DETECTION AND BIODEGRADATION OF EXPLOSIVES

Abstract: An enzyme capable of catalyzing the removal of nitrite from pentaerythritol tetranitrate (PETN) is provided. The enzyme (known as PETN reductase enzyme) is produced by culturing a novel strain of the Enterobacter cloacae bacterium isolated from nature. The strain designated PB2 has been deposited as NCIMB 40718. The amino acid sequence of the enzyme and the genetic sequence which encodes for this enzyme have also been determined. A PETN reductase enzyme encoded by the on gene is provided. A method for producing PETN reductase enzyme in large quantities and methods of bioremediation using the enzyme so produced are also provided. Additionally there is provided a method of detecting the presence of PETN in a sample together with a biosensor for use in such a method.

Description: Detection and Biodegradation of Explosives This invention relates to the field of explosives detection and biodegradation and in particular to a novel enzyme, to the amino acid sequence for the enzyme, to the gene which encodes the enzyme and to methods of producing the enzyme recombinantly. The invention further relates to a method of using the enzyme to catalyze the aerobic biodegredation of pentaerythritol tetranitrate (hereinafter referred to by the commonly used abbreviation PETN) and to a method and apparatus for the detection of PETN using the enzyme. The novel enzyme of this invention has also been demonstrated to liberate nitrite from glycerol trinitrate (GTN) and from ethylene glycol dinitrate (EGDN) which are further examples of nitrate ester species. The enzyme is referred to as a PETN reductase. Nitrate esters, though apparently extremely rare in nature, are produced in significant quantities by the chemical industry and comprise, for example, an important class of energetic materials having applicability as explosives and propellants. PETN itself has a diverse range of applications including as an explosive in blasting caps and detonators and in pharmaceutical compositions as the active ingredient of long-acting, slow onset coronary vasodilators for the prevention of angina attacks. The manufacture, handling and disposal of PETN can all lead to the contamination ofthe environment with PETN. There are concerns regarding the environmental fate of nitrate esters due to their relative recalcitrance and there therefore exists a need for a means of removing such contaminants from the environment without producing other undesirable pollutants. There is also an urgent requirement for a better method of detecting PETN as the currently proposed analytical systems rely mostly on use of bulky and sophisticated pieces of equipment such as gas chromatograms or mass spectrometers and/or require specially trained laboratory technicians for their application. It is an aim of this invention to provide an enzyme which is capable of catalyzing the biodegradation of PETN and which may be employed in a bioremediation system for the environmental decontamination ofthe PETN pollutant. It is a further aim to provide an enzyme which is useful for PETN detection systems. According to a first aspect ofthe invention therefore there is provided a PETN reductase enzyme which has the characteristics that, in the presence of nicotinamide adenine dinucleotide phosphate (NADPH hereinafter), it 1) catalyses the removal of nitrite from PETN; and 2) has reductase activity specifically at the nitrate ester linkage of PETN. The enzyme is further characterised by the fact that it has a pH optimum of 6.5 and that it has a M r of about 40,000 Daltons as determined by gel filtration. The subunit M r , as estimated by SDS-PAGE (polyacrylamide gel electrophoresis), was also 40 000. These results suggest that PETN reductase is a monomer of M r approximately 40,000. The PETN reductase enzyme of this invention is characterised by the essential features described above but may be further identified by additional characteristics such as its pH optimum, catalytic activity, thermal stability or molecular weight. Details of such further characteristics are given in Example 3 below but it must be stressed that these characteristics are variable to a degree depending upon the conditions under which the microorganism producing the enzyme is grown and upon the degree of purification ofthe crude product. Variations of this kind will be well understood by those skilled in the art. The purified enzyme is visibly yellow and shows a visible absoφtion spectrum characteristic of an oxidised flavoprotein. The flavin was liberated from PETN reductase by boiling followed by removal of denatured protein by centifugation, indicating that the flavin is not covalently bound. In two thin layer chromatography systems the liberated flavin comigrated with authentic flavin mononucleotide (FMN) and not with flavin adenine dinucleotide (FAD). Flavin standards subjected to the protocol used to liberate the flavin from PETN reductase showed no change; in particular, FAD was not hydrolysed to FMN. These results indicate therefore that the enzyme is a monomeric flavoprotein which binds FMN non-covalently. The amino acid sequence ofthe enzyme and the encoding genetic nucleotide sequence therefor have been established. According to a second aspect ofthe present invention therefore, there is provided a PETN reductase enzyme having the amino acid sequence shown in Figure 4 or a derivative thereof. By derivative herein is meant a version ofthe enzyme sequence of Figure 4 containing insertions, deletions and/or substitutions of the amino acid sequence such that the functionality ofthe enzyme is retained. Based on the evidence ofthe amino acid sequence it is possible to state that the enzyme is a member ofthe family of α/β-barrel flavoprotein oxidoreductases. In a third aspect, the present invention provides the gene (designated onr (for organic nitrate ester reductase)) which encodes the PETN reductase enzyme or a derivative thereof. By derivative ofthe gene is meant herein homologues ofthe gene having a coding sequence which is at least 70% identical to the onr gene, involving any and all single or multiple nucleotide additions, deletions and/or substitutions thereto. According to a fourth aspect ofthe invention there is provided a recombinant DNA molecule including the nucleotide sequence ofthe onr gene or a nucleotide sequence which is at least 70% identical to the nucleotide sequence ofthe onr gene. The nucleotide sequence ofthe onr gene as determined herein is set out in Figure 3. In a fifth aspect the present invention provides an enzyme comprising substantially the transcribed product ofthe onr gene. In a further aspect the present invention provides the PETN reductase enzyme which is encoded by the onr gene. It will be readily apparent to those skilled in the art that once the sequence ofthe genetic material which encodes for PETN reductase enzyme in the E. cloacae PB2 microorganism has been identified in accordance with this present invention, it will be possible according to well known techniques to transform a suitable host cell with the onr gene (or a derivative thereof) such that the host cell produces (expresses) the recombinant gene product ie. PETN reductase. This may be done by any suitable method such as splicing the gene into a vector and transforming said host cell with that vector. Accordingly the present invention therefore also provides a recombinant DNA vector containing the onr gene or a derivative thereof and a host cell transformed with the onr gene or a derivative thereof. This transformation may be performed using such a vector. The manner in which such vectors and recombinant DNA may be produced will be readily apparent to those skilled in the art given that the methods applicable, including the choice ofa suitable host cell and of suitable promoters are generally well understood in the field. Among host cells which might be used for the purpose, it may be appropriate to use E. cloacae PB2 cells transformed with additional copies ofthe onr gene. Using the host cell transformed with the onr gene or a derivative thereof and spliced behind a suitable promoter ofthe host cell, it will be possible to generate PETN reductase enzyme in industrially useful quantities, again by techniques which are well known in the art. There is also provided therefore, a method for the production of PETN reductase enzyme or a derivative thereof which comprises the steps of: transforming a host cell with the onr gene or a derivative thereof; growing the host cell under conditions appropriate for expression ofthe said onr gene product, and extracting the onr gene product from the growing medium or from the host cells after disruption thereof. Most conveniently the production process is run in a continuous or semi-continuous manner to continuously extract the enzyme produced from the growth medium for the host cell, employing techniques which are well understood in the art. Ifthe host cell produces the enzyme intracellularly, disruption ofthe cells in the culture will be necessary to extract the enzyme product. Suitable host cells may be provided by either prokaryotic or eukaryotic organisms. The action ofthe novel reductase enzyme ofthe present invention is to catalyze the reduction of PETN into pentaerythritol tri- and di-nitrates by attack at the nitrate ester linkage of PETN. The ability to specifically attack the nitrate ester linkage of PETN is a distinctive feature of this PETN reductase enzyme that is not possessed by commercially available reductases. A description ofthe mode of identification ofthe reaction products of PETN is set out in Example 2 below. The ability ofthe novel PETN reductase enzyme to catalyse the removal of nitrite from PETN in the presence of NADPH allows the enzyme to be used in the detection of PETN. According to a yet further aspect ofthe invention therefore, there is provided a method of detecting the presence of PETN in a sample which comprises subjecting the sample to the PETN reductase enzyme of this invention in the presence of NADPH and under conditions to permit reaction of any PETN present in the sample and detecting the occurrence of such reaction. Conveniently, detection ofthe reaction would be by means of a bioluminescence test using either bacterial or firefly luciferase, or by a colorimetric or amperometric method as is well known in the art. In a further aspect, therefore, the present invention also provides a biosensor for the detection of PETN in a sample which comprises means for contacting the sample with a PETN reductase enzyme in the presence of NADPH and means for detecting the occurrence ofa reaction, catalyzed by the enzyme, of PETN when PETN is present in the sample. The means for detecting the occurrence ofa reaction may conveniently comprise a bioluminescent transducer or an amperometric transducer. Such sensors can be used as the basis for highly convenient portable detectors for checking luggage, clothing etc. for traces ofPETN The methods of making biosensors that rely on amperometric or bioluminescent changes in the test reaction are well known in the art. For example, UK Patent Application Publication No. 2,231,332A (NRDC) describes such methods and their use in biosensors, the contents of which in relation thereof is hereby incoφorated by reference. Any of such methods may be of use in detecting the occurrence ofthe PETN degrading reaction and hence in the detection of PETN. Typically, in the case ofa bioluminescent biosensor, luciferase is used. This enzyme is responsible for the light-emitting reaction of luminous bacteria and catalyzes the reaction of molecular oxygen with reduced flavin and aliphatic aldehyde to form long-lived intermediates whose slow breakdown provides energy to give light emission with reasonably high quantum yield. In coupling the PETN reductase to such a bioluminescent system, the NADP + generated through the activity ofthe PETN reductase is detected by the oxidation of an alcohol such as decanol, octanol or hexanol, to its corresponding aldehyde in the presence of an alcohol dehydrogenase. The aldehyde is then detected by reaction with reduced flavin (FMNH 2 ) in the presence of oxygen together with luciferase to catalyse the reaction. The intensity ofthe emitted light provides a measure ofthe NADP + converted to NADPH which in turn provides a measure ofthe PETN concentration present. It is anticipated that using such a scheme, sensitivity to PETN will be in the range OJ nmol - OJμmol. A convenient colorimetic detection procedure uses a Griess reagent which generates a characteristic puφle colouration in the presence of nitrite. A standard curve comprises the step of inoculating the environment with a sample ofthe bacterial isolate of Enterobacter cloacae designated PB2 and allowing the isolate to consume the PETN present in the environment. The environment concerned may be, for example, a waste stream of material containing PETN originating from the destruction of an explosives charge containing PETN or a sample of PETN-contaminated earth or other material. In the former case bioremedial treatment may be conveniently carried out in a reactor vessel, whereas in the latter instance the isolate may be introduced directly into the environment by inoculating the contaminated soil with it. Other appropriate methods of effecting treatment will be readily apparent to those skilled in the art. The bacterium identified above will only produce the enzymic activity to which the present invention refers when it is cultured on PETN as the nitrogen source. Further characteristics ofthe deposited bacterium PB2 are listed below. Gram stain -ve Spores -ve Motility -hve Growth 37°C +ve 41°C +ve 45°C +ve Catalase +ve Oxidase -ve Fermentative in glucose OF +ve Colony moφhology: R Roouund, regular, entire, smooth, glossy cream, low convex, semi-translucent, Imm in diameter. Rapid Test (APP: 24 hours at 30°C β galactosidase + Arginine dihydrolase + 10 Lysine decarboxylase - Ornithine decarboxylase + Citrate utilisation + H 2 S production - Urease - Tryptophan deaminase - Indole production - Noges Proskauer + Gelatinase - Acid production from:- Glucose + Mannitol + Inositol - Sorbitol + Rhamnose + Sucrose + Melibiose + Amygdalin + L (+) Arabinose + Cytochrome oxidase - Further Tests. 30°C. 7 davs Methyl Red (37°C) Acid from Raffinose + Acid from α-Methyl-glucoside + Acid from Adonitol + Gelatin + PETΝ reductase can be produced by culturing E. cloacae on PETΝ as a nitrogen source. When grown on ΝH»ΝO 3 the activity can be induced by the addition of PETN. comprises the step of inoculating the environment with a sample ofthe bacterial isolate of Enterobacter cloacae designated PB2 and allowing the isolate to consume the PETN present in the environment. The environment concerned may be, for example, a waste stream of material containing PETN originating from the destruction of an explosives charge containing PETN or a sample of PETN-contaminated earth or other material. In the former case bioremedial treatment may be conveniently carried out in a reactor vessel, whereas in the latter instance the isolate may be introduced directly into the environment by inoculating the contaminated soil with it. Other appropriate methods of effecting treatment will be readily apparent to those skilled in the art. The bacterium identified above will only produce the enzymic activity to which the present invention refers when it is cultured on PETN as the nitrogen source. Further characteristics ofthe deposited bacterium PB2 are listed below. Gram stain -ve Spores -ve Motility +ve Growth 37°C +ve 41°C +ve 45°C +ve Catalase +ve Oxidase -ve Fermentative in glucose OF +ve Colony moφhology: R Roouund, regular, entire, smooth, glossy cream, low convex, semi-translucent, Imm in diameter. Rapid Test (APT): 24 hours at 30°C β galactosidase + Arginine dihydrolase + Lysine decarboxylase - Ornithine decarboxylase + Citrate utilisation + H 2 S production - Urease - Tryptophan deaminase - Indole production - Voges Proskauer + Gelatinase - Acid production from:- Glucose + Mannitol + Inositol - Sorbitol + Rhamnose + Sucrose + Melibiose + Amygdalin + L (+) Arabinose + Cytochrome oxidase - Further Tests. 30°C. 7 davs Methyl Red (37°C) Acid from Raffinose + Acid from α-Methyl-glucoside + Acid from Adonitol + Gelatin + PETN reductase can be produced by culturing E. cloacae on PETN as a nitrogen source. When grown on NH-,NO 3 the activity can be induced by the addition of PETN. However, this is not the case when grown on NHjCl. Cultivation is preferably anoxic at any usual temperature, eg within 20 to 40°C range, preferably 25 to 30°C. To obtain PETN reductase the cells can be disrupted in any conventional way. Preferably, a cell free extract is made. The enzyme is then recovered from the extract. Instead ofthe precise starting organism deposited, a mutant thereof, eg derived by gamma-ray irradiation or the use ofa chemical mutant, induction by culture on another medium etc. or a transconjugant thereof with another bacterium or an artificially produced variant can be used. The ability of any such organism to give the enzymic activity can be readily determined by the skilled person. In a further manner of use ofthe previously described activity ofthe PETN reductase of this invention, there is provided a method for producing pentaerythritol di- and tri-nitrates which may have useful pharmaceutical activity (biotransformation) by reacting PETN with the PETN reductase enzyme ofthe present invention, in the presence of NADPH. The invention will now be further described with reference to the following figures of which :- Figure 1 shows an alignment ofthe DNA inserts in pNER-Gl, pNER-G2 and pNER l; Figure 2 demonstrates in schematic manner the stategy used for sequencing onr and flanking DNA; Figure 3 shows the nucleotide sequence of onr and the deduced amino acid sequence of PETN reductase; Figure 4 sets out the amino acid sequence per se; and Figure 5 is a PETN reductase assay standard curve for PETN-contaminated soils and to the following examples which further illustrate the invention but are not to be regarded as restrictive thereof. EXAMPLE 1 Preparation of he enzvme activity from the bacterial strain Enterobacter cloacae PB2 1.Materials and Methods Enterobacter cloacae PB2 was isolated using techniques standard in the art, from samples collected from a natural source by enrichment with PETN as the nitrogen source. E. cloacae was grown in 1 litre of defined medium consisting of 10 mM potassium phosphate buffer, pH 7.3, containing 0.25 mM MgS0 4 , 5 mM glucose, 5 mM succinate, 10 mM glycerol, 2mM NH»NO 3 , PETN (10 mM) and trace elements (as described by Pfennig and Lippert, Arch. Microbiology. 1966, 55, 726-739.) supplemented with CaCl 2 *2H 2 0 (lOOmg/l). Flasks were incubated at 180 r.p.m in a shaking incubator at 30°C. For bulk preparation of bacteria, 1 litre of seed culture was aseptically added to a 75 litre culture vessel, containing 50 litres of sterile medium. The bulk cultures were incubated at 30°C, stirred at 150 r.p.m. with sterile aeration to maintain dissolved oxygen at 10% saturation. Cell free extracts were prepared from cells grown in the above manner. Cells were harvested from a 75 litre bulk culture, using continuous flow centrifugation (Sorval TZ-28 rotor, Sorval RC-5C centrifuge). Those obtained from a smaller volume culture were then pelleted by spinning at 10,000g for 15 min at 4°C in a Sorval RC-SC centrifuge fitted with a GS-3 rotor. These pelleted cells were resuspended in 2 ml of bis-Tris propane buffer (pH 7), per gram wet cell weight. Cells were disrupted by sonication in an MSE Soniprep (Fisons, Instruments, FSA Ltd.) using 6 x 12 μm bursts of 15 seconds, alternated with 30 seconds of cooling in melted ice. Cell debris and unbroken cells were removed by centrifugation at 20,000g for 20 min at 4°C in a Sorval RC-5C centrifuge using a SS-34 rotor, to give clarified cell free extract. 2 Chemicals PETN was ofthe highest purity and other chemicals were of analytical grade, and unless stated otherwise, were obtained from BDH Ltd. (Poole, U.K), Sigma Chemical Company Ltd. (Poole, U.K) or Aldrich (Gillingham, U.K). 3 Assays PETN reductase PETN reductase activity was determined by monitoring the disappearance of PETN by HPLC in 50 mM bis-Tris propane buffer (pH 7), containing PETN (47 μM, final concentration), 40 μl enzyme and NADPH (0.2 mM, final concentration) in a final volume of 1 ml. Alternatively, PETN degradation was also followed by monitoring the release of nitrite using Greiss reagent (Rosenblatt, Burrows, Mitchell and Parmer. 1991 : "Organic Explosives and Related Compounds" in The Handbook of Environmental Chemistry 3 (G), edited by O.Hutzinger, Springer-Verlag). The assay was carried out as described above and terminated by the addition of ferricyanide (0.5 mM, final concentration) and phenazine methosulphate (0.2 mM, final concentration). Sulphanilic acid (0.6 mM, final concentration) was added and left to stand for 15 min. N-1-naphthylethylenediamine (0.4 mM, final concentration) was then added and after 5 min the colour which developed was measured spectrophotometrically at 540 nm. The unit enzyme activity is defined as the amount of enzyme necessary to release 1 μmol of nitrite per min at 30°C. The degradation of PETN could also be determined by monitoring the oxidation of NADPH at 340 nm. Protein Protein was routinely assayed by the Coomassie dye-binding method of Bradford (Anal. Biochem. (1976) 72, 248-254) using commercially available reagent and Bovine Serum Albumin standard (Pierce Ltd.- obtained through Life Science Labs Ltd., Luton). An aliquate (20 μl) of sample containing 0.2-1 mg protein/ml was added to 1 ml of reagent and the reaction allowed to develop for 5 min at room temperature prior to reading the absorbance at 595 nm against a blank of buffer (20 μl) plus reagent (1 ml). Comparison to a standard curve of standard values (0-1 mg/ml) allowed calculation ofthe protein concentration in the sample. Gel filtration standards The following enzymes were used as molecular weight markers in gel filtration experiments: Bovine Serum albumin, Ovalbumin, Chymotrypsin and Ribonuclease A (molecular weights 67,000, 43,000, 25,000, 13,700 Daltons respectively). EXAMPLE 2 Purification of PETN reductase To the crude extract, obtained from 30g wet weight cells, enough ammonium sulphate was added to achieve 50% saturation. After stirring at 4°C for 5 min the resulting precipitate was removed by centrifugation at 20,000g for 20 min. Ammonium sulphate was added to the resulting supenatent to achieve 90% saturation. The resulting precipitate was collected by centrifugation at 4°C and redissolved in 4ml of 50 mM bis-Tris propane buffer (pH 7). The sample was desalted using a PD-10 column packed with Sephadex G-25M (Pharmacia) and concentrated to 8ml by ultrafiltration using an Amicon stirred ultrafiltration chamber equipped with a Diaflo type YM-3 membrane filter that retained proteins with molecular weights greater than 3,000 Daltons. The fast protein liquid chromatography (FPLC) system was used in combination with a Q-sepharose column to further purify the sample. The FPLC system consisted of two LKB P500 pumps (Pharmacia) combined with a model LCC-500 PLUS gradient controller (Pharmacia), a Rheodyne injection valve, a single path UN monitor (Pharmacia) and an LKB 2212 HELIRAC fraction collector. FPLC was carried out at room temperature, but the fractions collected were cooled on ice. The concentrate was applied to the Q-sepharose column (1 x 7 cm) which had previously been equilibrated with 50 mM bis-Tris propane (pH 8.5) at room temperature. The column, was washed extensively with buffer until no further absorbance at 280 nm was detected in the eluent, whence the reductase was eluted with 10 mM ΝaCl. Fractions (14ml) were collected at a flow rate of 1 ml/min, desalted and concentrated by ultrafiltration as previously described. The sample was then applied to a Mimetic Orange 2 affinity chromatography column (8 x 20 mm, Affinity Chromatography Ltd.) that had previously been equilibrated with 50 mM bis-Tris propane (pH 7) at 4°C. The column was washed with 2 column volumes of buffer. The third column volume contained the reductase activity which was collected. Results The specific activity ofthe PETN reductase was measured after the various stages of purification described above. The resulting data is set out in Table 1, from which it may be seen that in a cell free extract of E cloacae PB2 grown on PETN as a nitrogen source, PETN reductase was present at a specific activity of 0.025 unit/mg protein while ultimately it was purified 182 fold. Table I Volume Total Total Specific Recovery Purification Purification step (ml) protein activity activity of activity factor (mg) (units) (units/mg) (%) (-fold) Crude extract 40 361.6 9.04 0.025 100 - Ammonium sulphate 8 31.4 3.47 0J 10 39 4 fractionation Q-Sepharose ion exchange 10.5 15 0.83 0.720 9 29 chromatography Mimetic Orange 2 affinity 16 0J6 0.728 4.550 8 182 chromatography EXAMPLE 3 Characteristics of PETN reductase pH optimum Purified PETN reductase (50 μl, 0.5 μg protein) was incubated for 4 min at 30°C with 47 μM PETN in a range of buffers: 50 mM bis-Tris propane (pH 6.5, 7, 7.5 and 8), 50 mM 2-[N-moφholino]ethanesulphonic acid (MES) (pH 5.5, 6, 6.5) and 50 mM bis-Tris (pH 6.2, 6.3, 6.4, 6.5, 6.6, 6.7 and 6.8). The concentration of nitrite was then measured using Greiss reagent. PETN reductase displayed a pH optimum of 6.5. Km of enzvme The K m of PETN reductase was above the maximum solubility of PETN (47 μM). Molecular weight detemination The molecular weight ofthe native enzyme was determined by the method of Andrews (Biochem. J. (1964) 91, 222-223). Measurements were carried out on a Superose 6 HR 10/30 column (1 x 30 cm). Purified PETN reductase (10 μg) was mixed with marker proteins and added to the column. The column was eluted with bis-Tris propane buffer (pH 7) and 0.4 ml fractions collected. The elution volume of PETN reductase corresponded to a molecular weight of 40,000 Daltons. Molecular weight determination was also performed using SDS-PAGE. The purified PETN reductase ran as a distinct major band corresponding to a molecular weight of 42,000 Daltons. This similar value to that ofthe native enzyme implies that any effect of detergent/protein interactions in determining the molecular weight ofthe enzyme were minimal. EXAMPLE 4 Cloning and sequencing of the structural gene onr encoding PETN reductase. The structural gene encoding PETN reductase, designated onr (for organic nitrate ester reductase) was cloned by the use of degenerate oligonucleotide probes based on the N-terminal amino acid sequence ofthe purified protein. To obtain the N-terminal amino acid sequence of PETN reductase, purified enzyme (4.0 μg) was transferred from an SDS/polyacrylamide gel to a poly(vinylidene difluoride) membrane (ProBlott; Applied Biosystems, Foster City, CA, USA) using the Pharmacia PhastTransfer semi-dry blotting apparatus (Pharmacia Biotech, St. Albans, UK). The transfer buffer consisted of 25 mM tris(hydroxymethyl)aminomethane, 190 mM glycine, 10% w/v methanol. Transfer was with a current of 25 mA for 30 min. The N-terminal amino acid sequence was determined by automated Edman degradation by the Protein and Nucleic Acid Chemistry Facility, Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge. Based on elements of the amino acid sequence, the following oligonucleotide probes were designed: 1 ) ACTTT(G/C) AG(G/C)GG(G/C)GTGAA(G/C) AGTTTTTC(G/C)GC 2) GT(G/C)AG(G/C)GG(GC)GCCATGAA(G/C)AC(G/C)CGGTT Oligonucleotides were synthesized by the Protein and Nucleic Acid Chemistry Facility, Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge. Genomic DNA was prepared from E. cloacae PB2 as described by Ausubel et al. (Ausubel, F. M., Brent, R., Kingston, R. E. et al. (1994) Current Protocols in Molecular Biology, John Wiley and Sons, New York). Genomic DNA was digested to completion with various combinations of restriction endonucleases obtained from Boehringer- Mannheim (Lewes, E. Sussex, UK), Gibco/BRL (Paisley, Scotland, UK) and Promega (Southampton, Hants., UK). DNA fragments were separated by agarose gel electrophoresis using 0.8% (w/v) agarose gels and TAE buffer (Sambrook, J., Fritsch, E. F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd edn., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York), and transferred to nylon membranes (Hybond N+, Amersham, Little Chalfont, Bucks., UK) by alkaline capillary blotting according to the manufacturer's protocol. The oligonucleotide probes described above were end-labelled using [γ- 32 P]ATP (Dupont/NEN) and T4 Polynucleotide Kinase (Promega). Blots were prehybridized for 2 h at 42°C in a hybridization buffer consisting of 5 x SSC (where 1 x SSC is 0.15 M NaCl/0.015 M sodium citrate) with 5 x Denhardt's solution (where 1 x Denhardt's is 0.02% Ficoll 400/0.02% polyvinyl-pyrrolidone/0.02% bovine serum albumin) and 0.02 mg/ml sonicated denatured salmon sperm DNA. Labelled oligonucleotide probes were then added at 1 pmol/ml and allowed to hybridize overnight at the same temperature. Blots were washed four times for 15 min in 0.5 x SSC/0.1% (w/v) SDS at 45°C and exposed to Fuji RX100 X-ray film. Both oligonucleotide probes were found to hybridize to the same region of genomic DNA. A Bam lll/Hin dill fragment of 4.5 kb was selected for cloning. The vector used was pBluescript SK+ (Stratagene, Cambridge, UK). Genomic DNA was digested with Bam HI and Hin dill and DNA fragments of 4 to 5 kb were eluted from agarose gels using the US Bioclean system (United States Biochemical Coφoration, obtained through Amersham). Vector DNA was digested with the same enzymes, and vector and insert DNA were ligated using T4 DNA Ligase (Promega or Gibco/BRL). Electrocompetent Escherichia coli JMIO9 (obtained from Promega) was transformed with the ligation mixture by electroporation using a Bio-Rad Gene Pulser (Bio-Rad, Hemel Hempstead, Herts., UK). DNA from ampicillin-resistant transformants was transferred to Hybond-N+ membrane (Amersham) by colony blotting according to the manufacturer's protocol. Blots were screened using radiolabelled oligonucleotide probes as described above. One clone, designated pNER-Gl, was found to contain a 4.5 kb insert which hybridized to both probes. DNA sequencing demonstrated the presence of DNA encoding the N-terminal sequence of PETN reductase but showed that the Hin dill site fell within the open reading frame so that the 3' end of the gene was missing (Figure 1). A further oligonucleotide probe, GACGCCGTGGCCTTTGGCCGTGAC, was designed based on the DNA sequence near the Hin Dili site, and was used to screen various restriction digests of genomic DNA as described above in order to locate the missing region. Hybridization with this probe was at 50°C and blots were washed at 55°C, twice for 15 min with 1 x SSC/OJ % (w/v) SDS and twice for 15 min with 0.2 x SSC/OJ % (w/v) SDS. A Sal VCla I fragment of 0.5 kb was selected for cloning and was cloned as described above. This clone was designated pNER-G2. The regions of pNER-G 1 and pNER-G2 bearing the onr gene were ligated together in pBluescript SK+ to create an Nco l/Cla I insert of 1.5 kb bearing the entire onr gene. This construct was designated pNERl (Figure 1). Cell extracts from overnight cultures of E. coli JM109/pNERl grown in a rich medium were prepared and assayed for PETN reductase activity. PETN reductase appeared to form approximately 15% of soluble protein. Fragments of DNA from the region encoding PETN reductase were subcloned from pNER-Gl, pNER-G2 and pNERl in the vector pBluescript SK+ and sequenced using primers based on vector sequence. The sequencing strategy used is shown in Figure 2. DNA for sequencing was prepared using the Qiagen Plasmid Mini Kit (Qiagen Ltd., Dorking, Surrey, UK). DNA sequencing was peformed by the DNA Sequencing Facility, Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge using a Pharmacia ALF DNA sequencer (Pharmacia Biotech, St. Albans, UK). The nucleotide sequence of the onr gene and the deduced amino acid sequence of PETN reductase are shown in Figure 3. Considering Figure 1 further, it will be noted that all inserts are in the multi-cloning site of the vector pBlueseript SK+ (Stratagene). The dark arrow indicates the position of the onr gene encoding PETN reductase. The insert of pNERl was prepared by ligating together the Nco VStu I region of pNER-Gl with the Stu l/Cla I region of pNER-G2. In pNERl the Nco l/Cla I fragment is inserted between the Bam HI and Cla I sites of the multi-cloning site of pBluescript SK+. With particular reference to Figure 2, subclones were prepared in pBluescript SK+ and sequenced using primers based on vector sequence. Arrows indicate sequencing reactions. The dark arrow indicates the coding region. The positions of restriction sites used in sequencing are numbered, with 1 being the A of the ATG initiating the coding region. In Figure 3, nucleotides are numbered with 1 being the A of the ATG initiating the coding region. A putative ribosome-binding site is indicated. It should be noted that the N-terminal amino acid sequence of PETN reductase shows that in E. cloacae PB2 the initiating methionine is removed. The amino acid sequence is shown independently in Figure 4. Alternative ways of obtaining and cloning the gene will also be clear to the skilled person having knowledge ofthe gene sequence. For example suitable restriction enzymes may be employed to "cut" the DNA at restriction sites flanking the gene. Amplification of the gene may also be performed using PCR techniques employing suitably chosen primers flanking the gene. EXAMPLE 5 Identfication of whole cell degradation products Ethyl acetate extracts of supernatants from cultures grown with PETN contained PETN and three metabolites (as judged by HPLC). The metabolites were separated from PETN by TLC and found to have lower R f values (0.64, 0.53 and 0.23) than PETN (R f 0.81), indicating that the unknown metabolites were more polar than PETN. The identity ofthe unknown metabolites was investigated using electron impact (EI) mass spectrometry. The EI mass spectrum of metabolite 1 revealed a molecular ion of m/z 227 which is consistent with the empirical formula C5H 1 0N 2 O 8 . The mass spectrum contained a fragment ion at m/z 209. It is thought that this metabolite is pentaerythritol dinitrate (2,2-b/ ° s[(nitrooxy)methyl]- 1,3 -propanediol), a denitration product of PETN. The EI mass spectrum of metabolite 2 revealed a molecular ion of m/z 224 which corresponds to the empirical formula CsHgN 2 Og. The mass spectrum contained fragment ions at m/z 207, 170, 141, 99, 76, 74, 158, 46 and 44. This is believed to represent 3- hydroxy-2,2-£ s[(nitrooxy)methyl]propanal. The EI mass spectrum of metabolite 3 revealed a molecular ion of m/z 222 which corresponds to the empirical formula CsH6N 2 Og. The mass spectrum contained fragment ions at m/z 208, 177 and 91. This is believed to represent 2,2-bis[(nitrooxy)methyl]- propanedial. The proposed structures for these metabolites are as follows:- HOH 2 C CH 2 ONO 2 HOH 2 C CH 2 ONO 2 O 2 NOH 2 C CH 2 OH O 2 NOH 2 C CHO Metabolite 1 Metabolite 2 OHC CH 2 ONO 2 Metabolite 3 The identity of Metabolite 1 was further investigated using 1H NMR at 400mhz. The 1H NMR spectrum of pure PETN gave a single peak at 4.77 ppm which corresponds to the four equivalent methylene groups in PETN, whilst the 1H NMR spectrum ofthe unknown metabolite gave two separate peaks at 4.77 and 2.08 ppm. It is believed that the peak at 2.08 ppm corresponds to the methylene groups attached to the hydroxyl group in the proposed structural formula. The (EI) mass spectroscopy and 1H NMR analysis ofthe unknown metabolites foimed during PETN degradation by the bacterium suggest that at least two nitrogen atoms were used per PETN molecule; these metabolites provide no evidence for the removal ofa third nitrate group. EXAMPLE 6 Identification of the reaction products of PETN reductase Following treatment of PETN with purified PETN reductase and NADPH, an ethyl acetate extract ofthe reaction mixture contained PETN and two metabolites (as judged by HPLC). The metabolites were separated from PETN by TLC and found to have lower R f values (0.78 and 0.64) than PETN (R f 0.8 1). The identity of the unknown metabolites was investigated using (EI) mass spectrometry. The EI mass spectrum of metabolite A revealed a molecular ion of m/z 271 which corresponds to the empirical formula CsH 9 N 3 Oιo* The mass spectrum contained fragment ions at m/z 239 and 207. This is believed to represent pentaerythritol trinitrate. The EI mass spectrum and R f value of metabolite B were identical to those of Metabolite 1 isolated from culture supenatant (see Example 2). This metabolite was identified as pentaerythritol dinitrate (PEDN). It therefore appears that PETN reductase reductively liberates nitrite from PETN to form pentaerythritol trinitrate and then PEDN, which is not a substrate for this enzyme. The presence of aldehydes formed from these alcohols in culture supernatants (Example 2) suggests subsequent dehydrogenase activity by another enzyme. The specific activity of PETN reductase in crude extract was approximately 0.32 U/mg, equivalent to 9.7 mmol PETN(g soluble protein) "1 ^ 1 assuming complete conversion of PETN to PEDN. This is probably sufficient to account for the observed specific degradation rate of PETN by growing cells of 1.03 mmol PETN (g protein) "1 !! '1 . EXAMPLE 7 Use of PETN reductase enzyme as a colorimetric detector for PETN 1.Methodology This relies on the action of PETN reductase on PETN to produce nitrite which is then monitored by use ofa Griess reagent. There was added to a series of uncontaminated soil samples (John Innes No. 2, lg in each case) placed in clean glass boiling tubes, known concentrations of PETN (from 1 to 500μg) in HPLC acetone. Each ofthe samples was mixed thoroughly, placed in a vacuum oven and dried for 1 hour at room temperature. These deliberately contaminated soil samples together with other soil samples (lg) collected from ground which had been contaminated with either PETN or RDX/TNT mixtures were then each treated with 1.5 ml acetone per g of soil sample and shaken for 10 min. The soil was then allowed to settle under gravity after which 25 μl aliquots ofthe liquid were taken and added to 5ml Pyrex tubes containing a mixture of 12.8 μl of 7 mg/ml PETN reductase, 2μl of 20 mM NADPH (enzyme cofactor) and 220.2 μl of 50mM phosphate buffered saline. Each sample was mixed and then incubated for 10 min at room temperature. 200 μl of 1% sulphanilamide in 2.5% hydrochloric acid was then added to each tube (this forms a diazonium ion with nitrite) and incubated for a further 2 min prior to the addition of 40 μl of 0.5% N-(l-naphthyl)-ethylenediamine in water resulting in the generation ofa puφle-coloured product where PETN is present. 200 μl of each sample was taken and placed in a microtitre plate and the absorbance ofthe sample then measured on a Ceres 900 UV HDi reader. From those samples derived from soil specimens having known PETN concentrations a standard curve of absorbance against PETN concentration in soil could be plotted (Figure 5). Using this curve, optical densities obtained from samples of contaminated soils with unknown PETN content can be used to give an indication ofthe level of PETN contamination present within each sample. Table 2 gives data obtained with a series of samples as indicated. These show that the assay described responds specifically to the levels of PETN in soil samples, that it does not give false positives in the absence of PETN or the presence of other explosives (RDX/TNT) and that it is dependent on the presence ofthe PETN reductase enzyme. Table 2 Sample Sample Absorbance Amount of characteristic No. at 540 nm PETN/μg/g soil no enzyme, 100 μg 1 0.125 0 spiked soil 2 0J56 0 uncontaminated 3 0.137 0 soil 4 0.162 0 5 0J51 0 TNT/RDX 6 0J48 0 contaminated 7 0J31 0 soil 8 0J95 0 PETN 9 1.229 505 contaminated 10 0.482 95 soils 11 0.764 200 PETN 12 2J24 1200 contaminated 13 0.963 420 soils 14 0.805 280

Claims: Claims 1. A PETN reductase enzyme characterised in that: (1) it catalyses the removal of nitrite from PETN; and (2) it has reductase activity specifically at the nitrate ester linkage of PETN. 2. A PETN reductase enzyme according to claim 1 further characterised by one or more ofthe following features :- (3) it has a pH optimum of 6.5; and (4) it has a native molecular weight of about 40,000 Daltons, as determined by gel filtration chromatography. 3. An enzyme having the amino acid sequence shown in Figure 4 or a derivative thereof. 4. The gene (designated onr) which encodes the enzyme, or a derivative thereof. 5. A DNA molecule including the nucleotide sequence ofthe onr gene as shown in Figure 3 or a derivative of that sequence. 6. An enzyme comprising substantially the transcribed product ofthe onr gene. 7. PETN reductase enzyme which is encoded by the gene as claimed in claim 4. 8. A recombinant DNA vector containing the onr gene or a derivative thereof 9. A host cell transformed with the onr gene or a derivative thereof. 10. A host cell transformed with a DNA molecule as claimed in claim 5. 11. A host cell transformed with a vector as claimed in claim 8. 12. PETN reductase enzyme which is recombinantly produced. 13. A method for the production of PETN reductase enzyme or a derivative thereof which comprises the steps of: transforming host cells with the onr gene or a derivative thereof; suitably culturing said transformed host cells; and extracting the enzyme from the growth medium or from the host cells after disruption thereof. 14. A method as claimed in claim 13 where the host cell is transformed by means ofa recombinant DNA vector as claimed in claim 8. 15. A method as claimed in claim 13 or claim 14 where the host cell is grown on a continuous basis with the enzyme being continuously extracted from the growth medium. 16. A method as claimed in claim 13 or claim 14 where the host cells in the culture are disrupted after an appropriate period of growth in order to extract the enzyme therefrom. 17. A method of detecting PETN in a sample, comprising subjecting the sample to a reaction involving the removal of nitrite from PETN, the reaction being carried out in the presence of NADPH and a PETN reductase enzyme according to either claim 1 or claim 2, until NADP and nitrite are produced, and detecting the occurrence of said reaction. 18. A method of detecting PETN in a sample, comprising subjecting the sample to a reaction involving the removal of nitrite from PETN, the reaction being carried out in the presence of NADPH and a PETN reductase enzyme according to any one of claims 3, 6, 7 or 12, until NADP and nitrite are produced, and detecting the occurrence of said reaction. 19. A method according to claim 17 or claim 18 wherein the NADP liberated in the reaction is detected. 20. A method according to claim 19 wherein NADP is detected by a bioluminescence test. 21. A method according to claim 20 wherein the bioluminescence test uses either bacterial or firefly luminescence. 22. A method according to claim 19 wherein NADP is detected amperometrically. 23. A method according to claim 17 or claim 18 wherein the nitrite liberated in the reaction is detected colorimetrically. 24. A method according to claim 23 wherein Griess Reagent is used for colorimetric detection of nitrite. 25. A biosensor for the detection of PETN in a sample which comprises means for contacting the sample with a PETN reductase enzyme in the presence of NADPH and means for detecting the occurrence ofa reaction, catalysed by the enzyme, of PETN when PETN is present in the sample. 26. A biosensor for the detection of GTN and/or EDGN in a sample which comprises means for contacting the sample with a PETN reductase enzyme in the presence of NADPH and means for detecting the occurrence ofa reaction, catalyzed by the enzyme, of GTN and/or EDGN when either or both is present in the sample. 27. A biosensor according to claim 25 or claim 26 wherein the means for detecting the occurrence ofa reaction comprises a bioluminescent or an amperometric transducer or a colorimetric change. 28. A method for the bioremedial treatment of an environment which is contaminated by PETN, GTN and/or EGDN comprising the steps of adding to the environment a quantity of PETN reductase enzyme according to any of claims 3, 6, 7 or 12 and maintaining the mixture under conditions appropriate for degradation ofthe contaminant by the enzyme so as to allow the PETN, GTN and/or EGDN present in the material to be consumed. 29. A method according to claim 28 wherein the material is a waste stream containing PETN, GTN and/or EGDN. 30. A method according to claim 28 wherein the material is a soil or ground sample contaminated with PETN, GTN and/or EGDN. 31. A method according to any one of claims 28 to 30 wherein the PETN reductase enzyme is produced according to the method as claimed in any one of claims 13 to 16. 32. An Enterobacter cloacae bacterial strain referred to as "PB2" and deposited as NCIMB 40718, and mutants and variants thereof capable of producing enzymic activity which degrades PETN in the presence of NADPH. 33. A process of producing an enzyme according to claim 1, which comprises culturing the Enterobacter cloacae sp NCIMB 40718 according to claim 32, or a mutant or variant thereof, in the presence of PETN as nitrogen source, at a temperature of from 20 to 40°C, disrupting the cells and recovering the enzyme from the disrupted cells. 34. A method for the bioremedial treatment ofa PETN contaminated environment comprising the step of inoculating the environment with a sample ofthe bacterial isolate of Enterobacter cloacae as defined in claim 32 and allowing the isolate to consume the PETN present in the environment. 35. A method according to claim 34 wherein the environment is a waste stream containing PETN. 36. A method according to claim 34 wherein the environment is a soil or ground sample contaminated with PETN. 37. A method for producing pentaerythritol di- and tri-nitrates comprising reacting PETN with the PETN reductase enzyme of either claim 1 or claim 2 or of any of claims 3, 6, 7 or 12.

Inventors: BINKS PETER ROLAND, BRUCE NEIL CHARLES, FRENCH CHRISTOPHER EDWARD, NICKLIN STEPHEN, BINKS, PETER, ROLAND, BRUCE, NEIL, CHARLES, FRENCH, CHRISTOPHER, EDWARD, NICKLIN, STEPHEN
Applicants: BINKS PETER ROLAND, BRUCE NEIL CHARLES, FRENCH CHRISTOPHER EDWARD, NICKLIN STEPHEN, SECR DEFENCE, BINKS, PETER, ROLAND, BRUCE, NEIL, CHARLES, FRENCH, CHRISTOPHER, EDWARD, NICKLIN, STEPHEN, THE SECRETARY OF STATE FOR DEFENCE
Application year: 1996
Main classification: C12N15
IPC codes: A62D3, B09C1, C02F3, C06B21, C12N1, C12N9, C12N15, C12P13, C12Q1