WO2001040504A9 - Methods and compositions for detecting nitroaromatic compounds - Google Patents

Abstract

Nitroaromatic compounds present in various sample materials may be easily and inexpensively detected in a colorimetric assay according to the present invention. The invention includes a method of detecting nitroaromatic compounds, comprising placing a sample containing a nitroaromatic compound in the presence of a xenobiotic reductase enzyme and observing the formation of a colored product. The invention also includes xenobiotic reductase enzymes, DNA sequences that encode such enzymes and derivatives thereof. The invention also includes compositions and kits for performing the assay.

Description

METHODS AND COMPOSITIONS FOR DETECTING NITROAROMATIC COMPOUNDS

TECHNICAL FIELD

This invention relates to a method, enzyme, composition and kit for detecting the presence of nitroaromatic compounds. The invention further relates to a screening assay for microorganisms that contain enzymes that may be used for detecting the presence of nitroaromatic compounds.

BACKGROUND OF THE INVENTION

Xenobiotic nitroaromatic compounds such as trinitrotoluene (TNT) and picric acid have long been used in the manufacture of agricultural chemicals, pharmaceuticals, dyes, plastics and especially in explosives. Picric acid has been used as a primary component of blasting caps, which are used for the detonation of TNT.

Over the years, the large-scale manufacture, use and handling of such nitroaromatic compounds has exposed both soil and groundwater to extensive contamination by these products. Large amounts of these products were synthesized during the Second World War, and their manufacture and handling often led to extensive contamination. Sites contaminated by these products are targets for remediation. However, in order to determine if a particular site has had any contamination by these nitroaromatic products, samples taken from the site must be assayed. Preferably the assay used is compatible to being used on-site when the samples are taken. Numerous on-site assay methods for explosives such as TNT have been devised. Current on-site methods for detection of TNT in soil and environmental samples can be classified into two categories: colorimetric tests and immunoassays. However, these current tests have numerous disadvantages. Typical enzyme immunoassay (EIA) methods for TNT detection require expensive polystyrene microtitre plates coated with antibodies. Similar EIA methods require the use of magnetic particles. Other prior art methods use acetone to extract the TNT from the soil, and then incubation of diluted extracts with TNT- enzyme conjugate in microtitre wells coated with the antibody to detect TNT. These EIA methods require expensive components that may be difficult to use in rugged terrain situations.

Colorimetric methods for detection of nitroaromatics such as TNT also are known in the art. One such method is premised on the reaction of TNT with a base to produce a strongly colored Meisenheimer-complex, which can be quantified spectrophotometrically. For analysis, soil samples are extracted with methanol for one minute and then analyzed for color after the addition of a base. This methodology requires special equipment for performing the assay.

Other colorimetric methods for the detection of nitroaromatics are known. One such methodology places a sample of field-moist soil in methanol, requires shaking of the materials together, and then reacting the materials with sodium hydroxide. TNT detection is measured on a spectrophotometer by absorbance at 516 nm (e.g., detection of the colored Meisenheimer-complex). Other prior art colorimetric detection methods require acetone extraction of a soil sample that is suspected of being contaminated with nitroaromatics, and observing the formation of a Janowsky anion (reddish color for TNT derivative) when the acetone reacts with TNT in an alkaline environment. This methodology requires mixing of field-moist soil and acetone, shaking the mixture for three minutes, filtering the mixture through a 0.5 micrometer syringe filter, and reacting the extracted solution with potassium hydroxide and sodium sulfite. TNT concentration is estimated by absorbance at 540 nm (e.g., detection of the Janowsky anion derivative). When detecting nitroaromatics in other non- environmental settings, such as bomb and/or explosive material analysis, similar sample manipulations are required.

These colorimetric methods have several disadvantages. Many of them require complicated sample manipulation and the use of spectrophotometers to observe any color that is evolved. The tests may be indiscriminate, and may identify the presence of any nitroaromatic, rather than the nitroaromatic of interest, such as TNT. A need remains for a simple, inexpensive method for selectively detecting nitroaromatics such as TNT and picric acid.

SUMMARY OF THE INVENTION The present invention relates to a method of detecting selected nitroaromatic contaminants, preferably TNT and/or picric acid. According to the method a sample suspected of containing the nitroaromatic compound is mixed with an enzyme of the present invention, such that the nitroaromatic compound forms a colored product in the presence of the enzyme. The detection of this colored product indicates the presence of the selected nitroaromatic compound. This detection may be performed by any variety of means for detecting color, with the preferred method being a simple, visual detection whereby the sample and enzyme are compared to a simple color standard. The sample mixture may contain additional ingredients, including NADPH, solvent, buffer, and/or a preservative, with the preferred solvent being water.

The enzyme of the present invention can come from any number of biological sources. Typically, the enzyme is derived from an organism of a genera selected from the group consisting of Escherichia, Pseudomonas , Bacillus, Enterobacter, Rhodococcus, Mycobacteria, and Nocardiodes. Most preferably, the enzyme is derived from an organism of the species selected from the group consisting of Escherichia coli, Pseudomonas putida, Pseudomonas fluorescens , and Bacillus subtilis.

The enzyme may be in any form desired, including being present in the form of whole cells, lyophilized cells, cell free extract or isolated enzyme. The present invention is also directed at specific enzymes that are useful for detecting predetermined nitroaromatic compounds. These include all or a functional portion of an isolated or recombinant enzyme having the sequence shown in SEQ ID NO: 1 which encodes for the Pseudomonas putida xenA gene. The invention also includes enzymes having the sequence of SEQ ID NO:l, where the enzyme has one or more modifications, such that the modified enzyme has sufficient activity to produce a colored product from a selected nitroaromatic compound.

The invention also includes isolated DNA molecules that have the sequence of all or a functional portion of SEQ ID. NO: 7 such that the DNA molecule encodes an enzyme which has sufficient activity to produce a colored product from a selected nitroaromatic compound. The invention also includes DNA molecules having the sequence of SEQ ID NO: 7 having one or more modifications, where the modified DNA molecule encodes an enzyme which has sufficient activity to produce a colored product from a selected nitroaromatic compound. The present invention is also directed at specific enzymes that are useful for detecting selected nitroaromatic compounds. These include all or a functional portion of an isolated or recombinant enzyme having the sequence shown in SEQ ID NO: 2 which encodes for the Pseudomonas fluorescens xenB gene. The invention also includes enzymes having the sequence of SEQ ID NO:2, where the enzyme has one or modifications, such that the modified enzyme has sufficient activity to produce a colored product from a selected nitroaromatic compound.

The invention also includes isolated DNA molecules that have the sequence of all or a functional portion of SEQ ID. NO: 8 such that the DNA molecule encodes an enzyme which has sufficient activity to produce a colored product from a selected nitroaromatic compound. The invention also includes DNA molecules having the sequence of SEQ ID NO: 8 having one or more modifications, where the modified DNA molecule encodes an enzyme which has sufficient activity to produce a colored product from a selected nitroaromatic compound. The present invention is also drawn to a composition for detecting the presence of selected nitroaromatic compounds. The composition contains one or more enzymes of the present invention, as well as optional ingredients, including but not limited to, one or more solvents, NADPH, buffer(s) and preservative(s). The invention also relates to a kit for the colorimetric detection of a nitroaromatic compound. The kit comprises a reaction vessel, an enzyme of the present invention having sufficient activity to produce a colored product from a selected nitroaromatic compound, and a color standard for comparison purposes to determine if the nitroaromatic compound is present. The kit may also contain NADPH, one or more solvents, and other optional ingredients.

The invention also includes a method for screening microorganisms for the presence of enzymes that selectively form colored products with selected nitroaromatic compounds, preferably TNT or picric acid. The method comprises placing a selected microorganism in the presence of a nitroaromatic compound in a buffered solution and observing the microorganism for the formation of any colored product.

The invention also includes a method for producing derivatives of enzymes of the invention, such that derivatives exhibit specialized properties, such as improved solvent stability, catalytic properties, or thermal stability.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the nucleotide sequence (SEQ ID No: 7) and the amino acid sequence (SEQ ID No: 1) of the Pseudomonas putida xenA gene. Amino acid residues that correspond to the amino-terminal sequences determined by Edman degradation are shown in boldface type; -10 to -35 promoter element and ribosome- binding site as well as the transcription initiation site (+ 1) are indicated.

FIG. 2 shows the nucleotide sequence (SEQ ID No: 8) and the amino acid sequence (SEQ ID No: 2) of the Pseudomonas fluorenscens xenB gene. Amino acid residues that correspond to the amino-terminal sequences determined by Edman degradation are shown in boldface type; -10 to -35 promoter element and ribosome- binding site as well as the transcription site (+ 1) are indicated. FIG. 3 shows the formation of mono- and dihydride-Meisenheimer complexes from picric acid (R=OH) or TNT (R= CH₃).

FIGS. 4A and 4B are graphs showing the time course of the denitrification of 0.9 mM nitroglycerin (NG) and the culture densities, respectively.

DETAILED DESCRIPTION

The following terms are used throughout the application and are defined as follows:

Colored product - A product produced by the reaction of an enzyme according to the present invention with a selected nitroaromatic compound, such that the product produces a shift in visible wavelength from the nitroaromatic compound which may be detected.

Meisenheimer complex - A hydride-nitroaromatic complex that forms as a metabolite from reaction of an enzyme of the present invention with a selected nitroaromatic compound. Meisenheimer complexes are colored products. Reaction vessel - Any suitable container that may be utilized for holding the components of the present invention while the reaction takes place. Preferred vessels will be clear, noncolored containers including both glass and plastic (e.g. polypropylene) vessels.

Visual observation - An observation of colored product using only the human eye for observation, without mechanical aid.

The present invention relates to a novel method of screening for the presence of a selected nitroaromatic compound. The inventors have surprisingly and unexpectedly discovered a new class of enzyme, termed xenobiotic reductases, that form colored products, most likely in the form of Meisenheimer complexes, with only selected nitroaromatic compounds, such as picric acid and trinitrotoluene (TNT). The method comprises mixing a sample suspected of containing a selected nitroaromatic compound with an enzyme of the present invention, such that the nitroaromatic compound forms a colored product in the presence of the enzyme and observing the formation of the colored product. This novel nitroaromatic detection method provides a simple, low cost screening method for detecting the presence of selected nitroaromatics in contaminated samples. The detection method may be used in on-site field assays or in a laboratory setting. The enzymes of the present invention will form colored complexes with a number of different explosives that are classified as nitroaromatics, including, but not limited to, trinitrotoluene and picric acid.

The enzymes of the present invention are xenobiotic reductase enzymes. The nucleotide sequence and amino acid sequence of two of these enzymes, xenobiotic reductase A (XenA) and xenobiotic reductase B (XenB) are shown in FIG. 1 and FIG. 2, respectively, and further described in Blehert et al. , Journal Of Bacteriology, 181 :6254 (1999). A plasmid that contains XenB encoding sequences can be obtained, for example, from the American Tissue Culture Collection under Accession No. PTA-1067. The invention is also drawn to DNA molecules that encode the enzymes of the present invention. The DNA may be either genomic or cDNA. The invention also includes isolated DNA molecules that have the sequence of all or a functional portion of SEQ ID. NO:7 or SEQ ID NO:8 such that the DNA molecule encodes an enzyme which has sufficient activity to produce a colored product from a nitroaromatic compound. These portions of DNA molecules can be tested for activity in any manner well known in the art, including those methods described in the following Examples. The invention also includes modified DNA molecules which encode modified enzymes of the present invention. Such modified DNA molecules may be obtained in the manner described below, or by any other means well known in the art.

The xenobiotic reductase enzymes of the present invention may be isolated from a number of different microorganisms. The preferred genera from which xenobiotic reductases of the present invention are isolated are Escherichia, Pseudomonas, Bacillus, Enterobacter, Rhodococcus, Mycobacteria, and Nocardiodes. Of these genera, the preferred species from which the xenobiotic reductase enzymes are isolated are Escherichia coli, Pseudomonas putida, Pseudomonas fluorescens, Bacillus subtilis, with Pseudomonas putida and Pseudomonas fluorescens being the most preferred.

Any microorganism may be screened for the presence of the xenobiotic reductase gene by the methods described in the following Examples, or by any other means well known in the art, such as those described in Blehert, Characterization of Xenobiotic Reductases From Two Pseudomonas Species, University of Wisconsin-Madison Dissertation (1999). Such screening procedure entails placing the microorganism in the presence of the selected nitroaromatic compound, and observing the formation of any colored product. This screening methodology is also included within the present invention.

The xenobiotic reductase enzymes of the present invention have been surprisingly and unexpectedly discovered to form Meisenheimer complexes with select nitroaromatic compounds, such as trinitrotoluene and picric acid. Although the enzymes of the present invention will degrade a number of nitroaromatic compounds, the colored product Meisenheimer complex only forms with select nitroaromatic compounds. Table 1 shows the results of detecting various nitroaromatic compounds by placing them in the presence of P. fluorescens XenB. Thus, the xenobiotic reductases of the present invention are extremely useful for detecting nitroaromatic compounds that are contaminants, such as trinitrotoluene, as they selectively form colored products only with such materials. As shown in Table 1, XenB will decompose a number of nitroaromatic compounds, such as nitroglycerin, TNT and 2,4 dinitrotoluene. However, the enzyme only forms the colored product with TNT, thereby reducing false positive tests when testing a sample suspected of containing TNT. Table 1

DECOMPOSITION

COMPOUNDS TESTED ACTIVITY COLOR nitroglycerin YES NO

TNT (2,4,6-trinitrotoluene) YES YES

2,4 dintrotoluene YES NO

2,6 dintrotoluene NO NO

1,3 dinitrobenzene YES NO nitrobenzene NO NO

2-nitrotoluene NO NO

3-nitrotoluene NO NO

4-nitrotoluene NO NO

2-cyclohexenone YES NO

Nitramine YES NO

Picric Acid YES

It is believed that the Meisenheimer complex consists of a hydride- trinitrotoluene complex, as illustrated in FIG. 3. This complex yields a colored product that can easily be identified by visual observation, spectrophotometric techniques, or other methods well known in the art.

Typically, the method entails adding a sample suspected of containing the contaminant of interest, such as TNT, to the enzyme. The enzyme is often present in a solvent, and the enzyme and solvent are mixed together with the sample. The solvent may be any suitable organic solvent such as dichloromethane or ethyl acetate, or water, with water being the preferred solvent. Additional ingredients may also be added which include, but are not limited to, buffers and preservatives.

The enzyme can be present in any number of forms, including, but not limited to, whole cells, lyophilized cells, cell free extract and isolated enzyme. If the enzyme is present only as an isolated enzyme, NADPH will also be required. The color of the resultant colored product will depend not only on the specific nitroaromatic compound detected, but also on the form in which the detection enzyme is present. For example, TNT detection may result in a yellow colored product being detected when purified enzymes and/or cell extracted enzymes are used. A similar assay for TNT using whole cells containing the same enzyme will result in a red, rosy or orange colored product being detected. If the xenobiotic reductase enzyme is to be used as an isolated enzyme, it will typically be expressed either from its native bacterium or expressed as a heterologous gene construct in a host cell. For example, P. putida produces a large amount of XenA, approximately 16% of the soluble protein in the cell. The native P. fluorescens also produces a large amount of XenB. For heterologous expression of an enzyme of the present invention, the DNA sequence encoding the enzyme must be operably linked to regulatory sequences that control transcriptional expression in an expression vector and then, introduced into either a prokaryotic or eukaryotic host cell. In addition to transcriptional regulatory sequences, such as promoters and enhancers, expression vectors can include translational regulatory sequences and a marker gene which is suitable for selection of cells that carry the expression vector.

In the following Examples, the E. coli subclones expressed xenA and xenB without the aid of a plasmid-encoded expression promoter, suggesting that transcription was driven by a native promoter contained within the cloned inserts or by a plasmid encoded promoter, such as the lac promoter. However, other suitable promoters could be used, if desired. Suitable promoters for expression in a prokaryotic host can be repressible, constitutive, or inducible. Suitable promoters are well-known to those of skill in the art and include promoters capable of recognizing the T4, T3, Sp6 and T7 polymerases, the PR and PL promoters of bacteriophage lambda, the trp, recA, heat shock, lacUV5, tac, Ipp-lacλpr, phoA, gal, trc and lacZ promoters of E. coli, the α-amylase and the σ²⁸-specific promoters of B. subtilis, the promoters of the bacteriophages of Bacillus, Streptomyces promoters, the int promoter of bacteriophage lambda, the bla promoter of the β- lactamase gene of pBR322, and the CAT promoter of the chloramphenicol acetyl transferase gene. Prokaryotic promoters are reviewed by Glick, J. Ind. Microbiol. i:277 (1987); Watson et al , MOLECULAR BIOLOGY OF THE GENE, 4th Ed., Benjamin Cummins (1987).

Preferred prokaryotic hosts include E. coli, Clostridium, and Haemophilus, with E. coli being the preferred host, as detailed in the following Examples. Suitable strains of E. coli include DHl, DH4 , DH5, DH5α, DH5αF', DH5αMCR, DH10B, DH10B/p3, DHl IS, C600, HB101, JM101 , JM105, JM109, JM110, K38, RR1, Y1088, Y1089, CSH18, ER1451, BL21(DE3), BL21(DE3)plysS, BLR(DE3), BLR(DE3)plysS, and ER1647 (see, for example, Brown (Ed.), MOLECULAR BIOLOGY LABFAX, Academic Press (1991)). The preferred E. coli host is DH5α. Suitable Clostridia include Clostridium subterminale SB4 (ATCC No. 29748) and Clostridium acetobutylicum (ATCC No. 824), while a suitable Haemophilus host is Haemophilus influenza (ATCC No. 33391).

An alternative host is Bacillus subtilus, including such strains as BR151 , YB886, Mil 19, MI120, and B170. See, for example, Hardy, "Bacillus Cloning Methods," in DNA CLONING: A PRACTICAL APPROACH, Glover (Ed.), IRL Press (1985).

Methods for expressing proteins in prokaryotic hosts include those detailed in the following Examples. Other well-known methods known in the art may be used. See, for example, Williams et al. , "Expression of foreign proteins in E. coli using plasmid vectors and purification of specific polyclonal antibodies," in DNA CLONING 2: EXPRESSION SYSTEMS, 2nd Edition, Glover et al. (eds.), pages 15-58 (Oxford University Press 1995). Also see, Ward et al., "Genetic Manipulation and Expression of Antibodies," in MONOCLONAL ANTIBODIES: PRINCIPLES AND APPLICATIONS, pages 137-185 (Wiley-Liss, Inc. 1995); and Georgiou, "Expression of Proteins in Bacteria," in PROTEIN ENGINEERING: PRINCIPLES AND PRACTICE, Cleland et al. (eds.), pages 101-127 (John Wiley & Sons, Inc. 1996). An expression vector can be introduced into bacterial host cells using a variety of techniques including calcium chloride transformation, electroporation, and the like. See, for example, Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 1-1 to 1-24 (John Wiley & Sons, Inc. 1995).

The xenobiotic reductase enzyme of the present invention may be modified to increase its ability to form colored products under a variety of circumstances. For example, the enzyme may be modified to provide a variety of improved properties, including, but not limited to, solvent stability in a particular solvent, catalytic properties, and thermal stability. Mutation, deletion and/or addition of one or more nucleotides in relation to the native sequence may obtain these modifications for the DNA that encodes the enzyme. Such modifications may be made by any means well known in the art; oligonucleotide-directed mutagenesis, linker-scanning mutagenesis, mutagenesis using the polymerase chain reaction, DNA shuffling, and the like can obtain variants, for example. See Ausubel et al., pages 8.0.3-8.5.9; Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 8-10 to 8-22 (John Wiley & Sons, Inc. 1995); Chen et al.Vxoc. Natl Acad. Sci. U.S.A. 90:5618 (1993); and Arnold, Trends Biotechnol. 8:244 (1990). Also see generally, McPherson (ed.), DIRECTED MUTAGENESIS: A PRACTICAL APPROACH, IRL Press (1991).

The mutated enzymes produced from the modified DNA sequences may be screened for activity to determine if they retain the specific xenobiotic reductase activity. Such screening methodologies are well known in the art, and are further described in the following Examples. The enzymes of the present invention could therefore be modified to screen for enzymes that when combined with alternative specific nitroaromatic substrates, yield colored products.

The invention also comprises a composition that is useful for selected detection of nitroaromatic compounds. The composition would include an enzyme of the present invention, in any of the forms previously described. The composition would preferably include at least one solvent, as previously described. Also included would be any other optional ingredients as previously described. The invention also includes kits for detecting the presence of nitroaromatic compounds. The kit would include an enzyme according to the present invention, some or all of the optional ingredients previously mentioned for use for the nitroaromatic detection methodology, as well as a reaction vessel and optionally a color standard. The color standard could be any such standard used in the art, but would preferably be a simple color coded card which could be compared to the product in the reaction vessel after the enzyme and other optional ingredients were mixed with the sample that is suspected of containing the selected nitroaromatic compound. If high throughput testing were desired, the kit could contain one or more reaction vessels together with the enzyme and other optional ingredients, and the testing could be done using a spectrometer or other similar instrumentation.

The invention is also drawn to a method of screening microorganisms to see if they form colored products with selected nitroaromatic compounds. A number of screening methodologies can be used, including microtitre plate assays and overlay assays, as described in the following Examples. These methods provide an easy, inexpensive, quick determination of the presence of enzymes which form the desired colored complexes. Any organism that produces an enzyme which forms a colored product in the presence of selected nitroaromatic compounds can be determined by these methodologies.

This invention is illustrated further by the following nonlimiting Examples. All of the references listed in this application are incorporated by reference.

Example 1 - Methodologies and Materials for Isolating, Cloning and Sequencing Xenobiotic Reductase Enzymes/Genes

Bacterial strains, growth conditions, and plasmids

P. putida II-B, as taught by Blehert et al, (J. Bacteriol. 179:6912- 6920 (1997)) and Escherichia coli DH5α , as taught by Sambrook et al, Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989), were grown aerobically in Luria-Bertani (LB) medium at 37 °C. P. fluorescens I-C, as taught by Blehert et al, Q. Bacteriol. 179:6912- 6920 (1997)) was incubated aerobically in LB medium at 30°C. Plasmid pUC18, as taught by Sambrook et al, Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989), was used for cloning purposes. Cosmid pRK7813 was used for genomic library construction, according to the teachings of Jones et al, Gene 61 :299—306 (1987).

Preparation of cell extract

P. fluorescens I-C cells were harvested, washed in 100 mM potassium phosphate buffer (pH 7.0), and resuspended in the same buffer (2 ml of buffer per g [wet weight] of cells). All subsequent steps were conducted at 4°C. Cells were broken by two passages through a French pressure cell (SLM Instruments, Rochester, N.Y.) at 16,000 lb. /in². The lysate was centrifuged for 60 min at 25,000 x g, and the supernatant from the first centrifugation was then subjected to another centrifugation step for 60 min at 25,000 x g. The resultant supernatant, called the cell extract, was frozen in liquid nitrogen and stored at - 80°C until needed.

Nucleic acid isolation

Genomic DNA was purified by using Puregene reagents (Gentra Systems, Inc., Minneapolis, Minn.). Plasmid DNA was isolated by using the Wizard Plus Minipreps DNA purification system (Promega, Madison, Wis.). Total cellular RNA was isolated by using RNeasy Minipreps (Qiagen, Valencia, Calif.).

Electrophoresis methods

Protein samples were resolved by denaturing gel electrophoresis in 10% polyacrylamide resolving gels, using a Tris-glycine-sodium dodecyl sulfate (SDS) buffer system with 3-mercaptoethanol as a reducing agent, according to Laemmli, Nature 227:680-685 (1970). Proteins were visualized by staining with Coomassie brilliant blue R-250. DNA was visualized on ethidium bromide-stained agarose gels. Protein characterizations

Protein concentrations were determined by the Bio-Rad (Hercules, Calif.) protein assay, with bovine serum albumin as the standard. The amino- terminal sequence of the purified P. putida reductase was determined by automated Edman degradation at the Michigan State University Macromolecular Structure Facility. The amino-terminal sequence of the P. fluorescens reductase was determined at the Protein/Nucleic Acid Shared Facility at the Medical College of Wisconsin, Milwaukee. Electrospray ionization mass spectral analysis of the P. putida enzyme was conducted at the University of Wisconsin-Madison Biotechnology Center.

DNA sequencing

Sequencing reactions for inclusion as markers on primer extension gels were generated from double-stranded plasmid DNA containing the xenA or xenB gene by using the T7 Sequenase 2 kit (Amersham Life Science, Arlington Heights, 111.) and [³⁵S]dATP. All other sequencing reactions were conducted by ABI PRISM (Foster City, Calif.) dye terminator cycle sequencing. The xenA and xenB gene sequences were determined by a primer walking strategy.

5' labeling of oligonucleotides

Oligonucleotides used as probes or in primer extension analysis were 5' labeled with [γ-³²P]ATP, using T4 polynucleotide kinase (Gibco BRL,

Gaithersburg, Md.). After incubation at 37°C for 30 min., the reactions were stopped by addition of 5μl of 0.5 M EDTA (pH 8.0). Unincorporated nucleotides were removed from the labeled oligonucleotides with an Auto-Seq G-50 column (Pharmacia Biotech, Piscataway, N.J.).

Genomic library construction

Genomic DNA from P. putida and P. fluorescens was partially digested with Sau3A to generate fragments of 20 to 40 kb. These genomic SauiA fragments were ligated into the BamHl site of pRK7813, packaged by using the Gigapack IIXL (Stratagene, La Jolla, Calif.) packaging system, and transduced into E. coli DH5α. Genomic libraries consisting of approximately 1,500 E. coli DH5α subclones each were generated for P. putida and P. fluorescens and maintained on LB medium containing 15 μg of tetracycline per ml.

Genomic library screening The P. putida genomic DNA library was screened using [γ-³²P]ATP- labeled degenerate nonoverlapping oligonucleotides designed to be complementary to the amino-terminal sequence of the P. putida xenobiotic reductase: 5 '-CAR TAY ATG GCS GAR GAC GGI YTG AT-3' (SΕQ ID NO: 3) and 5'-TTC GAR CCI TAY ACC YTG AAG GAY GTI AC-3' (SΕQ ID NO:4) (where R = A or G, Y = C or T, S = G or C, and I = inosine). The probes were hybridized to DNA isolated from mixed cultures of library subclones, as taught by Donohue et al , J. Bacteriol. 168:962-972 (1986). Five-milliliter aliquots of LB medium supplemented with tetracycline (15 μg/ml) were inoculated with 10 E. coli DH5α genomic library subclones each and incubated overnight. Cosmid DNA was isolated from these mixed cultures, digested with EcσRI and Hindlll, and resolved on 0.7% agarose gels before transfer onto Magnacharge nylon membranes (MSI, Inc., Westboro, Mass.) by Southern blotting. Hybridization was carried out at 42 °C in 6X SSPΕ (IX SSPΕ is 0.18 M NaCI, 10 mM NaH_PO₄, and 1 mM ΕDTA [pH 7.7]) 5X Denhardt's solution, 0.5% SDS, and 100 μg of sonicated and denatured salmon sperm per ml. The membranes were washed in IX SSPΕ-0.1 % SDS at hybridization temperature prior to analysis with a Molecular Dynamics (Sunnyvale, Calif.) Storm 860 phosphorimaging system. Southern blots were stripped by incubation in 50% formamide-6X SSPE for 30 min. at 65°C. Stripped blots were then hybridized to the second oligonucleotide probe, as described above, and phosphor images were compared to identify DNA fragments that hybridized to both oligonucleotide probes. The colonies comprising a mixed culture containing a DNA fragment that hybridized to both probes were then screened individually until a single genomic library subclone was identified. The P. fluorescens genomic DNA library was screened by a colorimetric procedure. Individual E. coil DH5α genomic library subclones were inoculated in microtiter plate wells containing 200 μl of LB medium supplemented with tetracycline (15 μg/ml) and incubated overnight. Following incubation, 100 μl of 0.56 mM TNT solution was added to each well and allowed to stand at room temperature for 5 min. Wells were visually screened for library subclones that transformed TNT to a red hydride-Meisenheimer intermediate.

Analysis of NG denitration by P. putida, P. fluorescens, and the E. coli DH5α subclones Starter cultures grown in LB liquid medium were used to inoculate duplicate flasks containing LB medium supplemented with 0.9 mM NG and 100 μg of ampicillin per ml for plasmid selection. Culture density and NG denitration were measured initially and over a 5.5-h period with a Klett-Summerson (New York, N.Y.) photoelectric colorimeter with a red filter and by high-pressure liquid chromatography, by the method of Blehert et al, (J. Bacteriol. 179:6912—6920 (1997)), respectively. In vitro NG reductase activity was monitored by measuring the rate of NADPH oxidation at 340 nm in the presence of enzyme and NG. The assay buffer was 100 mM potassium phosphate (pH 7.0). A typical assay initially contained 300 μM NG and 130 μM NADPH in 1 ml of assay buffer. Reactions were initiated by the addition of enzyme and monitored for 1 min. One unit of enzyme activity was defined as the oxidation of 1 μmol of NADPH per min. at room temperature in the assay buffer, after correction for background NADPH oxidation in the absence of NG.

Example 2 - Identification and Subcloning of the P. putida Xxenobiotic Reductase Gene, xenA

The genomic library of DNA from P. putida II-B in pRK7813 was screened by Southern hybridization using degenerate oligonucleotide probes and a putative xenobiotic reductase-containing cosmid harboring an approximately 4.3 kb Accl fragment that hybridized to both probes was identified. This fragment was subcloned into pUC18 and transformed into E. coli DH5α, as taught by Hanahan, Techniques for Transformation of E. coli, In D. M. Glover (ed), DNA Cloning: A Practical Approach. IRL Press, Oxford, England (1985), and sequenced. Transformants denitrated NG, as shown in FIG. 4A, and grew, as shown in FIG. 4B, at rates equivalent to rates for P. putida. A 1 ,092-nucleotide open reading frame, as shown in FIG. 1, (SEQ ID NO: l) designated enA, was identified within the 4.3-kb subclone. The amino acid sequence deduced from the nucleotide sequence at the 5' end of xenA matched the amino terminus of the purified enzyme determined by Edman degradation, SALFEPYTLKDVTLRNRIAIPPMXQYMAEDGLINDXHQ (SEQ ID NO:5) (where X = unknown). After removal of the amino-terminal methionine, the predicted molecular weight of the deduced translation product of the xenA ORF was 39,702, in close agreement with the Mr of 39,704 determined by electro-spray mass spectroscopy after release of FMN from the protein by acid denaturation.

Example 3- Identification and Subcloning of the P. fluorescens Xenobiotic Reductase Gene, xenB

Purified P. fluorescens xenobiotic reductase transforms TNT to produce a red hydride-Meisenheimer intermediate (λ ax = 477 nm). E. coli DH5α genomic library transformants were screened for the ability to produce this red compound in the presence of TNT. A positive clone harboring an approximately 2.2kb Hindlll fragment of P. fluorescens I-C DNA was identified. This fragment was subcloned into pUC18, introduced into E. coli DH5α by the method of Example 3, and sequenced. Transformants denitrated NG, as shown in FIG. 4A, and grew at rates comparable to those for P. fluorescens, as shown in FIG. 4B. A 1,050-nucleotide ORF, as shown in FIG. 2 (SEQ ID NO:2), designated xenB, was identified within the subcloned fragment. The amino acid sequence deduced from the nucleotide sequence at the 5 ' end of xenB matched the amino terminus of the purified enzyme determined by Edman degradation, ATIFDPIKLGDIELSNRI (SEQ ID NO: 6). After removal of the amino-terminal methionine, the predicted molecular weight of the deduced translation product of the xenB ORF was 37,441 , in close agreement with the native Mr of 37,000 determined by sedimentation velocity measurements.

Example 4 - Expression of Recombinant xenA and xenB in E. coli

SDS-polyacrylamide gel electrophoresis analysis indicated that xenA and xenB were highly expressed in the E. coli DH5α subclones. Cell extracts of P. putida, P. fluorescens, and the E. coli subclones exhibited prominent protein bands that comigrated with pure xenobiotic reductase protein from either P. putida or P. fluorescens. In contrast, lysates from E. coli DH5α harboring the plasmid pUC18 lacking a DNA insert did not exhibit protein bands that comigrated with xenA or xenB. In vitro activity assays conducted with cell extract confirmed that the expressed proteins had catalytic activity and exhibited over 500-fold-greater specific activity than cell extracts from E. coli DH5α harboring the plasmid pUC18 lacking an insert, as shown below in Table 2.

Table 2 - NG Reductase Specific Activity of Cell Extracts

Cell extract Sp act (U/mg)^a P. putida 0.4

E. coli DH5α/pUC18 xenA subclone 0.6

P. fluorescens 0.4

E. coli DH5α/pUC18 xenB subclone 0.8

E. coli DH5α/pUC18 0.001 One unit of activity is defined as the oxidation of 1 μmol of NADPH per min. in the presence of 300 μM NG in 100 mM potassium phosphate buffer (pH 7.0) at room temperature.

Example 5 - Substrate Specificity of the Xenobiotic Reductases

Table 3 shows a comparison of the substrate specificities of purified xenobiotic reductases from P. putida and P. fluorescens. Both enzymes exhibited the greatest rates of NADPH oxidation when NG was provided as an electron acceptor, although TNT and 2-cyclohexen-l-one could be reduced to various degrees. The P. fluorescens xenobiotic reductase (XenA) exhibited five-fold-greater activity with TNT than did the P. putida enzyme (XenB). Conversely, the P. putida XenB exhibited approximately seven-fold-greater activity with 2-cyclohexen- l-one than did the P. fluorescens XenA enzyme.

As exemplified by a low rate of NADPH oxidation in the presence of TNT, P. putida XenA transformed TNT slowly. In contrast, P. fluorescens XenB rapidly transformed TNT.

Table 3 - Specific Activities of Purified Xenobiotic Reductases from P. putida and P. fluorescens with Several Substrates

Substrate Sp act (U/mg)^a

P. putida

NG 6.1

TNT 0.5

2-Cyclohexen- 1 -one 4.1

P. fluorescens

NG 6.8

TNT 2.5

2-Cyclohexen-l-one 0.6

One unit of activity is defined as the oxidation of 1 μmol of NADPH per min. in the presence of 300 μM NG, TNT, or 2-cyclohexen-l-one in 100 mM potassium phosphate buffer (pH 7.0) at room temperature.

Example 6 - TNT Assay with Whole cells of Pseudomonas fluorescens I-C

Concentration of TNT

P. fluorescens I-C cells (200 μl) that had been grown overnight were mixed directly with 100 μl of 0.56 mM TNT (190 μM final concentration). The reaction mixture turned red in 1 min and changed to yellow in about 40 min. A series of diluted TNT samples was tested to determine the minimum concentration of TNT required for a color detection. At a TNT concentration of 48 μM the reaction mixture turned pale red in 1 min and pale yellow in about 30 min. A TNT concentration of 19 μM produced a very faint yellow color only after 2 h. Reaction buffer

P. fluorescens I-C cells that had been grown overnight were harvested, washed twice with 100 mM phosphate buffer (pH 7), and resuspended in 200 μl of the same buffer. To the buffered cells, 100 μl of TNT (0.56 mM) was added. The reaction mixture turned red in 1 min and changed to yellow in 10 min. The color change to yellow was faster than when the overnight-cultured cells were directly used. When the washed cells were resuspended in 200 μl of LB medium and mixed with 100 μl of 0.56 mM TNT, the reaction mixture turned red in 1 min and changed to yellow in 5 min, which was yet faster than with cells suspended in phosphate buffer. The washed cells were resuspended in 200 μl of ddH2θ and mixed with 100 μl of 0.56 mM TNT. This reaction mixture turned pale red in 5 min and took more than 2 h to turn yellow. Therefore, the P. fluorescens strain is able to transform TNT even in ddH₂O although the reaction rate is slow.

Stability of Pseudomonas fluorescens I-C In order to determine the stability of the P. fluorescens I-C cells, overnight-grown cells (as cell suspensions in LB medium) and harvested cells (as cell pellets) were incubated at various temperatures (room temperature, 37°C, 42°C, 50°C, 4°C, on ice, -20°C, and -80°C) for various periods of time. Then, a 200 μl sample of the cell suspension was mixed with 100 μl of 0.56 mM TNT. The cell pellets were resuspended in 200 μl of LB medium, 100 mM phosphate buffer (pH 7.0), or ddH₂O, and mixed with 100 μl of 0.56 mM TNT. Reactions were then monitored for color changes, and the results are summarized in Table 4.

Table 4. - TNT Assay Under Various Conditions

Reaction Incubation Incubation Reaction time Reaction time solution temp. (°C) time (min) Red (min) Yellow (min)

LB RT^* 0 2 25

15 2 25

30 2 40

60 2 40

6h 2 40

24 h 3 40 Reaction Incubation Incubation Reaction time Reaction time solution temp. (°C) time (min) Red (min) Yellow (min)

1 week No change No change

Cell 37 60 2 25 suspension

(LB)

42 1 1 30

5 1 30

15 1 30

30 2 (weak) 20 (weak)

60 No change No change

50 1 1 20

5 No change No change

4 60 2 15

24 h 3 25

1 week 15 (weak) 15 (weak)

On ice 60 2 25

-20 60 No change No change

24 h No change No change

1 week No change No change

-80 24 h 3 35

1 week 5 (weak) 5 (weak)

Cell pellet RT 0 2 25

(resusp. in 60 2 30

LB)

24 h 8 (weak) 45

1 week No change No change

37 60 2 25

4 60 2 20

24 h 3 35 Reaction Incubation Incubation Reaction time Reaction time solution temp. (°C) time (min) Red (min) Yellow (min)

1 week 3 (weak) 40

-20 60 2 20

24 h 1.5 30

1 week 1 20

-80 24 h 2 40

1 week 1 20

Cell pellet RT 0 1 20

(resusp. in 60 0.8 20

24 h No change No change

1 week No change No change

4 60 1 15

24 h 2 25

1 week 3 (weak) 40

-20 60 1 15

24 h 1.5 30

1 week 1 20

-80 60 1 15

24 h 1 (strong) 25

1 week 1 20

Cell pellet RT 0 1 2 h

(resusp. in 60 0.5 50

24 h 10 (weak) No change

1 week No change No change

4 60 1 1 h

24 h 2 l h

1 week No change No change Reaction Incubation Incubation Reaction time Reaction time solution temp. (°C) time (min) Red (min) Yellow (min)

-20 60 1 (weak) 1 h

24 h 1.5 30

1 week 10 2 h

-80 60 1 (weak) l h

24 h 1 (weak) 1 h

1 week 1 40

^*RT = room temperature

The cell suspensions incubated at room temperature for 24 h transformed TNT to produce a red-yellow colored product. However, one day old cell pellets held at room temperature and resuspended in phosphate buffer or water were no longer active. Both cell suspensions and cell pellets incubated at room temperature for one week did not transform TNT.

When the cells were incubated at temperatures greater than 42°C, the cells lost the ability to transform TNT. When the overnight-grown cell suspensions were frozen at -20°C, they lost the capacity to transform TNT, whereas some capacity to transform TNT was maintained when the cell suspensions were frozen at -80°C. When the cell pellets were frozen at -20°C or -80°C, resuspension of the cell pellets in phosphate buffer yielded the clearest and the fastest color change. Resuspension of the cell pellets in LB medium produced a strong color change, whereas resuspension in water produced weak colors and required a greater time period to turn to yellow from red. Overall, cells stored at -80°C were most effective at maintaining the ability to give a color reaction with TNT.

Example 7 - Purified Enzyme TNT Detection Assay

A typical enzyme assay contained 300 nmoles NADPH, 100 nmoles TNT, 0.1 M potassium phosphate, pH 7.0, and 1 μg of purified reductase enzyme or cell-free extract prepared from the Pseudomonas strains or the recombinant E. coli strains, as taught in the previous Examples, in a final reaction volume of 700 μL. A bright yellow color appeared within 1 min at room temperature. Example 8 - TNT assay with Pseudomonas fluorescens I-C cell extract

Cell extract concentration

In a 300 μl reaction mixture containing 330 μM TNT, 1 mM NADPH, and 100 mM phosphate buffer, pH 7.0, various concentrations of the cell extract from Pseudomonas fluorescens I-C were added, ranging from 0.01 mg/ml to 1 mg/ml. At 1 mg/ml of the cell extract, the color immediately changed to bright yellow. The yellow intensity of the reaction decreased upon reducing the concentration of the cell extract, and the color change was barely visible at a concentration of 0.01 mg/ml of the cell extract.

TNT concentration

In a 300 μl reaction mixture containing 1 mM NADPH, 100 mM phosphate buffer, pH 7.0, and 0.1 mg/ml cell extract, various concentrations of TNT were added. The reaction mixture turned yellow in 10 seconds upon addition of 330 μM TNT. The addition of 33μM TNT caused the reaction mixture to turn pale yellow in 3-5 min. No color change was observed upon the addition of 3.3 μM TNT to the reaction mixture.

Phosphate buffer pH

With 1 mM NADPH, 330 μM TNT, and 0.1 mg/ml cell extract, TNT assays were performed in 100 mM phosphate buffer at pH 6, pH 7, and pH 8. All reactions produced a yellow color in 10 seconds. The same results were observed when assays were conducted in 100 mM Tris-HCl buffer.

Example 9 - Lyophilization of Pseudomonas fluorescens I-C

Overnight-grown cell suspensions and cell pellets were lyophilized and used in a TNT assay. When the lyophilized cell suspension was resuspended in LB medium and mixed with TNT immediately following lyophilization, the reaction mixture turned red in 20 min and yellow in 1 h. However, when the lyophilized cell suspension was stored at -80°C for a month and then tested with TNT, it turned very pale yellow in about 1 h without showing the red intermediate. The results were comparable when the lyophilized cell suspension was resuspended in phosphate buffer or water instead of LB medium.

When the cell pellets were lyophilized and resuspended in LB medium, phosphate buffer, or water, the cells in LB medium or phosphate buffer turned the reaction mixture red within 1 min and yellow in 5 min in the presence of TNT. The cells in water produced a pale red color in 5 min and yellow in 2 h.

The lyophilized cell pellets were stored at various temperatures and tested for their ability to transform TNT after one week and after one month of storage. The lyophilized cell pellets stored at room temperature for one week produced a yellow color in 15 min only when they were resuspended in LB medium. The cells resuspended in phosphate buffer or water did not produce a color change. Following storage at room temperature for one month, the cells failed to produce a color change in any of the above solvents. Storage of the lyophilized cells at 37°C produced identical results as room temperature storage. When the lyophilized cell pellets stored at 4°C for one week were resuspended in LB medium or phosphate buffer, both produced a red color in 1-2 min and a yellow color in 30 min. However resuspension in water produced a pale red color in 5 min and a yellow color in 2 h. Following one month of storage, the cells resuspended in LB medium produced a red color in 3 min and a yellow color in 10 min; the cells resuspended in phosphate buffer produced a red color in 5 min and a yellow color in 30 min; the cells resuspended in water produced a pale red color in 10 min and a yellow color in 3 h. These results indicate that the ability of the lyophilized cell to produce a colored product in the presence of TNT was not significantly diminished when stored at 4°C. When the lyophilized cell pellets stored at -80°C for one week were resuspended in LB medium or phosphate buffer, each produced a red color in 1 min and a yellow color in 5 min. However resuspension in water produced a pale red color in 2 min and a yellow color in 2 h. After one month of storage, the cells resuspended in LB medium and phosphate buffer produced a red color in 1 min and a yellow color in 30 min; the cells resuspended in water produced a pale red color in 1 min and a yellow color in 3 h, comparable to the results of cell pellets stored for one week. The lyophilized cells can be stored at either 4°C or -80°C without significantly impacting their ability to transform TNT. The results of the lyophilization experiments are summarized in Table 5.

In an attempt to improve results utilizing lyophilized cell pellets, cells were lyophilized in the presence of DMSO, glycerol, or skim milk. Overnight- grown cells were treated with 7% (v/v) DMSO and centrifuged. The supernatant was removed and the cell pellet was lyophilized. When these lyophilized cells were resuspended in LB medium and TNT added, the reaction mixture turned red in 5 min and yellow in 20 min, a slower reaction than that produced by non-treated lyophilized cells (red in 30 seconds; yellow in 5 min). When the cells were treated with 15% glycerol prior to lyophilization, the cells failed to produce a color change in the presence of TNT.

Cells were centrifuged and resuspended in 100 μl of 20% skim milk prior to lyophilization. The lyophilized cells were resuspended in LB medium and TNT added to the reaction mixture. The reaction mixture turned red in 3 min and yellow in 10 min, a slower reaction than produced by non-treated lyophilized cells (red in 30 seconds, yellow in 5 min). The color produced was turbid due to the presence of skim milk. When phosphate buffer or water was used to resuspend the cells, the TNT reaction product required a greater production time than with non- treated lyophilized cells. However, when skim milk-treated lyophilized cells were stored at room temperature or 37°C for a week and then resuspended in LB medium, phosphate buffer, or water, the cells produced a weak yellow product in 10-20 min in the presence of TNT, while non-treated lyophilized cells gave no change after one week of storage at room temperature or 37°C. Therefore, lyophilization in the presence of skim milk increases the stability of the cells, but it causes turbidity in the colored product. Table 5 -TNT Assay with Lyophilized Cells

Reaction Incubation Incubation Reaction time Reaction time solution temp. (°C) time (min) Red (min) Yellow (min)

Cell suspension RT^* 0 20 l h

(resusp. in LB) -80°C 1 month 50

Cell suspension RT 0 20 l h

(resusp. in -80°C 1 month 1 h

Cell suspension RT 0 20 l h

(resusp. in -80°C 1 month l h

Cell pellets RT 0 1 5 (resusp. in LB) 1 week - 15 (weak)

1 month No change No change

4°C 1 week 1 30

1 month 3 10

37°C 1 week - 15 (weak)

1 month No change No change

-80°C 1 week 1 5

1 month 1 30

Cell suspension RT 0 1 10

(resusp. in 1 week No change No change

1 month No change No change

4°C 1 week 2 30

1 month 5 30

37°C 1 week No change No change

1 month No change No change

-80°C 1 week 1 10

1 month 1 30

Cell suspension RT 0 5 (weak) 2 h

(resusp. in 1 week No change No change

1 month No change No change

4°C 1 week 5 (weak) 2 h

1 month 10 (weak) 3 h Reaction Incubation Incubation Reaction time Reaction time solution temp. (°C) time (min) Red (min) Yellow (min)

37°C 1 week No change No change

1 month No change No change

-80°C 1 week 2 (weak) 2 h

1 month 1 (weak) 3 h

Cells (skim RT 0 3 10 milk)

(resusp. in LB) 1 week - 5

37°C 1 week - 15

Cells (skim RT 0 3 15 milk)

(resusp. in 1 week 5 (weak) 50

37°C 1 week - 15

Cells (skim RT 0 3 l h milk)

(resusp. in 1 week 5 1.5 h

37°C 1 week 15 1 h

^*RT = room temperature

Example 10 -Overlay Assay Screening

Microorganisms were screened for the presence of xenobiotic reductase enzymes as follows. Cultures to be assayed were grown overnight in liquid medium. Cultures were serially diluted to give approximately 30-500 colony forming units (CFU) upon plating. 100 μl of appropriately diluted cultures were spread on solid medium plates, and incubated overnight or until colonies were visible. TNT was dissolved in solvent and added to melted top agar cooled to approximately 50° C. The final TNT concentration in the top agar was 0.4-0.5 mM. Approximately 10 ml of TNT-top agar was poured on the plates to be assayed. Colonies producing the Meisenheimer complex turned orange in approximately 2 min. The color persisted for a few hours.

Example 11 - Picric Acid Assay with Pseudomonas fluorescens I-C

XenB was purified from Pseudomonas fluorescens I-C by standard chromatographic methods. When 5.9 μg of purified XenB was added to a 1 ml reaction mixture containing 100 μM picric acid, 300 μM NADPH, and 100 mM phosphate buffer (pH 9.0), the reaction mixture produced a dark yellow-orange color in 30 min. Reactions were conducted at pH 9.0 because at pH 7.0 or pH 5.5, color changes were obscured by the bright yellow color of the added picric acid. The reactivity of picric acid with XenB was much slower than that of TNT.

It is understood that the invention is not confined to the particular embodiments set forth herein as illustrative, but embraces all such modified forms thereof as come within the scope of the following claims.

Claims

CLAIMSWhat is claimed is:

1. A method of screening for the presence of a nitroaromatic compound, comprising: (a) mixing a sample suspected of containing a selected nitroaromatic compound with an enzyme, such that the selected nitroaromatic compound forms a colored product in the presence of the enzyme; (b) observing the formation of any colored product that is formed.

2. The method of claim 1, wherein the enzyme is derived from an organism of the genera selected from the group consisting of Escherichia, Pseudomonas, Bacillus, Enterobacter, Rhodococcus, Mycobacteria, and Nocardiodes.

3. The method of claim 2, wherein the enzyme is derived from an organism of the species selected from the group consisting of Escherichia coli, Pseudomonas putida, Pseudomonas fluorescens , and Bacillus subtilis.

4. The method of claim 2, wherein the enzyme is derived from an organism of the species selected from the group consisting of Pseudomonas putida and Pseudomonas fluorescens.

5. The method of claim 1, wherein the enzyme is selected from the group consisting of all or a functional portion of isolated or recombinant SEQ ID NO: 1 and all or a functional portion of isolated or recombinant SEQ ID NO:2, such that the enzyme has sufficient activity to produce a colored product from the selected nitroaromatic compound.

6. The method of claim 5, wherein the enzyme comprises one or more modifications, such that the modified enzyme retains sufficient activity to produce a colored product from the nitroaromatic compound.

7. The method of claim 1, wherein the nitroaromatic compound is selected from the group consisting of trinitrotoluene and picric acid.

8. The method of claim 1, wherein (b) further comprises observing the colored product by visual observation.

9. The method of claim 1, wherein (a) further comprises adding a solvent to the sample.

10. The method of claim 1, wherein (a) further comprises adding NADPH to the sample.

11. A composition for detecting the presence of nitroaromatics, the compound comprising an enzyme, such that a nitroaromatic compound forms a colored product in the presence of the enzyme.

12. The composition of claim 11, wherein the enzyme is derived from an organism of the genus selected from the group consisting of Escherichia, Pseudomonas, Bacillus, Enterobacter, Rhodococcus, Mycobacteria, and Nocardiodes.

13. The composition of claim 11, wherein the enzyme is derived from an organism of the species selected from the group consisting of Escherichia coli, Pseudomonas putida, Pseudomonas fluorescens , and Bacillus subtilis.

14. The composition of claim 11, wherein the enzyme is derived from an organism of the species selected from the group consisting of Pseudomonas putida and Pseudomonas fluorescens.

15. The composition of claim 14, wherein the enzyme is selected from the group consisting of all or a functional portion of isolated or recombinant SEQ ID NO: 1 and all or a functional portion of isolated or recombinant SEQ ID NO:2, such that the enzyme has sufficient activity to produce a colored product from the nitroaromatic compound.

16. The composition of claim 15, wherein the enzyme comprises one or more modifications, such that the modified enzyme retains sufficient activity to produce a colored product from the nitroaromatic compound.

17. The composition of claim 11, wherein the nitroaromatic compound is selected from the group consisting of trinitrotoluene and picric acid.

18. A kit for the detection of nitroaromatic compounds, comprising: (a) a reaction vessel; (b) an enzyme having sufficient activity to produce a colored product from a nitroaromatic compound; and (c) a color standard for comparison purposes to determine if nitroaromatic compounds are present.

19. The kit of claim 18, wherein the enzyme is derived from an organism of the genus selected from the group consisting of Escherichia, Pseudomonas, Bacillus, Enterobacter, Rhodococcus, Mycobacteria, and Nocardiodes.

20. The kit of claim 18, wherein the enzyme is derived from an organism of the species selected from the group consisting of Pseudomonas putida and Pseudomonas fluorescens.

21. The kit of claim 20, wherein the enzyme is selected from the group consisting of all or a functional portion of isolated or recombinant SEQ ID NO: l and all or a functional portion of isolated or recombinant SEQ ID NO:2, such that the enzyme has sufficient activity to form a colored complex in the presence of the nitroaromatic compound.

22. A method of screening microorganisms for the presence of enzymes that form colored products with nitroaromatic compounds, comprising: (a) placing a selected microorganism in the presence of a selected nitroaromatic compound; (b) observing the microorganism for the formation of any colored product.

23. An enzyme having the sequence selected from the group consisting of all or a functional portion of isolated or recombinant SEQ ID NO: 1 and all or a functional portion of isolated or recombinant SEQ ID NO:2, such that the enzyme has sufficient activity to produce a colored product from trinitrotoluene.

24. The enzyme of claim 23, wherein the enzyme comprises one or more modifications, such that the modified enzyme retains sufficient activity to produce a colored product from trinitrotoluene.

25. A DNA molecule having the sequence selected from the group consisting of all or a functional portion of isolated or recombinant SEQ ID NO: 7 and all or a functional portion of isolated or recombinant SEQ ID NO: 8, such that the DNA molecule encodes an enzyme that has sufficient activity to produce a colored product from trinitrotoluene.

26. The DNA molecule of claim 25, wherein the DNA molecule comprises one or more modifications, such that the modified DNA molecule produces an enzyme having sufficient activity to produce a colored product from trinitrotoluene.