AU682433B2 - Enzyme based bioremediation - Google Patents

Description

WO 95/19440 PCT/AU95/00016

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Enzyme Based Bioremediation This invention relates to enzymes capable of hydrolysing organophosphate and/or carbamate pesticide residues. In particular, it relates to esterase enzymes purified from organophosphate resistant strains of Lucilia cuprina, and isolated DNA molecules encoding such enzymes.

Residues of organophosphates and carbamate pesticides are undesirable contaminants of the environment and a range of commodities. Areas of particular sensitivity include contamination of domestic water supplies, residues above permissible levels in meat and horticultural exports and contamination of health products like lanolin. Bioremediation strategies are therefore required for eliminating or reducing these pesticide residues. One proposed strategy involves the use of enzymes capable of immobilising or degrading the pesticide residues. Such enzymes may be employed, for example, in bioreactors through which contaminated water could be passed; in sheep or cattle dips to reduce problems with contaminated pasture and run off into water supplies; in the wool scour process to reduce contamination of liquid effluent, wool grease and lanolin; or in washing solutions after post harvest disinfestation of fruit and vegetables to reduce residue levels and withholding times.

Suitable enzymes for degrading pesticide residues include esterases. It is desirable that the esterases be relatively specific and hydrolyse the pesticide residues at a rapid rate.

Esterases in insects have been implicated in reproductive behaviour, pheromone and hormone metabolism, digestion, neurotransmission, and in the action of, and resistance to, insecticides, particularly organophosphates (OPs). Three different mechanisms of OP resistance in insects involving esterases have been proposed. One such mechanism involves possible alterations to the structure of an esterase to increase its ability to degrade OPs.

SUBSTITUTE SHEET (Rule 26) r~---PL~AI WO 95/19440 PCT/AU95/00016 2 This mechanism has been proposed for the house fly, Musca domestica and Lucilia cuprina. The proposed structural changes are thought to have resulted in the loss of activity for synthetic substrates, such as anaphthyl acetate and its related esters. For example, esterase E3 in L. cuprina has lost the ability to utilize a- and P-naphthyl acetate as substrates in all the OPresistant strains examined to date. However, concomittantly with this loss in ability to utilise a- and P-naphthyl acetate substrates, it would appear that the OP-resistant E3 esterase becomes capable of hydrolysing OPs into non-toxic products whereas the susceptible E3 esterase cannot. Thus, the E3 esterase from OP-resistant strains of L. cuprina may be a suitable enzyme for development as a catalytic bioremediant for organophosphates and/or carbamates.

The present inventors have now developed a method for purifying the E3 esterase from L. cuprina. Kinetic data obtained from assays using homogenates suggests that the E3 esterase from OP-resistant strains of L. cuprina, hydrolyses OPs quickly even under suboptimal conditions (prevalent in most bioremediation applications). Further, the inventors have isolated the gene encoding the E3 esterase from an OP-susceptible and resistant strains of L. cuprina, and identified a homologue of this gene in Drosophila melanogaster.

Accordingly, in a first aspect the present invention consists in an E3 esterase from an organophosphateresistant strain of Lucilia cuprina, in substantially pure form.

Preferably, the E3 esterase is from one of the isochromosomal OP-resistant L. cuprina strains selected from the group consisting of der-S, Inverell 22, Landillo 103 and Sunbury 5.2.

In a second aspect, the invention provides an isolated DNA molecule comprising a nucleotide sequence SUBSTITUTE SHEET (Rule 26)

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~1~1_ WO 95/19440 PCT/AU95/00016 3 encoding a Lucilia cuprina E3 esterase or portion thereof capable of hydrolysing organophosphates and/or carbamate pesticide residues.

Preferably, the isolated DNA molecule comprises a nucleotide sequence encoding an E3 esterase or portion thereof, from an OP-resistant strain of L. cuprina (such as those strains listed above). More preferably, the isolated DNA molecule includes a nucleotide sequence substantially as shown in Table 1 from an OP-resistant strain of L. cuprina.

The inventors have also identified a homologue of this gene in D. melanogaster. This homologue encodes esterase EST23 which shares biochemical, physiological and genetic properties with E3 esterase from L. cuprina. Like E3, the D. melanogaster EST23 is a membrane-bound aesterase which migrates slowly towards the anode at pH 6.8. Both enzymes have similar in vitro preferences for substrates with shorter acid side chain length.

Furthermore, they both show high sensitivity to inhibition by paraoxon and insensitivity to inhibition by eserine sulphate. The activity of each enzyme peaks early in development and again, in the adult stage. Both enzymes are found in the male reproductive system and larval and adult digestive tissues, the latter being consistent with a role for these enzymes in organophosphate resistance.

Fine structure deficiency mapping localised EST23 to cytological region 84D3 to E1-2 on the right arm of chromosome 3 (Spackman, Oakeshott, Smyth, K-A, Medveczky, K.M. and Russell, R.J. (1994) Biochemical Genetics 32: 39-62).

Homplogues of the E3 encoding sequence may also be present in the genome of other insects, and particularly other species of Diptera. Thus, it is to be understood that the invention also extends to these homologues.

The isolated DNA molecules according to the second aspect of the present invention may be cloned into a SUBSTITUTE SHEET (Rule 26) l~lm- i~l~p~ pr~ WO 95/19440 PCT/AIJ95/00016 4 suitable expression vector and subsequently transfected into a prokaryotic or eukaryotic host cell for expression of the esterase. A particularly suitable system involves baculovirus vectors and an insect cell line.

The invention further relates to methods for eliminating or reducing the concentration of organophosphate and/or carbamate pesticide residues in a contaminated sample or substance, involving the use of an esterase according to the first aspect or an esterase encoded by an isolated DNA molecule according to the second aspect.

It is also envisaged that as an alternative to using the esterase per se as a bioremediation agent the bioremediation agent may be an organism transformed with the DNA encoding the esterase. In such an arrangement the organism transformed such that it expresses the esterase would be used as the bioremediation agent.

In addition, the enzyme of the present invention may be used in in Tritro assays for identifying resistance breakers amongst an array of alternative organophosphates and esterase inhibitors. By using the enzyme of the present invention, organophosphates can be screened for resistance to the enzyme activity. Such organophosphates could then be used in situations where resistance is of concern.

In order that the nature of the present invention may be more clearly understood preferred forms thereof will now be described with reference to the following non-limiting examples.

Example 1: Determination in Lucilia cuprina of Diethyl Phosphate from Esterase Hydrolysis of Paraoxon Diethyl phosphate from esterase hydrolysis of paraoxon was determined accurately by capillary gas chromatography/chemical ionisation mass spectrometry, using specially synthesised diethyl- 2

H

10 phosphate as internal standard.

SUBSTITUTE SHEET (Rule 26) a WO 95/19440 PCT/AU95/00016 Samples of resistant and susceptible L. cuprina homogenates were incubated with paraoxon for defined periods then snap-frozen to quench further metabolism. A known quantity of internal standard was added to each sample, which was then extracted twice by vortex-mixing with dichloromethane (100pl) to denature the proteins and to remove lipophiles, including any remaining paraoxon. The aqueous layer was separated and evaporated to dryness under a nitrogen stream. The residue was vortex-mixed with 75ip acetonitrile for 15 min, transferred to a 100pl glass conical vial and again evaporated to dryness under nitrogen. The residue was taken up in 30pl acetonitrile and 5tl N-methyl-N-tertbutyldimethylsilyl trifluoroacetamide added. The capped vial was vortex-mixed for 30 min at room temperature 0 C) and the solution was then extracted with pentane The separated pentane layer was washed once with acetonitrile (10pl) and stored at -20 0 C prior to mass spectrometry. Samples were introduced to the mass spectrometer (VG 70-70) by way of a directly coupled Hewlett Packard 5790 gas chromatograph, using cool oncolumn injection at 30 0 C to a 5% phenyl methylsilicone column (DB5, 30m by 0.32mm ID, 1.0pm phase thickness) preceded by a 4m retention gap. Silylated diethyl phosphate and its internal standard were eluted during temperature programming and detected for quantitative analysis in the mass spectrometer by selected ion monitoring of their respective (M ions generated by positive-ion chemical ionisation using ammonia as reagent plasma.

The results of the GC/MS assay for degradation of paraoxon by crude homogenates of Lucilia strains indicate two significant processes. First, hydrolysis of paraoxon into the diethyl phosphate (DEP) and para-nitrophenol moieties occurs at a rapid rate. Within the first minute of the assay significantly more DEP was produced by the SUBSTITUTE SHEET (Rule 26) auPI ~s~~BIIlIIM Y s~ II IIC I WO 95/19440 PCT/AU95/00016 6 homogenate of the resistant strain (ca. 1.3 nmol by Inverell 22) than the susceptible strain (ca. 0.95 nmol LBB101). Each of these strains are iso-chromosomal for the fourth chromosome, and thus are homozygous for the alternate alleles of the resistance-conferring enzyme, E3.

Thus, the difference in hydrolysis is indicative of differences at that locus.

The second, and surprising, result is that free DEP, which is what the assay measures, is rapidly sequestered or enzymatically altered after its release from paraoxon by E3. This activity is indicated by the steadily decreasing amount of free DEP over the course of the experiment. This activity is apparently not as rapid as the hydrolysis by E3, but is more stable in that it continues to remove DEP from solution in the face of hydrolysis of paraoxon. That this activity is actually non-specific binding of DEP to heterogeneous protein in the homogenate is suggested by the loss of DEP from the boiled control, where no enzymatic activity is expected.

To the extent that our ability to monitor hydrolysis is compromised by the binding of DEP to heterogeneous protein, it may be the case that the hydrolysis is significantly more rapid than estimated.

Example 2: Purification of Esterase 3 (E3) from OP-Sensitive Lucilia cuprina Homogenisation, Differential Centrifugation and Solubilisation of E3 The starting material was 200g of previously frozen, adult L. cuprina. Heads were removed by sieving and the thorax and abdomen retained. The latter were homogenised in fractionation butter (50mM Tris/HCl buffer, pH KC1, 5mM Mg.acetate, 350mM sucrose, phenylthiourea) on ice in a Sorvall blender. The homogenate was clarified by filtration through gauze then centrifugation (15000g, 30 minutes). The homogenate was recentrifuged (120000g, 70 minutes) and the pellet was SUBSTITUTE SHEET (Rule 26) aBQaBB B~Bi~rs WO 95/19440 PCT/AU95/0t0016 7 r pended in 100mM imidazole/HCl (pH 7.0) containing ImM EDTA and 0.05% Triton X-100. This suspension was frozen (-20 0 C, overnight) and thawed to solubilise E3.

Insoluble material was removed by centrifugation (15000g, 30 minutes) and filtration (0.45pm).

Chromatographic Steps Three chromatographic purification steps were performed using the Pharmacia FPLC system to control buffer flow rates and gradients. Firstly, anion exchange was performed using DEAE-sepharose equilibrated with imidazole/HCl (pH 7.0) containing 0.1% v/v Triton X-100, v/v glycerol and E3 was eluted using a gradient of this solution containing 0-1M NaCl. E3 containing fractions were pooled and subjected to gel filtration using a Superdex 200 (Pharmacia) column equilibrated and eluted with 50mM imidazole/HCl (pH 7.0) containing 0.1% v/v Triton X-100 and 10% v/v glycerol. E3 containing fractions were pooled and a second anion exchange separation was performed using a Mono Q column (strong anion exchanger, Pharmacia) with the same buffers as the first anion exchange separation.

Electrophoretic Steps An E3 containing fraction from the final chromatographic separation was concentrated and subjected to non-denaturing polyacrylamide gel electrophoresis (PAGE) (Huahes and Raftos, 1985). The region of the gel containing E3 activity was excised. Separation by denaturing PAGE (Laemmli, 1970) and silver staining for total protein (Biorad Silver Stain kit) revealed that a single polypeptide of 70kDa was present in the region of the non-denaturing gel containing E3.

In a modification of the above protocol, a selective precipitation step is added after solubilisation of E3.

Insoluble material is removed by centrifugation as above then an equal volume of 16% polyethylene glycol (PEG, average MW 2000) is added in 10mM imidazole/HCl (pH SUBSTITUTE SHEET (Rule 26) U--"-811sll-Ip sU-P WO 95/19440 PCT/AU95/00016 8 containing 10% glycerol. The solution is incubated on ice for 1 hour then centrifuged (10000g, 15 minutes).

The 8% PEG precipitate is resuspended in about of 10mM imidazole/HCl (pH 7.0) containing 10% glycerol and subjected to isoelectric focussing (IEF). IEF is performed using a Biorad "Rotofor" apparatus. Three ml of ampholytes (Pharmalyte pH 4-6.5, Pharmacia) and glycerol were added to partially purified E3, bringing the total volume to 50ml, the volume of the Rotofor focussing chamber. An antifreeze solution at -8 0 C is circulated through the apparatus to achieve a temperature in the focussing chamber of around 2 0 C. The sample is focussed for 4 hours at 12 watts, during which time the voltage rises from around 300 to 900 volts. Twenty fractions are harvested and E3 is found to focus and precipitate at around pH 4.9. The E3 containing fractions are pooled and centrifuged (10000g, 15 minutes). The pellet is first resuspended and centrifuged in buffer lacking Triton X-100 (10000g, 15 minutes), then in the same buffer containing 1% Triton X-100. The supernatant from the last centrifugation is retained for anion exchange chromatography.

Anion exchange chromatography is performed as described above using the Mono Q column and the DEAE column is omitted. A further gel filtration step using a Pharmacia Superose 6 column) and electrophoresis as described above, may be required at this stage.

Example 3: Isolation and Cloning of the Gene Encoding OP-Sensitive L. cuprina E3 The E3 gene of L. cuprina has been mapped using classical genetic techniques to chromosome 4 (Raftos D.A., Pesticide Biochemistry and Physiology Vol. 26:302, 1986), and the likely homologue of E3 in D. melanogaster, EST23, has been mapped to the right arm of chromosome 3 in the vicinity of the gene encoding the major SUBSTITUTE SHEET (Rule 26) ,isll.-,-rPfiaPI r~g ll~slls~ WO 95/19440 PCT/AU95/00016 9 a-carboxylesterase, EST9. Chromosome 3R in D. melanogaster is homologous to chromosome 4 in L. cuprina. The EST9 gene had been mapped previously to cytological location 84D3-5. Fine structure deficiency mapping experiments were used to localise EST23 to cytological region 84D3 to El-2, the region encompassing EST9 (Spackman et al, 1994).

In order to clone the E3 gene from L. cuprina, it was decided to use the molecular genetic techniques available for D. mslanogaster to clone the E3 homologue and use these clones as probes to isolate the L. cuprina genes themselves.

The route which proved productive used a yeast artificial chromosome (YAC) clone (termed DY219) containing 300kb of DNA from the 84D3-10 region of chromosome 3R (Ajioka, Smoller, Jones, R.W., Carulli, Vallek, Garza, Link, A.J., Duncan, I.W. and Hartl, Chromosoma 100:495, 1991).

This resulted in the isolation of a 90kb stretch of DNA containing 11 regions of homology to consensus esterase oligonucleotide probes, defining 10 esterase genes.

In order to clone the homologous L. cuprina esterase genes, cluster-specific esterase primers were synthesised and used in PCR reactions to amplify the relevant genes from both L. cuprina genomic DNA and cDNA. Reactions were carried out under standard conditions: SUBSTITUTE SHEET (Rule 26) c ~ltllPs~Blr~lRllarm~ -i L I PCT/AU95/00016 WO 95/19440 Final concentration/amount Template DNA 100 1000ng primer A* In mole primer B* In mole Buffer 10mM Tris-HCI (pH 1.5mM MgCl 2 KC1.

dNTP's 0.2mM each Taq polymerase 2 units Total Volume Primer pa-.rs for experiments involving genomic DNA were: Primer A: 5' GGIWSIGARGAYTGYYTITAYYTNAAYGTNTA 3' Primer B: 5' YTGRTCYTTIARICCIGCRTTNCCNGGNAC 3' Primer pairs for experiments involving cDNA were: Primer A: 5' ATHCCITWTGCIVMICCICCIBTNGG 3' Primer B: as for genomic DNA experiment.

.0 Note: IUB codes for mixed positions are used.

I inosine, which was used in positions of 4-fold redundancy PCR conditions: 97 0 C 35" 45 0 C 60°C 97 0 C 35" 50°C 2' 72 0

C

2' 3 cycles 1' 27-37 cycles Reaction products were visualised by agarose gel electrophoresis.

Bands unique to 2 primer reactions from genomic DNA were gel-purified and subjected to a further 30 rounds of amplification. Resultant bands were then gel purified, cloned and sequenced. Bands derived from genomic DNA varied in size, the differences presumably resulting from the presence of introns at two potential sites between all four possible combinations of primers. The four major SUBSTITUTE SHEET (Rule 26) ~I r~r C-dPP~ I~BIR) ~IIJI WO 95/19440 PCT/AU95/00016 11 bands obtained were cloned and sequenced and all were shown to contain esterase encoding sequences.

cDNA derived from late larval fat bodies (known to be enriched for the E3 protein) were chosen as templates in PCR reactions. Bulk DNA was prepared from a cDNA library of the tissue and PCR reactions were carried out as for genomic DNA, except that the candidate esterase fragments could be identified directly by their characteristic size as predicted from D. melanogaster sequence data.

In summary, five esterase amplicons were isolated from L. cuprina genomic DNA. One of these (LcaE7) was also isolated from larval fat body cDNA and showed direct homology with gene DmaE7 of the D. melanogaster cluster.

This L. cuprina cluster member (LcaE7) was chosen as a candidate for the gene E3 as Northern blot analysis showed that it is expressed in the same life stages as those exhibiting E3 enzyme activity.

One cDNA has been cloned from a larval fat body cDNA library and six more have been cloned from a pupal cDNA library. One of the pupal cDNAs was probably full-length and therefore sequenced completely. Table 1 shows the DNA and inferred amino acid sequence of the OP-sensitive E3 (clone Lc743) and Table 2 shows the level of inferred amino acid similarity between D. melanogaster DmaE7 and LcaE7 (clone Lc743).

The pupal LcaE7 cDNA has now been expressed using a baculovirus vector transfected into an insect cell line (see below for details of method). The expression product was run on a PAGE and stained strongly with a- and Pnaphthyl acetate. This result confirmed that LcaE7 encodes a susceptible E3 esterase.

SUBSTITUTE SHEET (RULE 26) WO 95/19440 PC/AU95/06016 12 Table 1. Miiltiple nucleotide alignment of the four diazinon-resistant clones (LlO3A-D) and consensus (LlO3con) with the reference susceptible clone (Lc743) of LcaE7 (M3).

Dots indicate identity with the Lc743 susceptible clone and a dash in the sequence represents a missing nucleotide. Below the ruler is the aligned nucleotide sequence and above is the inferred amino acid sequence of Lc743 with t~e five replacements fbund in Lc7LlO3con indicated in bold text irmmediately below. Nucleotides are numbered from the translation start site.

Lc743 M N F N V S L M E K L K W K I K C I E N LlQ3con 1 +4.60 Lc7 43 ATGArnTCAACGTAGTTGATGGAGAAATTAAMTGGAAGATTAAATGCATTGAAAAT L103A L103B L103C L103D Ll03con Lc743 KF LNY R LT T NE TV VA ET EY G L103con 120 Lc 743 AAG=rTTAAACTATCGTTAACTACCAATGAAACGGTGG^TAGCTGAAACTGAATh.7GC L103A o L103B L103con Lc743 K V K G V/ K R L T V Y D D S Y Y S F R G '.103con 121 180 Lc 743 AAA(ITGAAAGGCGTAAACG7rTAACTGTGTACGATGATTCCTACTACAGTTITGAGG;GT L103A L103C L103D Ll03con Lc743 I P Y A Q P P V G E L Rc F K A P Q R P T' LlO3con 240 Lc 743 ATACCGTACGCCCAACCGCCAGTGGGTGAGC2'GAGATTTIAAAGCACCCCAGCGACCACA L103A L103B L103C

A-.

L103con SUBSTITUTE SHEET (Rule. 26) WO 95/19440 PCT/AU95/00016 13 Lc743 P W D G V R D C C N H K D K S V Q D F L103con 241 300 Lc743 CCCTGGGATGGTGTGCGTGATTGTTGCAATCATAAAGATAAGTCAGTGCAAGTTGATTTT :103A L103B L103C L103D Ll03con Lc743 I T G K V C G S E D C L Y L S V Y T N N L103con 301 360 Lc743 ATAACGGGCAAAGTGTGTGGCTCAGAGGATTGTCTATACCTAAGTGTCTATACGAATAAT L103A T..A L103B C L103C T..A L103D T..A C Ll03con T..A C Lc743 L N P E T K R P V L V Y I H G G G F I I L103con D 361 420 Lc743 CTAAATCCCGAAACTAAACGTCCCGTTTTAGTATACATACATGGTCGTGGTTTTATTATC L103A A L103B A L103C A L103D A L103con A Lc743 G E N H R D M Y G P D Y F I K K D V V L L103con 421 480 Lc743 GGTGAAAATCATCGTGATATGTATGGTCCTGATTATTTCATTAAAAAGGATGTGGTGTTG L103A L103B L103C L 103D L103con Lc743 I N I Q Y R L G A L G F L S L N S E D L Ll03con 481 Lc743 ATTAACATACAATATCGTTTGGGAGCTCTAGGTTTTCTAAGrTTAAATTCAGAAGACCTT L103A L103B L103C L 103D Ll03con SUBSTITUTE SHEET (Rule 26) WO 95/19440 PCTAIJ95OOOI6 14 LOU4 N V P C N A G L K D Q V M A L R W I K N LlO3con 541 Lc 743 AATGTGCCCGGTAATGCCGGCCT'rAAAGATCAAGTCATCGCCTTGCGTrGGATTAAAAAT L103A L103C L103D LlO3con Lc743 N C A N F G G N P D N I T V F G E S A G L103con Lc7 43 ATTGCGCCAACTTTGGTGGCAATCCCGATAATAT'ACAGTCTTTGGTGAAAGTGCCGGT L103A .0 L103B L103C L103D L1O3con Lc743 A A S T H Y M M L T E Q T R G L F H R G L103con Lc7 43 GCTGCCTCTACCCACTACATGATGTTAACCGAACAAACTCGCGGrCTITTCCATCGTGGT L103A L103B L103C L103D.. L103con Lc743 I L M S G N A I C P W A N T Q C Q H R A L103con Lc 743 ATACTAATGTCGGGTAATGCTA'TPGTCCATGGGCTAATACCCAATGTCAACATCGTCC L103A.. L103B L103D L1O3con Lc743 F T L A K L A G Y K G E n N D K D V L E L1O3con...... V Lc7 43 TTCACCTTAGCCAAATTGGCCGGCTATAAGGGTGAGGATAATGATAAGGATGTTIGGAA

G

G

SUBSTITT SBEET (Rule 26) WO 95/19440 PCT/A1195100016 Lc743 F L M K A K P Q D L I K L E E K V L T L L103con L Lc 743 TI'CTTATGAAAGCCAAGCCACAGGAT'ITAATAAAACTTGAGGAAAAAGTTTI'AACTCTA Lc743 EE R T NK V-MF P FG P TVE P YQ T LlO3con Lc 743 GAAGAGCGTACAM.TAAGGTCATGTT'TCCTTITGGTCCCACTGTTGAGCCATATCAGACC L103A L103B L103D LlO3con Lc7 43 GCTGATTGTGTCTTACCCAAACATCCTCGGGAAATGGT1'AAAACTGCTTGGGGTAkIT7CG CA CA L103C CA CA CA Lc743 I P T M M G N T S Y E G L F F T S I L K L103con.. 1021 1080 Lc 743 ATACCCACTATGATGGGTAACACTTCATATGAGGGTCTATTTTTCAC'TrCAATTCTTAAG GT GT Lc743 Q M P M L V K E L E T C V N F V P S E L LlO3con 1081 Lc7 43 CAAATGCCTATGCTTGTDAAGGAATTGGA.AACTTGTGTCAATTiTTGTGCCAAGTGAATTG L103A .0 L103B L103C L1.03D L1O3con SUBSTITUTE SHEET (Rule 26) WO 95119440 PCTAU95OOOI6 16 L~C743 A D A E R T A P E T L E M G A K I K K A L1O3con 1141 LC74 3 GCTGATGCTGAACGCACCGCCCCAGAGACCrrGGAAATGGGTGCTAAAATTAAAAAGGCT L103B L103C L103D L1O3con Lc743 H V T G E T P T A D N F M D L C S H I Y L103con 1201 Lc 743 CATGTTACAGGAGACACCAACAGCTGATAA!TTTATGGATCTTTGCTCTCACATCTAT C..C C..C Lc743 F W F P M H R L L Q L R F N H T S G T P LlO3con 1261 Lc 743 TTCTGGTTCCCCATGCATCGTTTGTTGCAAITACGTTTCAATCACACCTCCGGTACACCC Lc743 V Y L Y R F D F D S E D L I N P Y R I M L10O3con 1321 Lc 743 GTCTACTTGTATCGCTTCGACTTTGATTCGGAAGATCTTATTAATCCCTATCGTATTATG Lc743 R S G R G V K G V S H A D E L T Y F F W LlO3con 14 1381 Lc7 43 CGTAGTGGACGTGGTGTTAAGGGTTTAGTCATGCTGATGAATTACCTAITCTCTGG L103A L103B L103C L103D L103con SUBSTITUTE SHEET (Rule 26) WO 95/19440 PCTAU95/00016 17 Lc743 N Q L A K R M P K E S R E Y K T I E R M Ll03con I.

Lc7 43 AATCAATTGGCCAAACGTATGCCTAAAGAATCGCGTGAATACAAAACAATTGAACGTATG

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L103C Lc743 T G 1 W I Q F A T T G N P Y S N E I E G Ll03con 1501 Lc7 43 ACTGGTATATGGATACAATTTGCCACCACTGGTAATCCTTATAGCAATGAAATTGAAGGT L103A L103B L103C L103D.. L103con Lc743 M E N V S W D P I K K S D E V Y K C L N LlO3con Lc74 3 ATGGAAAATGTTTCCTGGGATCCAATTAAGAAATCCGACGAAGTATACAAGTGTTTGAAT T L103B T T. Lc743 I S D E L K M I D V P E M D K I K Q W E L1O3con 1621 Lc 743 ATTAGTGACGAATTGAAAATGATTATGTGCCTGAAATGGATAAGATTAACAATGGGAA C. Lc743 S M F E K H R D L F L103con 1713 Lc 743 TCGATGTTrGAAAAACATAGAGATTTATTTTAG L103A L103B L103C L103D L1O3con SUTBSTrrUTh. SHEET (Rule 26)

I

WO 95/19440 PC7IAJ9SIOOO16 Table 2. Comparison of the inferred amino acid sequences of the OPsensitive E3 of L. cuprina (clone Lc743; top line) and its Drosophila melanogaster homologue, DmcxE7 (bottom line).

1 MNFNVSLMEKLKWKIKC IENKFLNYRLTTNETVVAETEYGKVKGVKRLTV 1 MNKNLGFVERIIIRKRLKT IEHKVQQYRQSTNET VVADTEYGQVRG IKRLSL 51 YDDSyYSFEG:ZPYAQPPVGELRFKAPQRPTPWDGVRDCCNHKDKSVQVDF 100 51 YDVPYFSFEGIPYAQPPVGELRFKAPQRPIPWEGVRDCSQPKDKAVQVQF 100 101 ITGKVCGSEDCLYLSTYTNNLNPETKRPVLVY IHGGGF IIGENHRDM4YGP 150 101 VFDKVEGSEDCLYLNVYTNNVKPDKARPVMVVWII{GGGF IIGEANREW4YGP 150 DYFIKKDVVLINIQYRLGALGFLSLNSEDLNVPGNAGLKDQVMALRWIKN 200 151 DYFMCEDVVLVTIQYRLGALGFMSLKSPELNVPGNAGLKDQVLALKWIKN 200 201 NCANFGGNPDNITVFGESAGAASTHYM'flTEQTRGLFIIRGILMSGNAIC p 250 201 NCASFGGDPNCITVFGESAGGASTHYMfrLTDQTQGLFHRGILQSGSAICP 250 251 WAP..NTQCQHRAFTLAKLAGYKGEDNDKDVLEFLMKAKPQDLIKLEEKVLT 299 251 WAYNGDITENPYRIAKLVGYKGEDNDKDVLEFLQNVKaKDLIRVEENVLT 300 300 LEERTNKVMFPFG PTVEPYQTADCVL PKHPREMVKTAWGNS IPTMMGNTS 349 301 LEERMKIMFRFGPSLEPFSTPECVISKPPKEMMKflTAWSNSIPMFIGNTS 350 350 YEGLFFTSILKQMPM~LVKELETCVNFVPSELADAERTAPETLEMGAKIKK 399 351 YEGLLWVPEVKLMPQVLQQLDAGTPFIPKELLATEPSKEKLDSWSAQIRD 400 400 AHVTGETPTADNFMDLCSHIYFWFPMHRLLQLRFNi{TSGTPVYLYRFDFD 449 401 VHRTGSESTPDNYMDLCSIYYFVFPALRVVESREAYAAGAPVYFYRYDFD 450 450 SEDLINPYRIMRSGRGVKGVSHADELTYFFWNQLAKMPKESREYKeTIER 499 451 SEELIFPYRIMRMGRGVKGVS {ADDLSYQFSSLLARRLPKESREYRNIER 500 500 MTGIWIQFATTGNPYSNEIEGMENVSWDPIKKSDEVYKCLNISDELF 4 ID 549 501 TVGIWTQFAATGNPYSEKINGMDTLTIDPVRKSDAVIKCLNISDDLKFID 550 550 VPE KIKQWESMFEKHRDLF. 570 551 LPEWPKLKVWESLJYDDNKDLLF 572 SUBSfTUTE SHEET (Rule 26) s;BDBPsa. WO 95/19440 PCT/AU95/00016 19 Example 4: Sequence of an OP-Resistant Allele of LcaE7 (E3) a) Cloning the OP-resistant allele of LcaE7 (E3).

A RT-PCR (reverse transcriptase-PCR) approach was used to clone a cDNA allele of LcaE7 from a diazinon resistant strain of L. cuprina (Llandillo 103) which is homozygous for the fourth chromosome.

Methods: Adults from the Llandillo 103 strain were aged for three days before collection and stored at -70 oC. RNA was prepared using a modified protocol of Chigwin et al.

(Chigwin, J. Przybyla, A. MacDonald, R. J. Rutter, W. 1979, Biochemistry 18, 5294). About 100 adults were thoroughly homogenised in 15ml of solution D (4M guanidinium thiocyanate, 25mM sodium citrate, pH sarkosyl, 0.1M p-mercaptoethanol) using a Sorvall Omnimix blender. The resulting homogenate was filtered through glasswool and 6 ml layered on top of 5ml of 4.8M CsCl, made up in 10mM EDTA, pH 8, in an SW41 ultrascentrifuge tube. These were spun at 35,000 rpm in an SW41 rotor for 16hr at 15 OC. The supernatent was removed and the RNA pellet resuspended in 400il of DEPC-treated The RNA was precipitated by the addition of 800il of ethanol and 10p of 4M NaCI and stored under ethanol at 20 OC. Before use the RNA pellet was washed in 75% ethanol and air dried before resuspension in DEPC-treated PolyA+ RNA was prepared from 500pg of total RNA using affinity chromotography on oligo-dT cellulose (Pharmacia; Sambrook, Fritsch, E. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory Press, USA). The resulting mRNA was again precipitated, washed and resuspended in of DEPC-treated H20. Oligo-dT primed cDNA was made from l.g of mRNA using reverse transcriptase (Superscript II, BRL) as per the manufacturers instructions in a 204l volumn reaction. 200ng of cDNA was used as template in a SUBSTITUTE SHEET (Rule 26) b- 9p1~ WO 95/19440 PCT/AU95/00016 PCR reaction using primers designed from the 5' (Lc743 atgaatttcaacgttagtttgatgga and complementry 3' (Lc743 5' ctaaaataaatctctatgtttttcaaac ends of the coding region of the LcaE7 gene (clone Lc743). Reactions used the proof reading UlTma thermostable polymerase (Perkin-Elmer) and contained 500pmoles of each primer, of each dNTP, 10mM Tris-HC1, pH 8.8, 10mM KC1, 0.002% Tween 20 2mM MgC12, and 200ng of template. Two drops of mineral oil were layered over each 50pl reaction.

Six units of UlTma enzyme was added after a 5 minute "hot start" at 97 °C and was followed by 40 cycles of seconds at 97 OC, 1 minute at 60 OC and 2 minutes at 72 oC. A final cycle of 72 OC for 8 minutes was included. The 1.7 kb major product was gel purified and cloned into the EcoRV cleavage site of the pBSK- plasmid vector (Stratagene) using conventional cloning techniques (Sambrook, Fritsch, E. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory Press, USA). Ten units of the restriction enzyme EcoRV was included in ligation reactions to cleave any self-ligated vector.

b) Sequence of the OP-resistant allele of LcaE7 (E3).

Four clones were chosen for sequencing (Lc7L103 A-D), three of which were derived from independent PCR reactions. A set of twelve 21-mer sequencing primers (sequence shown below) were designed from the existing LcaE7 sequence: SUBSTITUTE SHEET (Rule 26) L I llPl 31111 WO 95/19440 WO 9519440PCT/AU9/O0O16 primer seq primer name 5' position in Lc743 sequence j ggatggtgtgcgtgattgttg MF 246 aaaaggatgtggtgttgatta 7F2 465 actaatgtcgggtaatgctat 7F3 723 cactatgatgggtaacacttc 7F4 1026 tgttacaggagaaacaccaac 7F5 1203 agaat,:gcgtgaatacaaaac 7F6 1468 acggtataccctcaaaactgt 7R1 187 tcccaaacgatattgtatgtt 7R2 505 acatcatgtagtgggtagagg 7R3 686 ccgaggatgtttgggtaagac 7R4 981 tatcagctgttggtgtttctc 7R5 1232 acgcgattctttaggcatacg 7R6 1477 These, in conjuction with the end primers Lc743 and Lc743 were used in dye-terminator sequencing reactions (ABt) conducted following manufacturer's instructions in 25pLl capillary tubes inr a Corbett Research capillary thermal cycler, except that S0pmoles of primer was used per reaction, a "hot start" of 96 0 C for 3 minutes SUBSTITUT SHEET (Rule 26) WO 95/19440 PCT/AU95/00016 22 was included and 30 cycles were completed for each sequencing reaction. Dye primer reactions were also conducted on all four clones using the ABI M13 forward and reverse primers as per ABI protocols using the same template DNA. Sequencing reactions were resolved by electrophoresis on an ABI 370A automatic sequencing machine as per the manufacturer's instructions. This resulted in both strands being sequenced entirely.

Results: Table 1 shows a nucleotide alignment of the four resistant clones (Lc7L103A-D) compared with the reference susceptible clone (Lc743) of LccE7. A consensus sequence of the OP-resistant LcaE7 allele was determined (Lc7L103con). Differences between resistant clones were assumed to be errors incorporated by the UlTma polymerase.

c) Sequence of the oxyanion hole region of various LcE7 alleles When comparing the susceptible sequence (Lc743) with that of the resistant Llandillo 103 consensus sequence (Lc7Li03con), thirteen silent and five replacement differences where identified. The positions of the five replacement differences where mapped onto the homologous positions in the primary amino acid sequence of acetylcholine esterase (AChE; Sussman, Harel, M., Frolov, Ocfner, Goldman, Toker, L. and Silman, 1991, Science 253, 872) from the electric ray, Torpedo californica, by aligning the primary amino acid sequence of the two proteins. The homologous amino acids where highlighted on a three-dimentional model of T. californica AChE. Only one replacement site difference resulted in a change in the active site region of the enzyme (oxyanion hole): the glycine to aspartic acid substitution at nucleotide position 411 (Table 1).

SUBSTITUTE SHEET (RULE 26) WO 95/19440 PCT/AU95/00016 23 Methods: This nucleotide position was then sampled over a range of strains which are homozygous for chromosome IV and of known diazinon resistance status. Genomic DNA was prepared from either eggs using the method of Davis, L.

Dibner, M. and Batley, J. (1986. Basic Methods in Molecular Biology, Elsavie- Science Publ. Co., New York, Section 5.3 or from adult flies using a C-TAB method (Crozier, Y. Koulianos, S. Crozier, R. H., 1991, Experientia 47, 968-969). lpg samples were then used as templates in PCR reactions using 100pmoles of the primers 7F1 and 7R4. Also included in the reactions were 0.2mM of each dNTP, 10mM Tris-HCl, pH 8.3, 50mM KC1, MgCl2. Two drops of mineral oil were layered over each 50pl reaction. 2.5 units of Taq polymerase was added after a "hot start" of 97 0 C for 3 minutes while an annealing temperature of 55 0 C was maintained. An initial extention at 72 0 C was held for 2 minutes. This was followed by 34 rounds of 97 0 C for 35 seconds, 55 0 C for 1 minute and 72 0

C

for 1 minute. A final extention of 72 0 C for 9 minutes was included. A single product of about 1kb was produced. This was purified for sequencing using QIAquick spin columns (Qiagen), following manufacturer's instructions. 1g of template was used in dye-terminator sequencing reactions using the 7R2 primer as described above.

Results: Of the 14 strains assayed, all seven diazinon susceptible strains (LS2, Llandillo 104, LBB101 and four malathion resistant strains, der-R, Woodside 5.2, Hampton Hill 6.1, Hampton Hill 6.2) possess a G at nucleotide postion 411, whereas all six diazinon resistant strains (Llandillo 103, Gunning 107, der-S, Q4, Sunbury 5.2, Strathfieldsaye 4.1) possess an A at this position, resulting in a Gly to Asp substitution at amino acid position 137.

SUBSITUTE SHEET (RULE 26)

I

WO 95/19440 PCT/AU95/00016 24 Example 4: Hydrolytic Activity of the E3 Enzyme a) In vitro expression of LcaE7 alleles Methods: The susceptible (clone Lc743) and resistant (clone Lc7L103D) alleles of LccE7 were cloned into the baculovirus transfer vector, Bacpac 8 (Clonetech), 3' of the polyhedrin promoter. Transfec-ions were conducted using a lipofection method with polybrene (Sigma) according to King, L. A. Possee, R. D. (The Baculovirus Expression System: A Laboratory Guide, Chapman Hall, London, 1992). One g of DNA of each of the resulting constructs together with 200 ng of Bacpac 6 baculovirus DNA (Clonetech), linearised by digestion with the restriction enzyme BSU 361 (Progema), was incubated in a solution of hepes buffered saline containing polybrene (Sigma) at room temperature for 10 minutes. The solution was then used to transfect a single well of a six well tissue culture plate pre-seeded 2 hr previously with 104 Sf9 (Spodoptera frugiperda) cells in 1.5 ml Grace's medium (King, L. A. Possee, R. D, The Baculovirus Expression System: A Laboratory Guide, Chapman Hall, London, 1992). After 12 hr, the medium was removed, made up to 10% DMSO and placed back over the cells for minutes. This was then replaced with 3 ml of Grace's medium containing 10% fetal calf serum. Construct plus polybrene, linearised virus plus polybrene and polybrene only controls were conducted in parallel with transfections. The transfections were harvested 4-5 days after infection and the cells isolated by centrifugation at 500g for 5 minutes. Aliquots of the resulting supernatent were immediately stored on ice for the following chlorfenvinphos hydrolysis assay work or frozen at -20 0 C as virion stocks.

SUBSTITUTE SHEET (Rule 26) r~ II WO 95/19440 PCT/AU95/00016 b) Radiometric partition assay for OP hydrolysis Methods: Enzyme samples were diluted in 0.1 M imidazole-HC1 buffer pH 7.0 ("imidazole buffer") to a final volume of 4l. Reactions were started by the addition of 25 p1 of 14 C-ethyl]-chlorfenvinphos (CFVP, 306.5 MBq/mmole, Internationale Isotope Minchen) diluted in imidazole buffer from a 7.5mM stock solution in ethanol. The final chlorfenvinphos concentration was typically 50 or 75 gM for routine assays but can be much lower for the determination of kinetic parameters. The reaction was incubated at 30 0 C and stopped by the addition of 300 i dichloromethane and 150 l of imidazole buffer containing gM diethylphosphate (Eastman Kodak) followed by vigourous vortex mixing. The reactions were centrifuged to separate phases and 150 il of the upper, aqueous phase was taken for scintillation counting to determine the amount of 14 C-diethylphosphate produced by hydrolysis of CFVP. Incubations with boiled enzyme were also performed to control for non-enzymic hydrolysis of CFVP.

Results: Whole-fly homogenates: Assays were carried out on whole-fly homogenates using 50 M CFVP. Homogenates derived from an OP-resistant strain of L. cuprina (RM2-6 [der-S]) exhibited an initial rate of hydrolysis of 7.7 pmol/min/mg protein. The boiled control hydrolysed CFVP at a rate of 0.48 pmol/min/mg protein. Homogenates derived from an OP-susceptible strain (LS2) hydrolysed CFVP at the same rate as the boiled control, indicating the absence of CFVP hydrolytic enzymic activity in OP-susceptible L.

cuprina.

SUBSTITUTE SHEET (Rule 26) ncervl3a WO 95/19440 PCT/AU95/00016 26 Preliminary kinetic experiments indicated a Vmax of approximately 13pmol/min/mg protein for the hydrolysis of CFVP by homogenates derived from the resistant strain.

(ii) LcaE7 4E3) expressed in vitro: Enzyme expressed from the OP susceptible allele (Lc743) exhibited no hydrolysis of CFVP. However, this enzyme was able to hydrolyse a-naphthol acetate (aNA). In contrast, cells expressing the OP resistant allele (Lc7L103D) hydrolysed CFVP with a Vmax of approximately 2.0 nmol/min/mg protein, but did not have elevated, or indeed any, aNA hydrolytic activity.

Preliminary kinetic experiments indicated that the Km of the CFVP hydrolysing enzymes is approximately 16 uM in both the RM2-6 homogenate and cells expressing the Lc7L103D allele.

c) Radiometric partition assay for malathion hydrolysis Methods: Malathion carboxylesterase (MCE) activity was assayed using the partition method of Ziegler, Whyard, Downe, A. E. Wyatt, G. R. Walker, V. K., (Pesticide Biochemistry and Physiology 28: 279, 1987) as modified by Whyard, Russell, R. J. Walker, V. K.

(Biochemical Genetics 32: 9, 1994). Supernatants (6041) from cell cultures containing recombinant baculovirus (as well as controls) were added to 15l of dilution buffer imidazole-HCl, pH7.0) in duplicate microfuge tubes.

Reactions were started by the addition of 751 dilution buffer containing [1 4 C]-malathion [Amersham; 103 mCi/mmole, 280nCi, labelled at both the methylene carbons of the succinate moiety, adjusted to 37.54M by the addition of unlabelled malathion Riedel-de-Ha6n Ag., Seelze, Germany]. The assay mixture was incubated at for one hour, then 300gl of dilution buffer was added and SUBSTITUTE SHEET (Rule 26) i- WO 95/19440 PCT/AU95/00016 27 the undegraded malathion extracted three times with 90041 of chloroform. The concentration of carboxylic acids of malathion in 300l of aqueous phase was determined by liquid scintillation. Protein concentrations in the cell supernatants were determined by the method of Bradford, Analytical Biochemistry 72:..48 (1976) with bovine serum albumin as the standard. The non-enzymatic degradation of malathion and/or degradation by enzymes produced by the cells was corrected for by subtracting the activity of supernatant from cells infected with nonrecombinant baculovirus.

Results: Initial rates of malathion hydrolysis by the supernatant of cells expressing the OP susceptible allele, Lc473, was 3.3 pmole/min/gl from an in..tial concentration of 4 gM malathion. However, the enzyne is inhibited by malathion, with a half-life of about 20 minutes, in the presence of 4 gM malathion. This has been shown both by determining the amount of 14 C-malathion hydrolysed after time intervals and by determining the rate of c-NA hydrolysis after of preincubation of the enzyme with nonradiolabeled malathion for various times. In the absence of malathion there was only slight loss of enzyme activity under these conditions for at least 20 hours. It is clear that g2eater rates of hydrolysis occur with greater concentrations of malathion but these assays did not take inhibition of the enzyme into account. Malathion hydrolysis (0.5 pmoles/min/gl) was also detected in the supernatant of cells expressing the D. melanogaster homologue, DmaE7.

The enzyme expressed from the OP resistant allele of LcaE7, Lc7L103D, was not tested for malathion hydrolysis because strains resistant to general OPs are susceptible to malathion (Smyth, Boyce, T- Russell, R. J.

and Oakeshott, J. in preparati,n). The OP resistant SUBSTITUTE SHEET (Rule 26) s -d p a~-sa II WO 95/19440 PCT/AU95/09016 28 form of LccE7 (E3) would not therefore be expected to hydrolyse malathion.

Example 5: Restriction Fragment Length Polymorphism (RFLP) Analysis of L. cuprina in the Vicinity of the LcaE7 (E3) Gene An effort was also made to generate accurate genomic restriction maps for a number of representatives of each of the allelic classes of LcaE7, and to examine the maps for restriction patterns which are diagnostic for resistance. This data could then form the basis of a quick screen for the OP resistance alleles among field strains of L. cuprina.

Methods: Fourth chromosomes of L. cuprina were isolated from field and laboratory populations and made homozygous via a crossing scheme. Individual wild-caught or laboratory flies were mated to flies heterozygous for Bal IV. Bal IV is a fourth chromosome carrying the dominant, homozygous lethal mutation Sh (short setae), the recessive marker gl (golden halteres) and multiple inversions (numbers 6, 8, and 12) to suppress recombination between this chromosome and wild type chromosomes when occurring together in heterozygotes. Single Sh/+ flies from the Fl generation were crossed again to Bal IV and Sh/+ flies from that cross selfed to generate lines homozygous for the fourth chromosome.

Dose-mortality responses were determined by topical application of 1 l of increasing concentrations of diazinon in acetone to the thorax of adult flies.

Total DNA was isolated from eggs of each strain by the method of L. G. Davis, M. D. Dibner, and J. F. Batley, (1986. Basic Methods in Molecular Biology, Elsavier Science Publ. Co., New York, Section 5.3 Restriction SUBSTITUTE SHEET (RULE 26) c- p~ WO 95/19440 PCTAU95/00016 29 enzyme maps were created by single and double digestion of DNA with restriction enzymes following manufacturer's recommendations. Digested DNA was electrophoresed in 0.8% agarose gels in 0.5X TBE pH 8.0 and transferred to uncharged nylon membrane (Genescreen®) by the method of D.

F. Westneat, W. A. Noon, H. K. Reeve, and C. F. Aquadro (1988. Nucleic Acids Research. 16, 4161) after acid depurination in 0.25M HCI for 7 min. The membranes were probed with 32P labeled DNA via random primed extension P. Feinberg and B. Vogelstein, 1983. Analytical Biochemistry 132, 6-13 using LcaE7 cDNA as template in the hybridisation solution of Westneat et al. (1988) at 0 C overnight. The membranes were washed in 40 mM phosphate buffer pH 7.2, 1 mM EDTA, 1 SDS twice at room temperature for 5 min., then twice at 55 0 C for 15 min.

prior to autoradiography.

Results: Across all lines examined to date, three different haplotype classes have been discovered for LcaE7 using seven restriction enzymes (Table Differences among haplotypes are the result of both gains and losses of restriction sites and changes in fragment sizes resulting from insertions or deletions of DNA sequence. Insertion and deletion variation occurs only within the susceptible (halplotype A) class (Table Other than this size variation, there is little apparent sequence variation within each class of LcaE7 allele.

Through a combination of restriction site differences, and fragment size differences resulting from apparent insertions and deletions, haplotypes can be used to predict diazinon resistance status using the data gathered here. In particular, for most haplotypes, Eco RI restriction fragment sizes appear to be diagnostic for resistance status, and could be used to assay resistance levels in the field.

SUBSTITUTE SHEET (Rule 26) ~u I s~u~ WO 95/19440 FCT/AU95/00016 Because of the generally low amount of variation found within each haplotype class, restriction site or sequence differences discovered in cDNA sequence data from the different classes should both have value as diagnostics for diazinon resistance. However, the presence of the oxyanion hole mutation (glycine to aspartic acid at nucleotide position 411) is not completely congruent with haplotype class as defined by these restriction sites. In particular, the chromosomes of susceptible line Flinders Island B5.2a and that of the resistant line Gunning 107 appear identical at the RFLP level, although they differ in their oxyanion hole sequence. This difference, itself, however, can be used to distinguish the two alleles via restriction digests with the enzyme Hph I, which recognises the mutant sequence (GGTGAn8) but not the susceptible sequence (GGTGG...) at site 411.

SUBSTITUTE SHEET (Rule 26) i Y~ I II _~bC-~PLBS~U WO 95/19440 PCT/AU95/00016 Table 3.

Line Diazinon resistance status Flinders Island Susceptible B5.2a Hampton Hill Susceptible 6.1 LS2 Susceptible LBB101 Susceptible Llandillo 104 Susceptible der-R Susceptible Woodside 5.2 Susceptible RopRmal-1 Susceptible M27.1.4.1 Susceptible Belpor 1.2 Susceptible Oxyanion hole residue @137 Glycine Glycine Glycine Glycine Glycine Glycine Haplotype class

A

A

A'

A"'

B

B

B

B

B

CFVP

hydrolysis no no Gunning 107 Llandillo 103 Sunbury 5.2 RM 2-6 (der-S) Strathfieldsaye 4.1 Q4 Resistant Resistant Resistant Resistant Resistant Resistant Aspartic Acid Aspartic Acid Aspartic Acid Aspartic Acid Aspartic Acid Aspartic Acid yes yes yes indicates not yet determined.

indicates the presence of the resistance associated mutation at nucleotide 411.

indicate various insertions and deletions that change fragment sizes but not homologous restriction site sequences.

As will be clear to persons skilled in the art the present inventors have developed a protocol whereby a SUBSTTUTE SHEET (Rule 26)

-PI~~

WO 95/19440 PCT/AU95/00016 32 resistant E3 esterase can be obtained in a substantially pure form. Such a purified enzyme can then be used in a probing strategy to obtain a nucleotide sequence encoding this resistant enzyme. Further, the present inventors have elucidated cDNA sequences encoding resistant E3s.

The present inventors have also developed a genetic test to -creen for organophosphate resistance.

It will be appreciated by persons skilled in the art that numerous variations and/or modifications may be made to the invention as shown in the specific embodiments without departing from the spirit or scope of the invention as broadly described. The present embodiments are, therefore, to be considered in all respects as illustrative and not restrictive.

SUBSTITUTE SHEET (Rule 26) heh.

Claims (10)

1. E3 esterase from Lucilia cuprina, in substantially pure form.

2. An E3 esterase as claimed in claim 1 in which the E3 esterase is from one of the isochromosomal OP-resistant L. cuprina strains selected from the group consisting of der-S, Inverell 22, Landillo 103 and Sunbury 5.2.

3. An isolated DNA molecule comprising a nucleotide sequence encoding a Lucilia cuprina E3 esterase nr portion thereof capable of hydrolysing organophosphates and/or carbamate pesticide residues.

4. An isolated DNA molecule as claimed in claim 3 in which the isolated DNA molecule comprises a nucleotide sequence encoding an E3 esterase or portion thereof, from an OP-resistant strain of L. cuprina. An isolated DNA molecule as claimed in claim 3 or claim 4 in which the isolated DNA molecule comprises a nucleotide sequence substantialy as shown in Table 3.

6. A cell which expresses E3 esterase in which the cell is transformed with a DNA molecule as claimed in in any one of claims 3 to

7. A cell as claimed in claim 6 in which the cell is a prokaryotic cell or an insect cell.

8. An E3 esterase produced by a cell as claimed in claim 6 or claim 7.

9. A method of eliminating or reducing the concentration of organophosphate and/or carbamate pesticide residues in a contaminated sample or substance, the method comprising contacting the sample or substance with an E3 esterase as claimed in claim 1 or claim 2 or an E3 esterase encoded by the DNA molecule as claimed in any one of claims 3 to A method of eliminating or reducing the concentration of organophosphate and/or carbamate pesticide residues in a contaminated sample or substance, SUBSTITUTE SHEET (Rule 26) 1. se~-s~ ~sea BS~f~bPY WO 95/19440 PCT/AU95/00016 34 the method comprising contacting the sample or substance with a cell as claimed in claim 6 or claim 7.

11. A method of assessing the susceptibility of a strain of L. cuprina to organophosphates comprising analysing the genotype of the strain in respect to LcaE7.

12. A method as claimed in claim 11 in which the analysis is by restriction fragment length polymorphisms. SUBSTITUTE SHEET (Rule 26) Bk INTERNATIONAL SEARCH REPORT u1111111 1uPo nluil I|IIL uIn oL IUi PCT/AU 95/00016 A. CLASSIFICATION OF SUBJECT MATTER Int. C1. 6 C12N 15/55, 9/16, 9/18, C12Q 1/68, C02F 1/58, 3/00 According to International Patent Classification (IPC) or to both national classification and IPC B. FIELDS SEARCHED Minimum documentation searched (classification system followed by classification symbols) ELECTRONIC DATABASES AS BELOW Documentation searched other than minimum documentation to the extent that such documents are included in the fields searched AU: IPC: C12N 9/16, 9/18, 15/55 Electronic data base consulted during the international search (name of data base, and where practicable, search terms used) DERWENT WPAT, BIOT: CHEMICAL ABSTRACTS CASM KEYWORDS: LUCILIA, CUPRINA, BLOWFLY, PLY, DIPTERA, DROSOPHILA, INSECT, ESTERASE, HYDROLASE, ENZYME, E3, ORGANOPHOSPHATE, PESTICIDE C. DOCUMENTS CONSIDERED TO BE RELEVANT Category Citation of document, with indication, where appropriate, of the relevant passages Relevant to Claim No. P,X Biochemical Genetics, Vol. 32 No. 1-2 issued February 1994, M. E. Spackman 1-12 et al.: "A cluster of esterase genes on chromosome 3R of Drosophila melanogaster includes homologues of esterase genes conferring insecticide resistance in Lucilia cuprina.", pages 39-62, whole document P,X Biochemical Genetics, Vol. 32 No. 1-2 issued February 1994, S. Whyard et al.: 1-12 "Insecticide resistance and malathion carboxyesterase in the sheep blowfly, Lucilia cuprina," pages 9-24, whole document Further documents are listed X See patent family annex. in the continuation of Box C. Special categories of cited documents later document published after the international filing date or priority date and not in conflict document defining the eneral state of the art which is with the application but cited to understand the not considered tobe ofparticular relevance principle or theory underlying the invention earlier document but published on or after the document of particular relevance; the claimed internat'otal filing date invention cannot be considered novel or cannot be documerit which may throw doubts on priority claim(s) considered to involve an inventive step when the or wthih is cited to establish the publication date of document is taken alone another citation or other special reason (as specified) document of particular relevance; the claimed document referring to an oral disclosure, use, invention cannot be considered to involve an exhibitirn or other means inventive step when the document is combined docuim~t published prior to the international filing date with one or more other such documents, such but later 'tian the priority date claimed combination being obvious to a person skilled in the art document member of the same patent family Date of the actuil completion of the international search Date of mailing of the international search report April 1995 (05.04.95) 2G A 9q5 o, qS) Name and maiing address of the ISA/AU Authorized officer AUSTRALIAN INDUSTRIAL PROPERTY ORGANISATION PO BOX 200 WODEN ACT 2606 AUSTRALIA Ross Osborne Facsimile No. 06 2853929 Telephone No. (06) 2832404 Form PCT/ISA/2Ii0 (continuation of first sheet (July 1992) coprow INTERNATIONAL SEARCH REPORT InternationalI application No, PCT/IAU 95100016 C(Continuation). DOCUMENTS CONSIDERED 'rO BE RELEVANT Category* Citation of document, with indication, where appropriate of the relevant passages Relevant to Claim No. Y WO, A, 90/02177 (AMGEN INC) 8 March 1990 (08.03.90) page 2 line 1 to 1-12 page 4 line 33 Y WO, A, 89/02920 (LITTLE INC) 6 April 1989 (06.04.89) page 2 lines 3-15, 1-12 claims 1, 12, 15-29 Y Pesticide Biochemistry and Physiology Vol. 41 No. 3, 1991 A. G. Parker et al. 1-12 "Biochemistry and physiology of esterases in organophos-phate susceptible and resistant strains of the Australian sheep blowfly, Lucilia cuprina," pages 305-3 18. whole document Y Biochemical Genetics Vol. 30 No. 3-4 issued April 1992, J. Lai-Fook et al.: 1-12 "Genetics of the hemolytuph esterases of Lucilia cuprina (Diptera: calliphoridae)" pages 123-130, whole document Form PCT/ISAJ21O (continuation of second sheet)(July 1992) coprow INTERNATIONAL SEARCH REPORT iIUInIUIonIu aIpIPniiaiun iW. PCT/AU 95/00016 This Annex lists the known publication level patent family members relating to the patent documents cited in the above-mentioned international search report. The Australian Patent Office is in no way liable for these particulars which are merely given for the purpose of information. Patent Document Cited in Search Patent Family Member Report WO 9002177 EP 394393 JP 3501086 WO 8902920 EP 381701 END OF ANNEX Form PCT/ISA/210(patent family annex)(July 1992) coprow I~aP ~sl ~4181111PBq ll~