terminal amino acid sequence of this enzyme does not show a high degree of sequence similarity with nitroreductases from other enteric bacteria. This enzyme catalyzed the two-electron reduction of several nitroaromatic compounds with very high specific activities of NADPH oxidation. In the enzymatic transformation of TNT, 2-amino-4,6-dinitrotoluene and 2,2′,6,6′-tetranitro-4,4′-azoxytoluene were detected as transformation products. Although this bacterium utilizes the direct ring reduction and subsequent denitration pathway together with a nitro group reduction pathway, metabolites in direct ring reduction of TNT could not easily be detected. Unlike other nitroreductases, nitroreductase I was able to transform hydroxylaminodinitrotoluenes (HADNT) into aminodinitrotoluenes (ADNT), and could reduce ortho isomers (2-HADNT and 2-ADNT) more easily than their para isomers (4-HADNT and 4-ADNT). Only the nitro group in the ortho position of 2,4-DNT was reduced to produce 2-hydroxylamino-4-nitrotoluene by nitroreductase I; the nitro group in the para position was not reduced.     

No detectable reaction of the anion radical metabolite of nitrofurans with reduced glutathione or macro-molecules

The initial metabolite formed by most mammalian nitroreductases is the nitro anion free radical. We, as well as others, have proposed that nitroheterocyclic anion radicals covalently bind to protein, DNA, or thiol compounds such as reduced glutathione (GSH). Our results indicate that even at 100 mM GSH does not affect the steady-state concentration of the nitro anion free radical of N-[4-(5-nitro-2-furyl)-2-thiazolyl]acetamide (NFTA) in rat hepatic microsomal or xanthine oxidase incubations. The steady-state ESR amplitude of the anion radical is also unchanged by the addition of BSA or DNA. Similar results are obtained with nitrofurazone and nitrofurantoin. The reactive chemical species which binds to tissue macromolecules and GSH upon the reduction of nitrofurans remains unknown, but the anion free radical metabolite can be excluded from consideration.     

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.     

A flavoprotein encoded in Selenomonas ruminantium is characterized after expression in Escherichia coli

Selenomonas ruminantium is an obligate anaerobe that is very important for the provision of vitamin B12 to ruminants, which are particularly dependent upon this cofactor. One important use for vitamin B12 in anaerobic bacteria is for the utilization of glycerol as carbon source. A new flavoprotein has been found expressed by Escherichia coli from a plasmid created as part of a gene library of S. ruminantium. The 2.5-kb fragment of chromosomal DNA responsible for protein expression contains parts of two operons. Only one polypeptide (the flavoprotein) encoded by the S. ruminantium DNA is produced in E. coli in large amounts. The gene for the flavoprotein has been identified and is probably transcribed as part of an operon involved in glycerol metabolism in S. ruminantium. The flavoprotein has been purified and its molecular properties have been examined. Sequence analysis showed that this protein is a divergent member of the family of nitroreductases. Pure protein is a homodimer with a molecular weight of 44,500, containing one molecule of FMN per dimer. Like other nitroreductases, this protein forms a complex with pyridine nucleotide (NADPH), but unlike other nitroreductases, it fails to be reduced in this complex at a biologically significant rate. It has none of the common catalytic properties of other members of the nitroreductase family.     

Kinetic studies of four types of nitroheterocyclic radicals by pulse radiolysis. Correlation of pharmacological properties to decay rates

The chemical properties of the nitro radical of four types of nitroheterocyclic compounds, nitrofurans, 2-nitroimidazoles, 4(5)-nitroimidazoles, 5-nitroimidazoles, having radiosensitizing and cytotoxic properties, have been studied by pulse radiolysis. The acid-base equilibria involving the nitro radical, the imidazole ring and some residues on the heterocycle have been determined. The pH-dependence of the rate of the disproportionation reaction of the nitro radical have been extensively studied. While the nitro radical derived from nitrofurans, 4- and 5-nitroimidazoles had a second-order decay, those of the 2-nitroimidazoles were found to decay through simultaneous first-order and second-order processes. Intrinsic second-order rate constants of the decay of the radical species in its various acidic and basic forms, could be determined. The intrinsic rate constants that determine the overall decay rates in the physiologically important 6 to 7.5 pH-range could be related to the one-electron redox potential E7(1). The implication of such chemical properties to enzyme-catalyzed reduction processes and to the mechanisms of radiosensitization and cytotoxicity of nitroheterocyclic compounds are briefly discussed. Pharmacological properties such as in vitro radiosensitization efficiency or metabolic reduction rates could be related to two of the nitro radical intrinsic disproportionation rates.     

Correlation of kinetic parameters of nitroreductase enzymes with redox properties of nitroaromatic compounds

The well-established mechanism of regeneration of the parent nitro compound by the reaction of the nitro anion radical with oxygen in aerobic systems is the basis of the correlation of kinetic parameters of purified flavoenzymes with electron affinities of some selected nitroaryl and nitroheterocyclic compounds. We have found that there is a linear relationship between log Vmax/Km and the one-electron reduction potentials of these compounds and that the measured values of redox dependence for these compounds is similar to that determined by other methods. Our results support the proposal of a rate-determining single electron-transfer as the initial step in the reduction of nitro compounds by purified flavoenzymes and are discussed in terms of the Marcus electron transfer theory.     

Purification and characterization of an oxygen-insensitive NAD(P)H nitroreductase from Enterobacter cloacae

The reductive products of several nitroaromatic compounds have been found to be toxic, mutagenic, and carcinogenic. The nitroreductases present in intestinal microflora have been implicated in the biotransformation of these compounds to their deleterious metabolites. A "classical" nitroreductase has been purified from Enterobacter cloacae 587-fold using a protocol which yields approximately 1 mg of purified nitroreductase from 10 liters of cell culture. An analysis of the physical properties of the nitroreductase indicates that the enzyme is active as a monomer with a calculated molecular mass of 27 kDa. FMN has been identified as a required flavin cofactor and is present at a stoichiometry of 0.88 mol of FMN bound/mol of active enzyme. The enzyme was found capable of reducing nitrofurazone under aerobic conditions indicating that the mechanism involves an obligatory two-electron transfer. Thus, this enzyme can be classified as an oxygen-insensitive nitroreductase. The purified nitroreductase can utilize either NADH or NADPH as a source of reducing equivalents and can reduce a variety of nitroaromatic compounds including nitrofurans and nitrobenzenes as well as quinones. Studies in which the rates of nitroreduction for a series of para substituted nitrobenzene derivatives were determined suggest that a linear free energy relationship exists between the rate and the redox midpoint potential of the substrate.     

Standardization and regulation of the rate of the superoxide-generating reaction of adrenaline autoxidation used for evaluation of pro/antioxidant properties of various materials

The superoxide-generating reaction of adrenaline autoxidation is widely used for determination of superoxide dismutase activity and pro/antioxidant properties of various materials. There are two variants of the spectrophotometric registration of the products of this reaction. The first one is based on registration of adrenochrome (a product of adrenaline autoxidation) at 347 nm; the second approach employs nitro blue tetrazolium (NBT) and registration of diformazan (a product of NBT reduction) at 560 nm. In the present work, recommendations for the standardization of the reaction rate in both variants have been given. The main approach consists in the use of a pharmaceutical form of 0.1% adrenaline hydrochloride solution. Although each of two adrenaline preparations available in the Russian market has some individual features in kinetic behavior of adrenaline autoxidation, they are applicable for the superoxide generating system. Performing measurements at 560 nm, the reaction rate can be regulated by lowering concentration of added adrenaline, whereas during spectrophotometric registration at 347 nm, this is not applicable. These features of the adrenaline autoxidation reaction may be attributed to the multistage process of adrenaline conversion to adrenochrome and also to coupled electron transfer from adrenaline and intermediate products of its oxidation to oxygen, carbon dioxide, and carbonate bicarbonate ions. This results in formation of corresponding radicals detectable by adding NBT.     

Purification and characterization of 1-nitropyrene nitroreductases from Bacteroides fragilis

We isolated four nitroreductases from Bacteroides fragilis GAI0624 and examined their physicochemical and functional properties. Two major enzyme activities were found in the adsorbed and unadsorbed fractions from DEAE-cellulose column chromatography. The adsorbed fraction was subjected to Sephadex G-200 column chromatography, and two further activities were separated. One has high nitroreductase activity (nitroreductase I), and the other has low activity and relatively high molecular weight (nitroreductase III). The nitroreductase I fraction was subjected to hydroxylapatite and chromatofocusing column chromatography, and nitroreductase I was purified about 416-fold with a yield of 6.77%. The unadsorbed fraction from DEAE-cellulose column chromatography was subjected to Sepharose 2B and Sepharose 6B column chromatography. Two enzyme activities were obtained by the Sepharose 6B column chromatography. One has high activity (nitroreductase II), and the other has low activity (nitroreductase IV). Nitroreductase II was rechromatographed by Sepharose 6B gel filtration and purified about 178-fold with a yield of 9.65%. The four enzymes (nitroreductases I, II, III, and IV) were shown to be different by several criteria. Their molecular weights, determined by gel filtration, were 52,000, 320,000, 180,000, and 680,000, respectively. The substrate specificity, the effect on mutagenicity of mutagenic nitro compounds, of nitroreductases I, III, and IV was relatively high for 1-nitropyrene, dinitropyrenes, and 4-nitroquinoline 1-oxide, respectively, but nitroreductase II had broad specificity. Nitroreductase activity required a coenzyme; nitroreductases II, III, and IV were NADPH linked, but nitroreductase I was NADH linked. All enzyme activity was enhanced by addition of flavin mononucleotide and inhibited significantly by dicumarol, p-chloromercuribenzoic acid, o-iodosobenzoic acid, sodium azide, and Cu2+.(ABSTRACT TRUNCATED AT 250 WORDS)     

Purification and characterization of 1-nitropyrene nitroreductases from Bacteroides fragilis.

We isolated four nitroreductases from Bacteroides fragilis GAI0624 and examined their physicochemical and functional properties. Two major enzyme activities were found in the adsorbed and unadsorbed fractions from DEAE-cellulose column chromatography. The adsorbed fraction was subjected to Sephadex G-200 column chromatography, and two further activities were separated. One has high nitroreductase activity (nitroreductase I), and the other has low activity and relatively high molecular weight (nitroreductase III). The nitroreductase I fraction was subjected to hydroxylapatite and chromatofocusing column chromatography, and nitroreductase I was purified about 416-fold with a yield of 6.77%. The unadsorbed fraction from DEAE-cellulose column chromatography was subjected to Sepharose 2B and Sepharose 6B column chromatography. Two enzyme activities were obtained by the Sepharose 6B column chromatography. One has high activity (nitroreductase II), and the other has low activity (nitroreductase IV). Nitroreductase II was rechromatographed by Sepharose 6B gel filtration and purified about 178-fold with a yield of 9.65%. The four enzymes (nitroreductases I, II, III, and IV) were shown to be different by several criteria. Their molecular weights, determined by gel filtration, were 52,000, 320,000, 180,000, and 680,000, respectively. The substrate specificity, the effect on mutagenicity of mutagenic nitro compounds, of nitroreductases I, III, and IV was relatively high for 1-nitropyrene, dinitropyrenes, and 4-nitroquinoline 1-oxide, respectively, but nitroreductase II had broad specificity. Nitroreductase activity required a coenzyme; nitroreductases II, III, and IV were NADPH linked, but nitroreductase I was NADH linked. All enzyme activity was enhanced by addition of flavin mononucleotide and inhibited significantly by dicumarol, p-chloromercuribenzoic acid, o-iodosobenzoic acid, sodium azide, and Cu2+.(ABSTRACT TRUNCATED AT 250 WORDS)     

A model for NADH-tetrazolium reductase

Summary In the presence of light, reduced nicotinamide adenine dinucleotide (NADH) and riboflavin formed a complex which was able to reduce certain tetrazolium salts. Neither NADH (10^–3 M) nor riboflavin (10^–4 M) alone was able to induce tetrazolium reduction in the presence of oxygen, but in a nitrogen atmosphere photoreduction of riboflavin induced reduction of tetrazolium salts. Only electrophilic nitro and thiazolyl substituted tetrazolium salts with more positive redox potentials were reduced by the NADH-riboflavin complex, and only monoformazans were produced from the ditetrazolium salts. The reduction kinetics of these tetrazolium salts are given, and the spectral area capable for induction of electron transfer in the NADH-riboflavin complex is screened. It is concluded that the electron transfer in flavin nucleotide dependent dehydrogenase systems will probably proceed without direct interference with the apoenzyme. This may have practical implications for the histochemistry of tetrazolium reductases especially as regards fixation. The catalytic action of light on tetrazolium reduction should also be taken into consideration when tetrazolium salts are used as electron acceptors in a histochemical reaction.