Shirley F. Nishino

Aerobic Degradation of Dinitrotoluenes and Pathway for Bacterial Degradation of 2,6-Dinitrotoluene

ABSTRACT An oxidative pathway for the mineralization of 2,4-dinitrotoluene (2,4-DNT) by Burkholderia sp. strain DNT has been reported previously. We report here the isolation of additional strains with the ability to mineralize 2,4-DNT by the same pathway and the isolation and characterization of bacterial strains that mineralize 2,6-dinitrotoluene (2,6-DNT) by a different pathway.Burkholderia cepacia strain JS850 andHydrogenophaga palleronii strain JS863 grew on 2,6-DNT as the sole source of carbon and nitrogen. The initial steps in the pathway for degradation of 2,6-DNT were determined by simultaneous induction, enzyme assays, and identification of metabolites through mass spectroscopy and nuclear magnetic resonance. 2,6-DNT was converted to 3-methyl-4-nitrocatechol by a dioxygenation reaction accompanied by the release of nitrite. 3-Methyl-4-nitrocatechol was the substrate for extradiol ring cleavage yielding 2-hydroxy-5-nitro-6-oxohepta-2,4-dienoic acid, which was converted to 2-hydroxy-5-nitropenta-2,4-dienoic acid. 2,4-DNT-degrading strains also converted 2,6-DNT to 3-methyl-4-nitrocatechol but did not metabolize the 3-methyl-4-nitrocatechol. Although 2,6-DNT prevented the degradation of 2,4-DNT by 2,4-DNT-degrading strains, the effect was not the result of inhibition of 2,4-DNT dioxygenase by 2,6-DNT or of 4-methyl-5-nitrocatechol monooxygenase by 3-methyl-4-nitrocatechol.

Biodegradation of the nitramine explosive CL-20.

ABSTRACT The cyclic nitramine explosive CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) was examined in soil microcosms to determine whether it is biodegradable. CL-20 was incubated with a variety of soils. The explosive disappeared in all microcosms except the controls in which microbial activity had been inhibited. CL-20 was degraded most rapidly in garden soil. After 2 days of incubation, about 80% of the initial CL-20 had disappeared. A CL-20-degrading bacterial strain, Agrobacterium sp. strain JS71, was isolated from enrichment cultures containing garden soil as an inoculum, succinate as a carbon source, and CL-20 as a nitrogen source. Growth experiments revealed that strain JS71 used 3 mol of nitrogen per mol of CL-20.

Escherichia coli NsrR Regulates a Pathway for the Oxidation of 3-Nitrotyramine to 4-Hydroxy-3-Nitrophenylacetate

Chromatin immunoprecipitation and microarray (ChIP-chip) analysis showed that the nitric oxide (NO)-sensitive repressor NsrR from Escherichia coli binds in vivo to the promoters of the tynA and feaB genes. These genes encode the first two enzymes of a pathway that is required for the catabolism of phenylethylamine (PEA) and its hydroxylated derivatives tyramine and dopamine. Deletion of nsrR caused small increases in the activities of the tynA and feaB promoters in cultures grown on PEA. Overexpression of nsrR severely retarded growth on PEA and caused a marked repression of the tynA and feaB promoters. Both the growth defect and the promoter repression were reversed in the presence of a source of NO. These results are consistent with NsrR mediating repression of the tynA and feaB genes by binding (in an NO-sensitive fashion) to the sites identified by ChIP-chip. E. coli was shown to use 3-nitrotyramine as a nitrogen source for growth, conditions which partially induce the tynA and feaB promoters. Mutation of tynA (but not feaB) prevented growth on 3-nitrotyramine. Growth yields, mutant phenotypes, and analyses of culture supernatants suggested that 3-nitrotyramine is oxidized to 4-hydroxy-3-nitrophenylacetate, with growth occurring at the expense of the amino group of 3-nitrotyramine. Accordingly, enzyme assays showed that 3-nitrotyramine and its oxidation product (4-hydroxy-3-nitrophenylacetaldehyde) could be oxidized by the enzymes encoded by tynA and feaB, respectively. The results suggest that an additional physiological role of the PEA catabolic pathway is to metabolize nitroaromatic compounds that may accumulate in cells exposed to NO.

Biodegradation of 3-Nitrotyrosine by Burkholderia sp. Strain JS165 and Variovorax paradoxus JS171

ABSTRACT The cascade of reactive nitrogen species generated from nitric oxide causes modification of proteins, lipids, and nucleic acids in a wide range of organisms. 3-Nitrotyrosine is one of the most common products of the action of reactive nitrogen species on proteins. Although a great deal is known about the formation of 3-nitrotyrosine, the subsequent metabolism of this compound is a mystery. Variovorax paradoxus JS171 and Burkholderia sp. strain JS165 were isolated from soil slurries when 3-nitrotyrosine was provided as the sole carbon, nitrogen, and energy source. During growth on 3-nitrotyrosine stoichiometric amounts of nitrite were released along with approximately one-half of the theoretically available ammonia. The catabolic pathway involving oxidative denitration is distinct from the pathway for tyrosine metabolism. The facile isolation and the specific, regulated pathway for 3-nitrotyrosine degradation in natural ecosystems suggest that there is a significant flux of 3-nitrotyrosine in such environments.

The biochemistry of the metabolic poison propionate 3‐nitronate and its conjugate acid, 3‐nitropropionate

3‐Nitropropionate (3‐NPA) is a nitro aliphatic compound found in numerous plants and fungi. The nitro compound exists in equilibrium with its conjugate base, propionate 3‐nitronate (P3N) and has a pKa approaching the physiological range of 9.1. Since 1920, more than 30 species of plant and fungi have been identified as producing 3‐NPA as a means of defense from herbivores. Glycoside products containing moieties of 3‐NPA found in parts of the plants most accessible to herbivores can be easily hydrolyzed to free 3‐NPA by bacterial enzymes in the gut of animals. In addition to providing a defense mechanism, the nitro compound is an intermediate in the nitrification process of leguminous plants. The synthesis of 3‐NPA in these plants and fungi is poorly understood. P3N, which readily forms from 3‐NPA at physiological pH, is a potent inhibitor of the key enzyme succinate dehydrogenase in the Krebs cycle and electron transport chain. Inhibition of succinate dehydrogenase in humans and livestock causes neurotoxicity and in some cases death. Several enzymes catalyze the oxidation of 3‐NPA or P3N; all contain a noncovalently bound flavin cofactor and are found in the organisms that produce 3‐NPA. With kcat/Km values of >106 M−1 s−1, nitronate monooxygenases can quickly and efficiently oxidize P3N to malonic semialdehyde as a means of protecting the organism from killing itself. Although it was discovered almost a century ago, the biochemistry and physiological role of 3‐NPA/P3N are just emerging.

Catabolism of Nitroaromatic Compounds

Nitroaromatic compounds, though rare in nature, are versatile and favored tools of the synthetic chemist and became widely distributed in the biosphere after the advent of the industrial revolution. Compounds such as nitrobenzene (NB) consistently rank among the most commonly used industrial chemicals in the world, because it is the gateway to the production of aniline and thus to dyes, resins, inks, and rubber. Dinitrotoluene (DNT) is similarly the precursor to toluenediisocyanate which in turn is the major monomer used to manufacture polyurethane foams, elastomers, and coatings. 2,4,6-Trinitrotoluene (TNT) became the most widely used military explosive in the world shortly after the development of practical methods to manufacture substantial quantities of the explosive. Other nitroaromatic compounds have gained widespread use as pesticides and herbicides.

Growth of Bacteria on 3-Nitropropionic Acid as a Sole Source of Carbon, Nitrogen, and Energy

ABSTRACT 3-Nitropropionic acid (3NPA) is a widespread nitroaliphatic toxin found in a variety of legumes and fungi. Several enzymes have been reported that can transform the compound, but none led to the mineralization of 3NPA. We report here the isolation of bacteria that grow on 3NPA and its anion, propionate-3-nitronate (P3N), as the sole source of carbon, nitrogen, and energy. Experiments with resting cells, cell extracts, and purified enzymes indicate that the pathway involves conversion of 3NPA to P3N, which upon denitration yields malonic semialdehyde, nitrate, nitrite, and traces of H2O2. Malonic semialdehyde is decarboxylated to acetyl coenzyme A. The gene that encodes the enzyme responsible for the denitration of P3N was cloned and expressed, and the enzyme was purified. Stoichiometry of the reaction indicates that the enzyme is a monooxygenase. The gene sequence is related to a large group of genes annotated as 2-nitropropane dioxygenases, but the P3N monooxygenase and closely related enzymes form a cluster within COG2070 that differs from previously characterized 2-nitropropane dioxygenases by their substrate specificities and reaction products. The results suggest that the P3N monooxygenases enable bacteria to exploit 3NPA in natural habitats as a growth substrate.

Using Compound-Specific Isotope Analysis to Assess Biodegradation of Nitroaromatic Explosives in the Subsurface

Assessing the fate of nitroaromatic explosives in the subsurface is challenging because contaminants are present in different phases (e.g., bound to soil or sediment matrix or as solid-phase residues) and transformation takes place via several potentially competing pathways over time-scales of decades. We developed a procedure for compound-specific analysis of stable C, N, and H isotopes in nitroaromatic compounds (NACs) and characterized biodegradation of 2,4,6-trinitrotoluene (TNT) and two dinitrotoluene isomers (2,4-DNT and 2,6-DNT) in subsurface material of a contaminated site. The type and relative contribution of reductive and oxidative pathways to the degradation of the three contaminants was inferred from the combined evaluation of C, N, and H isotope fractionation. Indicative trends of Δδ(15)N vs Δδ(13)C and Δδ(2)H vs Δδ(13)C were obtained from laboratory model systems for biodegradation pathways initiated via (i) dioxygenation, (ii) reduction, and (iii) CH3-group oxidation. The combined evaluation of NAC isotope fractionation in subsurface materials and in laboratory experiments suggests that in the field, 86-89% of 2,4-DNT transformation was due to dioxygenation while TNT was mostly reduced and 2,6-DNT reacted via a combination of reduction and CH3-group oxidation. Based on historic information on site operation, our data imply biodegradation of 2,4-DNT with half-lives of up to 9-17 years compared to 18-34 years for cometabolic transformation of TNT and 2,6-DNT.

Remediation of dinitrotoluene contaminated soils from former ammunition plants: soil washing efficiency and effective process monitoring in bioslurry reactors

A pilot-scale bioslurry system was used to test the treatment of soils highly contaminated with 2,4-dinitrotoluene (2,4-DNT) and 2,6-dinitrotoluene (2,6-DNT). The treatment scheme involved a soil-washing process followed by two sequential aerobic slurry reactors augmented with 2,4-DNT- and 2,6-DNT-mineralizing bacteria. Test soils were obtained from two former army ammunition plants, the Volunteer Army Ammunition Plant (VAAP, Chattanooga, TN) and the Badger Army Ammunition Plant (BAAP, Baraboo, WI). Soil washing was used to minimize operational problems in slurry reactors associated with large particulates. The Eimco slurry reactors were operated in a draw-and-fill mode for 3 months and were monitored for the biodegradation of 2,4-DNT and 2,6-DNT, nitrite production, NaOH consumption, and oxygen uptake rate. Results show that soil washing was very effective for the removal of sands and the recovery of soil fines containing 2,4-DNT and 2,6-DNT. Bioslurry reactors offered rapid and nearly complete degradation of both DNT isomers, but require real time monitoring to avoid long lag periods upon refeeding. Results found a significant discrepancy between the measured DNT concentrations and calculated DNT concentrations in the slurry reactors because of solids profiles in the slurry reactors and the presence of floating crystal of DNTs. Based on the actual amount of dinitrotoluene degradation, nitrite release, NaOH consumption, and oxygen uptake were close to the theoretical stoichiometric coefficients of complete DNT mineralization. Such stoichiometric relationships were not achieved if the calculation was based on the measured DNT concentrations due to the heterogeneity of DNT in the reactor. Results indicate that nitrite release, NaOH consumption, and oxygen uptake rates provide a fast assessment of 2,4-DNT degradation and microbial activity in a slurry reactor, but could not be extended to a second reactor in series where the degradation of a much lower concentration of 2,6-DNT degradation was achieved.

Cytochrome P450 Initiates Degradation of cis-Dichloroethene by Polaromonas sp. Strain JS666

ABSTRACT Polaromonas sp. strain JS666 grows on cis-1,2-dichoroethene (cDCE) as the sole carbon and energy source under aerobic conditions, but the degradation mechanism and the enzymes involved are unknown. In this study, we established the complete pathway for cDCE degradation through heterologous gene expression, inhibition studies, enzyme assays, and analysis of intermediates. Several lines of evidence indicate that a cytochrome P450 monooxygenase catalyzes the initial step of cDCE degradation. Both the transient accumulation of dichloroacetaldehyde in cDCE-degrading cultures and dichloroacetaldehyde dehydrogenase activities in cell extracts of JS666 support a pathway for degradation of cDCE through dichloroacetaldehyde. The mechanism minimizes the formation of cDCE epoxide. The molecular phylogeny of the cytochrome P450 gene and the organization of neighboring genes suggest that the cDCE degradation pathway recently evolved in a progenitor capable of degrading 1,2-dichloroethane either by the recruitment of the cytochrome P450 monooxygenase gene from an alkane catabolic pathway or by selection for variants of the P450 in a preexisting 1,2-dichloroethane catabolic pathway. The results presented here add yet another role to the broad array of productive reactions catalyzed by cytochrome P450 enzymes.