WO2003023033A1 - Modified monooxygenase - Google Patents

Abstract

A monoxygenase comprises: (a) CYP101 having the mutations L244A and V247L; (b) a homologue thereof in which the equivalent amino acids to L244 and V247 have been substituted to increase the coupling efficiency or oxidation rate of pentachlorobenzene compared to the unmodified homologue. The monoxygenase may be used in a process for oxidising a substrate which is a halo aromatic compound.

Description

MODIFIED MONOOXYGENASE

Field of the Invention

The invention relates to a process for enzymatically oxidising halogenated aromatic compounds, and to modified enzymes for use therein.

Background to the Invention

Chlorinated aromatic compounds such as the chlorobenzene and polychlorinated biphenyls (PCBs) are among the most wide-spread organic contaminants in the environment due to their common application as solvents, biocides, and in the heavy electrical industry. They are also some of the most problematic environmental pollutants, not only because of the health hazards (lipid solubility and hence accumulation in fatty tissues, toxicity and carcinogenicity) but also because of their slow degradation in the environment. Whilst microorganisms have shown extraordinary abilities to adapt and evolve to degrade most of the organic chemicals released into the environment, the most chemically inert compounds such as PCBs do persist for two main reasons. First, these compounds have very low solubility in water and therefore their bioavailability is low. Research into this problem has focussed on the use of detergents and other surfactants to enhance their solubility and bioavailability. Second, these compounds require activation by enzymatic oxidation or reduction, and it can take a long time for the necessary genetic adaptations by microorganisms to occur, and even then the organisms may not be stable and viable.

Summary of the Invention

We have now found, according to the present invention, that a modified monoxygenase, in particular modified P450_cam, can be used to oxidise halogenated aromatic compounds. New mutants of the monoxygenase with substitutions in the active site have enhanced oxidation activity. Suitable monoxygenases can be expressed in microorganisms, animals and plants which are going to be used to oxidise the halogenated aromatic compounds. The present invention provides a monoxygenase enzyme comprising (a) CYPIOI in which leucine at position 244 is substituted by alanine and valine at position 247 is substituted by leucine, (b) a homologue thereof in which the equivalent amino acids to L244 and V247 have been substituted to increase the coupling efficiency or oxidation rate of pentachlorobenezene compared to the unmodified homologue.

The present invention also provides a process for oxidising a substrate which is a halo aromatic compound, which process comprises oxidising said substrate with a monooxygenase enzyme of the invention. The process may be carried out in a cell that expresses:

(a) the enzyme

(b) an electron transfer reductase; and

(c) an electron transfer redoxin.

Detailed description of the Invention

The enzyme is a mutant of a monooxygenase. The monooxygenase is generally a prokaryotic or eukaryotic enzyme. Typically it is a heme containing enzyme and/or a P450 enzyme. The monooxygenase may or may not be a TfdA (2,4-dichlorophenoxy) acetate/α-KG dioxygenase. The monooxygenase is generally of microorganism (e.g. bacterial), fungal, yeast, plant or animal origin, typically of a bacterium of the genus Pseudomonas. These organisms are typically soil, fresh water or salt water dwelling. In the case of a mutant monooxygenase the non-mutant form may or may not be able to oxidise the substrate.

The monooxygenase of the present invention has improved coupling efficiency or oxidation rate for aromatic compounds and in particular for chlorinated benzene derivatives. In particular, the monooxygenase of the present invention demonstrates improved coupling efficiency or oxidation rates for pentachlorobenzene. The coupling efficiency is defined as the proportion of NADH consumed that lead to the formation of products i.e. the yield of the reaction based on NADH consumed, and is given as a percentage.

The monooxygenase typically has a coupling efficiency of at least 1%, such as at least 2%, 4%, 6% or more, typically 10, 20, 30, 40 or 50% or more, up to 70, 80 or 90% or more. The monooxygenase typically has a product formation rate of at least 5 min^"1, such as at least 8, 10, 15 , 20, 25, 50, 100, 150 min^"1 or more. The coupling efficiency or product formation rate is typically measured using any of the substrates or conditions mentioned herein. Thus they are typically measured in the in vitro conditions described in the Examples, in which case the relevant monooxygenase, would be present instead of, but at the same concentration as, modified P450_cam-

Typically, the monooxygenase is derived from P450_cam (also known as CYPIOI) of Pseudomonas putida, having the polypeptide sequence of SEQ ID No 1, in which leucine at position 244 is substituted with alanine and valine at position 247 is substituted with leucine, hereinafter referred to as the L244A/V247L mutant. The invention also encompasses allelic variants and homologues, in particular species homologues of CYPIOI, and also fragments of any thereof.

A species homologue has sequence homology with SEQ ID No 1, and is typically P450_BM-₃ of Bacillus megaterium (e.g. the polypeptide sequence shown in SEQ ID No. 2), P450_tcrp of Pseudomonas sp, P450_eryF of Saccharopollyspora erythraea, or P450 105 Dl (CYP105) of Streptomyces griseus strains.

Any of the homologous proteins mentioned herein are typically at least 10% homologous to a natural monooxygenase on the basis of amino acid identity, or at least 80 or 90% and more preferably at least 95%, 97% or 99% homologous thereto over at least 20, preferably at least 30, for instance at least 40, 60 or 100 or more contiguous amino acids. The contiguous amino acids may include the active site. This homology may alternatively be measured not over contiguous amino acids or nucleotides but over only the amino acids in the active site. Homologues as referred to herein may also relate to fragments of CYPIOI including the active site. Such fragments may be up to 50 amino acids in length but more typically at least are 100, 150, 200 or 250 amino acids in length, such as 300 or 350 amino acids in length.

Homology can be measured using known methods. For example, the UWGCG Package provides the BESTFIT program which can be used to calculate homology (for example used on its default settings) (Devereux et al (1984) Nucleic Acids Research 12, p 387-395). The PILEUP and BLAST algorithms can be used to calculate homology or line up sequences (typically on their default settings), for example as described in Altschul S.F. (1993) J Mol Evol 36:290-300; Altschul, S, F et al (1990) J Mol Biol 215:403-10.

Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pair (HSPs) by identifying short words of length W in the query sequence that either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighbourhood word score threshold (Altschul et al, supra). These initial neighbourhood word hits act as seeds for initiating searches to find HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Extensions for the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment. The BLAST program uses as defaults a word length (W) of 11 , the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1992) Proc. Natl. Acad. Sci. USA 89: 10915-10910) alignments (B) of 50, expectation (E) of 10, M=5, N=4, and a comparison of both strands.

The BLAST algorithm performs a statistical analysis of the similarity between two sequences; see e.g., Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90: 5873-5787. One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a sequence is considered similar to another sequence if the smallest sum probability in comparison of the first sequence to the second sequence is less than about 1, preferably less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001. The naturally occurring homologue of CYPIOI or a variant of either thereof will have at least two substitutions, at positions equivalent to leucine at position 244 and valine at position 247 of CYPIOI . Such mutations will typically be substitution to alanine and leucine at each position respectively. The mutations at these equivalent positions are selected to improve the coupling efficiency or oxidation rates of aromatic compounds by the mutated enzymes compared to their unmutated counterparts. Preferably, improved efficiencies or oxidation rates are seen for chlorobenzene substrates and in particular for pentachlorobenzene.

Molecular modelling and mutagenesis studies can be carried out on homologues of CYPIOI, as described in the examples for CYPIOI, for example, to increase the space close to the haem associated with position 244 of CYPIOI and to decrease the space associated with position 247 of CYPIOI. The 'equivalent' side chain in the homologue is one at the homologous position. This can be deduced by lining up the CYP101/P450_cam sequence and the sequence of the homologue based on the homology between the two sequences. The PILEUP, BLAST and BESTFIT algorithms can be used to line up the sequences (for example as described in Altschul S. F. (1993) J Mol Evol 36:290-300; Altschul, S, F et al (1990) J Mol Biol 215:403-10 and (Devereux et al (1984) Nucleic Acids

Research 12, p387-395)). These algorithms can also be used to calculate the levels of homology discussed herein (for example on their default settings). The equivalent amino acid will generally be in a similar place in the active site of the homologue as amino acids 244 and 247 in P450_cam. The monooxygenase may have 1, 2, 3, 4 or more other mutations, such as substitutions, insertions or deletions. The other mutations may be in the active site or outside the active site. An amino acid 'in the active site' is one which lines or defines the site in which the substrate is bound during catalysis or one which lines or defines a site through which the substrate must pass before reaching the catalytic site. Therefore such an amino acid typically interacts with the substrate during entry to the catalytic site or during catalysis. Such an interaction typically occurs through an electrostatic interaction (between charged or polar groups), hydrophobic interaction, hydrogen bonding or van der Waals forces.

The amino acids in the active site can be identified by routine methods to those skilled in the art. These methods include labelling studies in which the enzyme is allowed to bind a substrate which modifies ('labels') amino acids which contact the substrate. Alternatively the crystal structure of the enzyme with bound substrate can be obtained in order to deduce the amino acids in the active site.

Typically the mutations are in the 'second sphere' residues which affect or contact the position or orientation of one or more of the amino acids in the active site. The insertion is typically at the N and/or C terminal and thus the enzyme may be part of a fusion protein. The deletion typically comprises the deletion of amino acids which are not involved in catalysis, such as those outside the active site. The monooxygenase may thus comprise only those amino acids which are required for oxidation activity. The other mutations in the active site typically alter the position and/or conformation of the substrate when it is bound in the active site. The mutation may make the site on the substrate which is to be oxidized more accessible to the haem group. Thus the mutation may be a substitution to an amino acid which has a smaller or larger, or more or less polar, side chain. The other mutations typically increase the stability of the protein, or make it easier to purify the protein. They may prevent the dimerisation of the protein, for example by removing cysteine residues from the protein (e.g. by substitution of cysteine at position 334 of P450_cam, or at an equivalent position in a homologue, preferably to alanine). They typically allow the protein to be prepared in soluble form, for example by the introduction of deletions or a poly-histidine tag, or by mutation of the N-terminal membrane anchoring sequence. The mutations typically inhibit protein oligomerisation, such as oligomerisation arising from contacts between hydrophobic patches on protein surfaces.

The discussion below provides examples of the positions at which substitutions may be made in CYPIOI or P450_cam, in addition to the modifications at positions 244 and 247. The same substitutions may be made at equivalent positions in the homologues. Standard nomenclature is used to denote the mutations. The letter of the amino acid present in the natural form is followed by the position, followed by the amino acid in the mutant. To denote multiple mutations in the same protein each mutation is listed separated by hyphens. The mutations discussed below using this nomenclature specify the natural amino acid in P450_cam, but it is to be understood that the mutation could be made to a homologue which has a different amino acid at the equivalent position.

An additional mutation is typically an amino acid substitution at amino acid 87, 98, 101, 185, 248, 296, 395, 396 or a combination of these. The following combinations of substitutions are preferred:

(i) Substitutions at position 96 to A, L, F, and W, preferably the substitution Y96F.

(ii) Substitutions at position 87 to amino acids of different side chain volume, such as substitutions (typically of F) to A, L, I or W. (iii) Substitution at position 101 to amino acids with different side-chain volume, such as substitutions (typically of T) to A. This substitution increases the space close to the haem.

(iv) Substitution at position 87 to amino acids of different side-chain volume, such as substitutions (typically of F) to A, L, I and W, combined with substitutions at position 96 to amino acids of different side-chain volume such as (typically Y to) A, L, F, and W. These combinations alter the space available in the upper part of the substrate pocket compared to the wild-type enzyme, for example, from Y96W-F87W (little space) to Y96A-F87A (more space), as well as the location of the space, for example from one side in Y96F-F87A to the other in Y96A-F87W. (v) Substitution at position 96 to F combined with substitutions at positions 185 and 395. Both T185 and 1395 are at the upper part of the substrate pocket, and substitution with A creates more space while substitution with F will reduce the space available and push the substrate close to the haem.

(vi) Other substitutions at combinations of positions 87, 96, 101, 295, 296, 395 and 396 with combinations of A, L, F, and W in addition to the L244A and N247L substitutions. The aim is to vary the size and shape of the hydrophobic substrate binding pocket.

Mutations are generally introduced into the enzyme by using methods known in the art, such as site directed mutagenesis of the enzyme, PCR and gene shuffling methods or by the use of multiple mutagenic oligonucleotides in cycles of site-directed mutagenesis. Thus the mutations may be introduced in a directed or random manner. Typically the mutagenesis method produces one or more polynucleotides encoding one or more different mutants. In one embodiment a library of mutant oligonucleotides is produced which can be used to produce a library of mutant enzymes.

The invention also provides a polynucleotide which comprises a sequence which encodes the mutant enzyme of the invention. The polynucleotide is typically DNA or RNA, and may be single or double stranded. The polynucleotide may be able to hybridise with a polynucleotide encoding the naturally, occurring form of any mutant discussed herein. It typically hybridises with the relevant polynucleotide at a level significantly above background. The signal level generated by the interaction is typically at least 10 fold, preferably at least 100 fold, as intense as 'background' hybridisation. The intensity of interaction may be measured, for example, by radiolabelling the probe, e.g. with P. Selective hybridisation is typically achieved using conditions of medium to high stringency, such as 0.1 to 0.2 x SSC at 55°C up to 60°C or 65°C. Polynucleotides of the invention can be incorporated into a recombinant replicable vector. The vector may be used to replicate the nucleic acid in a compatible host cell. Thus one method of making polynucleotides of the invention comprises introducing a polynucleotide of the invention into a replicable vector, introducing the vector into a compatible host cell, and growing the host cell under conditions which bring about replication of the vector. The vector may be recovered from the host cell. Suitable host cells are described below in connection with expression vectors.

Preferably, a polynucleotide of the invention in a vector is operably linked to a control sequence which is capable of providing for the expression of the coding sequence by the host cell, i.e. the vector is an expression vector.

The term "operably linked" refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner. A control sequence "operably linked" to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences.

Such vectors may be transformed into a suitable host cell to provide for expression of the mutant enzyme. The vectors may be, for example, plasmid, virus or phage vectors provided with an origin of replication, optionally a promoter for the expression of the said polynucleotide and optionally a regulator of the promoter. The vectors may contain one or more selectable marker genes, for example an ampicillin resistance gene in the base of a bacterial plasmid or a neomycin resistance gene for a mammalian vector. Vectors may be used in vitro, for example for the production of RNA or used to transfect or transform a host cell.

Promoters and other expression regulation signals may be selected to be compatible with the host cell for which the expression vector is designed. For example, E. coli promoters include lac, tac, trc, trp and T7 promoters, and yeast promoters include S. cerevisiae GAL4 and ADH promoters, S. pombe nmtl and adh promoters. Mammalian promoters include the metal lothionein promoter which can be induced in response to heavy metals such as cadmium. The expression vectors are possible for use in insect or mammalian cells. For use in insect cells, strong baculovirus promoters such as the polyhedrin promoter are preferred. For expression in mammalian cells, strong viral promoters such as the SV40 large T antigen promoter, a CMV promoter or an adenovirus promoter may also be used. All these promoters are readily available in the art.

Expression vectors of the invention are typically introduced into host cells using conventional techniques including calcium phosphate precipitation, DEAE- dextran transfection, or electroporation.

The expression vector may contain a selectable marker and/or such a selectable marker may be co-transfected with the expression vector and stable transfected cells may be selected. Suitable cells include cells in which the abovementioned vectors may be expressed. Such cells may be prokaryotic or eukaryotic. These include microbial cells typically bacteria such as E. coli, preferably the strains DH₅oc , JM109, NM522 and BL21DE3 or Pseudomonas, typically putida, mammalian cells such as CHO cells, COS7 cells or HeLa cells, insect cells or yeast such as Saccharomyces. Baculovirus or vaccinia expression systems may be used.

Cell culture can take place under standard conditions. Generally the cells are cultured in the presence of assimible carbon and nitrogen sources. Commercially available culture media for cell culture are widely available and can be used in accordance with manufacturers instructions.

The monooxygenases of the present invention can be used for oxidising a substrate which is a halo aromatic compound, the process comprising oxidising the substrate with the monooxygenase enzyme of the invention.

The halo aromatic compound is typically a benzene or biphenyl compound. The benzene ring is optionally fused and can be substituted. The halogen is typically chlorine. In many cases there is more than one halogen atom in the molecule, typically 2 to 5 or 6. Generally 2 of the halogen atoms will be ortho or para to one another. The compound may or may not contain an oxygen atom such as a hydroxy group, an aryloxy group or a carboxy group. The compound may or may not be chlorophenol or a chlorophenoxyacetic compound.

Specific compounds which can be oxidised by the process of the present invention include 1, 2; 1,3- and 1 ,4-dichlorobenzene, 1, 2, 4; 1, 2, 3- and 1, 3, 5- trichlorobenzene, 1, 2, 4, 5- and 1 , 2, 3, 5- tetrachlorobenzene, pentachlorobenzene, hexachlorobenzene, 3,3'-dichlorobiphenyl and 2, 3, 4, 5, 6- and 2, 2', 4, 5, 5'- pentachlorobiphenyl. In a particularly preferred aspect of the present invention, hexachlorobenzene or pentachlorobenzene is oxidised, most preferably pentachlorobenzene. Other compounds which can be oxidised by the process include recalcitrant halo aromatic compounds, especially dioxins and halogenated dibenzofurans, and the corresponding compounds where one or both oxygen atoms is/are replaced by sulphur, in particular compounds of the formula:

which possess at least one halo substituent, such as, 2,3,7,8 tetrachlorodibenzodioxin. The oxidation typically gives rise to 1, 2 or more oxidation products. These oxidation products will generally comprise 1 or more hydroxyl groups. Generally, therefore, the oxidation products are phenols which can readily be degraded. It is particularly noteworthy that pentachlorobenzene and hexachlorobenzene can be oxidised in this way since they are very difficult to degrade. In contrast the corresponding phenols can be readily degraded by a variety of Pseudomonas and other bacteria. The atom which is oxidized is generally a ring carbon.

The process is typically carried out in the presence of the natural cofactors of the monooxygenase. Thus typically in addition to the enzyme and the substrate the process is carried out in the presence of an electron transfer reductase, an electron transfer redoxin, cofactor for the enzyme and an oxygen donor. In this system the flow of electrons is generally: cofactor → electron transfer reductase → electron transfer redoxin → enzyme.

The reductase is generally an electron transfer reductase which is able to mediate the transfer of electrons from the cofactor to redoxin, such as a naturally occurring reductase or a protein which has homology with a naturally occurring reductase, such as at least 70% homology; or a fragment of the reductase or homologue. The reductase is typically a reductase of any of the organisms mentioned herein, and is typically a flavin dependent reductase, such as putidaredoxin reductase.

The redoxin is generally an electron transfer redoxin which is able to mediate the transfer of electrons from the cofactor to the monooxygenase via the reductase. The redoxin is typically a naturally occurring electron transfer redoxin or a protein which has homology with a naturally occurring electron transfer redoxin, such as at least 70% homology; or a fragment of the redoxin or homologue. The redoxin is typically a redoxin of any of the organisms mentioned herein. The redoxin is typically a two-iron/two sulphur redoxin, such as putidaredoxin.

The cofactor is any compound capable of donating an electron to reductase, such as NADH. The oxygen donor is any compound capable of donating oxygen to monooxygenase, such as dioxygen.

Typically the monooxygenase, reductase and redoxin are present as separate proteins; however they may be present in the same fusion protein. Typically only two of them, preferably reductase and redoxin, are present in the fusion protein. Typically these components are contiguous in the fusion protein and there is no linker peptide present.

Alternatively a linker may be present between the components. The linker generally comprises amino acids that do not have bulky side chains and therefore do not obstruct the folding of the protein subunits. Preferably the amino acids in the linker are uncharged. Preferred amino acids in the linker are glycine, serine, alanine or threonine. In one embodiment the linker comprises the sequence N-Thr-Asp-Gly- Gly-Ser-Ser-Ser-C. The linker is typically from at least 5 amino acids long, such as at least 10, 30 or 50 or more amino acids long.

In the process the concentration of monooxygenase, reductase or redoxin is typically from 10^"8 to 10^"2M, preferably from 10^"6 to 10^"4M. Typically the ratio of concentrations of monooxygenase: reductase and/or monooxygenase: redoxin is from 0.1 :01 to 1 :10, preferably from 1 :0.5 to 1 :2, or from 1 :0.8 to 1 : 1.2. Generally the process is carried out at a temperature and/or pH at which the enzyme is functional, such as when the enzyme has at least 20%, 50%, 80% or more of peak activity. Typically the pH is from 3 to 11, such as 5 to 9 or 6 to 8, preferably 7 to 7.8 or 7.4. Typically the temperature is 10 to 90^°C, such as 25 to 75°C or 30 to 60^°C.

In the process different monooxygenases may be present. Typically each of these will be able to oxidise different substrates, and thus using a mixture of monooxygenases will enable a wider range of substrates to be oxidised.

In one embodiment the process is carried out in the presence of a substance able to remove hydrogen peroxide by-product (e.g. a catalase).

In one embodiment the process is carried out in the presence of the enzyme, substrate and an oxygen atom donor, such as hydrogen peroxide iodosylbenzene or t-butylhydroperoxide, for example using the peroxide shunt.

In one embodiment in the process the monooxygenase, reductase and redoxin together are typically in a substantially isolated form and/or a substantially purified form, in which case together they will generally comprise at least 90%, e.g., at least 95%, 98% or 99% of the protein in the preparation.

The process may be carried out inside or outside a cell. The cell is typically in culture, at a locus, in vivo or in planta (these aspects are discussed below).

The process is typically carried out at a locus such as in land (e.g. in soil) or in water (e.g. fresh water or sea water). When it is carried out in culture the culture typically comprises different types of cells of the invention, including those expressing monooxygenase of the invention. Generally such cells are cultured in the presence of assimible carbon and nitrogen sources.

Typically the cell in which the process is carried out is one in which the monooxygenase does not naturally occur. In another embodiment the monooxygenase is expressed in a cell in which it does naturally occur, but at higher levels than naturally occurring levels. The cell may produce 1, 2, 3, 4 or more different monooxygenases of the invention. These monoxygenases may be capable of oxidising different halo aromatic compounds. Typically the cell also expresses any of the reductases and/or redoxins discussed above. Components reductase and redoxin may be expressed in the cell in a similar manner. Typically monooxygenase, reductase and redoxin are expressed from the same vector, or may be expressed from different vectors. They may be expressed as three different polypeptides. Alternatively they may be expressed in the form of fusion proteins. The cell typically expresses more than one type of monooxygenase.

In one embodiment the three genes encoding the three proteins of the P450_ca system, i.e. carnA, camE, and camC are placed in the mobile regions of standard transposon vectors and incorporated into the genome of Pseudomonas and Flavobacteria. Alternatively plasmid vectors for expressing these genes may be used, in which case the P450_cam gene cluster will be extra-chromosomal.

The cell may be prokaryotic or eukaryotic and is generally any of the cells or of any of the organisms mentioned herein. Preferred cells are Pseudomonas, Flavobacteria or fungi cells (e.g. Aspergillus). In one embodiment the cell is one which in its naturally occurring form is able to oxidise any of the substrates mentioned herein. Typically the cell is in a substantially isolated form and/or substantially purified form, in which case it will generally comprise at least 90%, e.g. at least 95%, 98% or 99% of the cells or dry mass of the preparation.

The invention provides a transgenic animal or plant whose cells are any of the cells of the invention. The animal or plant is transgenic for the monooxygenase gene and typically also an appropriate electron transfer reductase and/or redoxin gene. They may be homozygous or heterozygous for such genes, which are typically transiently introduced into the cells, or stably integrated.(e.g. in the genome). The animal is typically a worm (e.g. earthworm) or nematode. The plant or animal may be obtained by transforming an appropriate cell (e.g. embryo stem cell, callus or germ cell), fertilising the cell if required, allowing the cell to develop into the animal or plant and breeding the animal or plant true if required. The animal or plant may be obtained by sexual or asexual (e.g. cloning) propagation of an animal or plant of the invention or of the FI organism (or any generation removed from the FI, or the chimera that develops from the transformed cell).

As discussed above the process may be carried out at a locus. Thus the invention also provides a method of treating a locus contaminated with a halo aromatic compound comprising contacting the locus with a monooxygenase, cell, animal or plant of the invention. These organisms are then typically allowed to oxidise the halo aromatic compound. In one embodiment the organisms used to treat the locus are native to the locus. Thus they may be obtained from the locus (e.g. after contamination), transformed transfected (as discussed above) to express the monooxygenase (and optionally an appropriate electron transfer reductase and/or redoxin).

In one embodiment the locus is treated with more than one type of organism, e.g. with 2, 3, 4, or more types which express different monooxygenases which oxidise different halo aromatic compounds. In one embodiment such a collection of organisms between them is able to oxidise all halobenzenes, e.g. all chlorobenzenes.

The organisms (e.g. in the form of the collection) may carry out the process of the invention in a bioreactor (e.g. in which they are present in immobilised form). Thus the water or soil to be treated may be passed through such a bioreactor. Soil may be washed with water augmented with surfactants or ethanol and then introduced into the bioreactor.

The invention is hereinafter described in more detail with reference to the following examples. Examples Materials and methods General Enzymes for molecular biology were from New England Biolabs, UK. Buffer components were from Anachem, UK. General reagents were from Sigma/Aldrich or Merck, UK. NADH was from Roche Diagnostics, UK. 1,3,5,-TCB, PeCB, HCB and PCP were from Sigma/Aldrich. UV/Nis spectra were recorded on a CARY IE spectrophotometer equipped with a Peltier cell temperature controller (± 0.1 °C). HPLC analyses were performed on a Gilson system. Cytochrome P450_cam (CYP101 ) is (P00183) EC1.14.15.1, putidaredoxin reductase is (P16640) EC1.18.1- and putidaredoxin is (P00259), No EC number but given as PDX.

Enzymes and molecular biology

General DNA and microbiological manipulations were carried out by standard methods [Sambrook, 1989]. CYPIOI and the physiological electron transfer co-factor proteins putidaredoxin and putidaredoxin reductase were expressed in Escherichia coli and purified following literature methods [Westlake, 1999; Peterson, 1990; Yasukochi, 1994]. The purified proteins were stored at -20 °C in buffers containing 50% glycerol. Immediately before use in activity assays the proteins were buffer exchanged into 50 mM Tris, pH 7.4 on a 5-mL PD-10 gel filtration column (Amersham Pharmacia Biotech). Site-directed mutagenesis was carried out using the Stratagene QuikChange kit. Mutants were identified and fully sequenced by automated DNA sequencing on an ABI 377XL Prism DNA sequencer by the DNA sequencing facility at the Department of Biochemistry, University of Oxford. All CYPIOI enzymes described in this work also contained the C334A mutation to prevent protein dimerisation via disulphide bond formation [Nickerson, 1997], although this mutation is not essential. For convenience, the C334A base mutant is referred to as 'wild-type', and the Y96F/C334A double mutant as Y96F, etc.

CYPIOI crystallisation and substrate soaking experiments

Crystals of the F87W/Y96F/V247L mutant were obtained at 291 K by the vapour diffusion method. Immediately prior to crystallisation the mutant was further purified by size exclusion chromatography on a Superdex 75 (Amersham-Pharmacia

Biotech) column (26 mm i.d. x 80 cm), eluting with 40 mM phosphate, buffer, pH 7.4, containing 1 mM camphor, 10 mM β-mercaptoethanol, 200 mM KC1 at a flow rate of 0.8 mL(min)^"1. The protein was buffer exchanged into 100 mM cacodylate, pH 6.5, 150 mM KC1, and concentrated to 8 mg(mL)^"1 by ultrafiltration. A 1 μiL aliquot of this solution was mixed with 1 μL of 30% PEG8000 in buffer A (100 mM cacodylate, 200 mM sodium acetate), and suspended over 1 mL of 18-24% PEG8000 in buffer A. Diffraction quality crystals of CYPIOI appeared within 24 hours. Crystals were captured with a fibre loop and soaked in 100 mM MES buffer, pH 6.5, 100 mM sodium acetate, 100 mM KC1, 20% PEG8000 containing 100 μM 1,3,5- TCB (added as a 100 mM stock in ethanol) for 5 days.

Data collection and structure refinement

Immediately prior to data collection, crystals were soaked in a cryoprotecting solution consisting of 100 mM MES buffer, pH 6.5, 100 mM KC1, 100 mM sodium acetate, 20% glycerol, 20% PEG8000 and flash frozen at 100 K in a stream of nitrogen gas. X-ray diffraction data were collected at 100 K on a MAR345 image plate. Initially it appeared that the crystals belonged to the space group E21 with unit cell dimensions a = 66.86, b = 61.99, c = 95 A3 A, β = 90.54°. Further refinement showed that the crystals belonged to the space group P_\ with unit cell dimensions a = 62.47, b = 66.90, c = 95.54 A, α = 98.72° and β = γ = 90°. The structure was solved by molecular replacement based on the crystal structure of wild-type CYPIOI with camphor bound (protein databank code: 2cpp). Difference map showed disk-shaped electron density above the heme, with the density due to the three chlorine atoms clearly visible. This density was modelled with the 1,3,5-TCB substrate and the structure refinement rapidly converged.

NADH turnover rate determinations

All incubations were carried out at 30 °C. Incubation mixtures (1.7 mL) contained 50 mM Tris, pH 7.4, 200 mM KC1, 1 μM CYPIOI, 10 μM putidaredoxin, 1 μM putidaredoxin reductase, and 30 μgm^"1 bovine liver catalase [Stevenson, 1996]. The mixtures were oxygenated and then equilibrated at 30 °C for 2 min. The PeCB and HCB substrates were added as 5 mM stocks in ethanol to a final concentration in an incubation mixture of 50 μM. NADH was added to 320 μM (final ₃₄₀ = 2.00) except for the F87W/Y96F/L244A/V247L mutant for which NADH was added to 50 μM. The absorbance at 340 nm was monitored. The maximum concentration of ethanol in an incubation reaction was 1% v/v, and control experiments showed that ethanol at concentrations up to 10%) v/v did not induce any increase in NADH consumption above background.

The NADH consumption rates were calculated using ε₃₄₀ = 6.22 mM^''cm^"'. The reduced forms of putidaredoxin and putidaredoxin reductase are susceptible to air oxidation. The amount of NADH consumed by these background reactions were determined from incubations containing all components except CYPIOI and substrate and subtracted from the observed rates to calculate the true CYPIOI and substrate-dependent rates [Nickerson, 1997].

Metabolite assays After all the NADH had been consumed in an incubation reaction, 2- naphthol was added to the mixture to act as an internal standard for the solid phase extraction and HPLC analysis steps. The organics were adsorbed onto a Varian Bond-Elut Cι₈ column (1 mL matrix volume) which had been equilibrated by washing with 1 mL methanol followed by 1 mL 50 mM Tris, pH 7.4. The column was then washed with 1 mL 50 mM Tris, pH 7.4, and dried under vacuum for 5 min. Bound organics were eluted from the column with 1 mL acetonitrile.

The polychlorinated benzenes and their metabolites were separated by reverse phase HPLC using acetonitrile/water (pH 3.0) gradients developed on a Cl 8 column (2.5 mm i.d. x 250 mm). The flow rate was maintained at 1 mL-(min)^"1, and the eluent was monitored at 220 nm. A 360 μL aliquot of the acetonitrile eluent from the Bond-Elut column was mixed with the 440 μL of water (pH 3.0), and 400 μL of the mixture (45% v/v acetonitrile in water) was injected onto the column. The acetonitrile concentration was increased from 45%) to 75% over 10 min, and then maintained at 15% for 8 min. The retention time of the PCP product was 16.5 min. The PCP concentration in incubation mixtures were calculated by calibrating the concentration response of the HPLC detector. Mixtures containing different concentrations of PCP and all the components of a normal incubation except NADH and substrate were extracted and analysed as for normal incubations. The plot of the peak area ratios for PCP to the 2-naphthol internal standard against product concentration gave a linear calibration plot which passed through the origin. The absolute concentration of PCP produced by enzymatic turnover in an incubation mixture was thus readily determined. The coupling efficiency was the percentage of NADH consumed that lead to PCP formation.

Results and discussion

The structure of the F87W/Y96F/V247L mutant with 1,3,5-TCB bound Crystals of the F87W/Y96F/V247L mutant obtained from cacodylate buffer and PEG8000 initially appeared in the same P_\ as crystals of the wild-type obtained from Tris buffer and PEG4000 [Schlichting, 2000]. However, on refinement, while the crystals were in the same monoclinic form the point group was P_\, due to the substrate soaking step, rather than P_\, but the unit cell dimensions were also virtually identical. Soaking the crystals in the well solution with 100 μM 1,3,5-TCB added did not give crystals with this substrate bound in the active site. The soaking conditions were varied and we found that MES buffer gave the best results.

Crystals of the F87W-Y96F-V247L mutant with 1,3,5-TCB bound in the active site diffracted, and the structure was readily solved by molecular replacement methods. The electron density of the first 8 residues was not observed. Otherwise the mutant retained all the structural features of the wild-type [Poulos, 1987]. The Cα backbone of the mutant was superimposable on that of the wild-type, with an RMS deviation of 0.38 to 0.46 A. Protein-heme contacts such as those between the side- chains of Rl 12, H355 and D297 and the heme propionate groups were present. The heme was ruffled and the 5-coordinate iron atom was out of the porphyrin plane and towards the proximal ligand. The iron cysteine thiolate sulphur distance refined to 2.07 to 2.23 A (2.2 A in the wild-type, but at the resolution of the mutant structure bond length errors are in the region of ±0.2 A). There was large positive electron density in the proposed cation binding site. As found for the wild-type, the ligands were the four backbone carbonyls of residues 84, 93, 94 and 96, and two water molecules, one of which was hydrogen-bonded to the carboxylate side-chain of E84. The active site structure of wild-type CYPIOI with bound camphor, and of the F87W/Y96F/N247L mutant with bound 1,3,5-TCB, were compared. There are no water molecules in the active site of camphor-bound wild-type CYPIOI, and none was found for the mutant with 1,3,5-TCB bound. The 1,3,5-TCB substrate was almost parallel to the heme, and the two aromatic systems were in van der Waals contact. The substrate was located over pyrroles A and D, and the CHA meso carbon. There was strong van der Waals interaction between Cl-3 and Cl-5 and pyrroles A and D. This binding mode also placed C-4 of 1,3,5-TCB over the heme iron. The predicted product for 1,3,5-TCB oxidation would be 2,4,6-trichlorophenol (2,4,6- TCP), as observed experimentally. The effective exclusion of water and close approach of a C-H bond to the haem iron were also consistent with the high coupling efficiency of 57% (Jones, 2000 and 2001).

Of the amino acid residues that lined the CYPIOI active site, the planes of the aromatic side-chains of the wild-type and mutant at the 87 and 96 positions were superimposable. The indole ΝH group of W87 in the mutant pointed towards the heme and the phenyl ring slightly upwards and towards the L247 side-chain. The indole nitrogen was 3.4 A away from Cl-1 of the 1,3,5-TCB substrate, indicative of a hydrogen bond. This chlorine atom was also within weak hydrogen bonding distance (3.4 A) of a carboxylate oxygen of D297. These two interactions combined to pull this end of the 1,3,5-TCB molecule slightly upwards and away from being parallel to the porphyrin plane. This movement also forced the V396 side-chain to move up by 0.5 A.

The extra bulk of the leucine side-chain at the 247 position forced the F98 phenyl side-chain to rotate by 20° to avoid steric hindrance. The W87 and L247 side- chains approached each other to within 4.5 A, compared to 6.5 A between Y96 and V247 in the wild-type structure, and effectively closed off the top of the active site of the mutant to substrate binding. We would therefore expect 1,3,5-TCB to be forced to bind close to the heme, resulting in faster substrate oxidation. As Poulos noted previously [Poulos, 1987], the structure of CYPIOI does not show an obvious substrate access channel, and dynamic fluctuations are required to allow entry of a potential substrate. The close approach of the W87 and L247 side-chains indicated that the structural fluctuations are sufficient to move both out of the way to enable the incoming 1,3,5-TCB substrate to bind in the active site. Closer to the heme, the larger radius of 1,3,5-TCB compared to camphor forced the geminal methyls of the L244 side-chain to move sideways by 0.7 - 0.9 A to accommodate the substrate, and these methyl groups were within 4 A of Cl-3. The V295 side-chain was in van der Waals contact with Cl-5. The T101 side-chain did not contact 1 ,3,5-TCB but, as reported recently for the same monoclinic crystal form [Schlichting, 2000], this side-chain was rotated compared to the wild-type structure of the orthorhombic form [Poulos, 1987], such that it formed a hydrogen bond (3.0 A) with the heme propionate of pyrrole ring D.

The 1 ,3,5-TCB binding orientation and enzyme-substrate contacts suggested other mutations which could enhance the activity of CYPIOI for the oxidation of the most heavily chlorinated benzenes. Viewed from the top of the active site, the L244 side-chain fitted neatly between Cl-1 and Cl-3 of 1,3,5-TCB. There was no room to accommodate another chlorine atom in PeCB and maintain the highly favourable, parallel binding orientation observed for 1,3,5-TCB. One solution would be to introduce the L244A mutation to create space to allow PeCB and HCB to bind in this parallel orientation. We therefore prepared the F87W/Y96F/L244A, F87W/Y96F/V247A and F87W/Y96F/L244A/N247L mutants to examine the effect of mutations at the L244 and V247 positions on the PeCB and HCB oxidation activity of CYPIOI .

Polychlorinated benzene oxidation activity of CYPIOI mutants

The rates of ΝADH turnover and product formation, and the derived coupling efficiencies for PeCB and HCB oxidation by the CYPIOI enzymes are given in Table 1. Wild-type CYPIOI showed slow ΝADH oxidation activity but no products were observed, while all the mutants oxidised both PeCB and HCB to PCP. Since a PCP formation rate as slow as 0.001 min^"1 was detectable, we conclude that the rate for the wild-type must be an order of magnitude or so slower than 0.001 min^"1. We note that camphor is oxidised by the wild-type at a rate of 1000 min^"1 with 100%) coupling efficiency under identical conditions. Considering the PeCB data first, the results showed that the crystal structure- based protein engineering was successful, with the F87W/Y96F/L244A/V247L mutant oxidising PeCB at a rate of 289 min^"1 and with 90% coupling efficiency. Further investigation showed that the calibration was not, in fact, linear. On adjustment, the F87W/Y96F/L244A/N247 L mutant oxidation rate for PeCB was 82.5 min^"1, with a coupling efficiency of 24%). This activity was nearly 8% of the camphor oxidation rate of wild-type CYPIOI, and entirely consistent with the argument that the L244A mutation created space close to the heme to bind the larger PeCB molecule in the parallel orientation proposed to promote chlorinated benzene oxidation. The necessity of the V247L mutation was clearly demonstrated by the much lower activity and coupling of the F87W/Y96F/N247A mutant, and the increased coupling but reduced ΝADH turnover rate of the F87W/Y96F/L244A mutant.

The present crystal structure offered a framework for rationalising the role of different active site residues in the substrate specificity of CYPIOI. We noted previously that the Y96F mutation most likely promoted the oxidation of a wide variety of hydrophobic organic compounds by increasing the hydrophobicity of the substrate binding pocket. Introducing the F87W mutation increased both the ΝADH turnover rate and coupling efficiency for PeCB oxidation 10-fold (Table 1 below).

Table 1: The catalytic parameters for the oxidation of pentachlorobenzene and hexachlorobenzene by wild-type and mutants of CYPIOI. The data are means of at least 3 experiments, with all data for each parameter being within 15% of the mean. % HS (± 5%) is the high spin heme content in the presence of excess substrate. N is the ΝADH turnover rate, & the product formation rate (pentachlorophenol for both PeCB and HCB), and both rates are given in nmol (nmol CYP101)^-1 min^-1. n.d:. no product observed.

A previous molecular dynamics study on the reductive dehalogenation of pentachloroethane by the F87W mutant suggested that the indole NH group formed a hydrogen bond with the T185 side-chain, thus orienting the indole phenyl ring towards the heme and reducing the active site volume [Manchester, 1995]. The structure with 1,3,5-TCB bound showed that the indole NH group did not form a hydrogen bond with the T185 side-chain, but instead with a chlorine of the 1,3,5- TCB substrate. This interaction could strengthen substrate binding, and also orient the indole phenyl ring towards the side-chain at the 247 position to close off partially the top of the substrate binding pocket, thus promoting PeCB binding closer to the heme.

The side-chain at the 247 position played a very important role. Closer examination of the structure of the wild-type and the mutant showed that there is a hydrophobic region near the top of the CYPIOI substrate binding pocket, defined by the side-chains of residues 87, 96, 98, 181 and 247, and capped by F193. This pocket is approximately 6 A across in the wild-type structure. Although too small to accommodate the entire PeCB molecule, it was sufficiently large, even with the F87W mutation, to bind part of it so that the PeCB was located further away from the heme, resulting in reduced rate and coupling. The V247A mutation would enlarge this pocket sufficiently to bind PeCB, which would explain the very low activity of the F87W/Y96F/N247A mutant. The V247L mutation, as in the F87W/Y96F/V247L mutant, would close off this pocket to PeCB binding, forcing it to bind closer to the heme. This gave rise to increased ΝADH turnover activity but interestingly the coupling efficiency was not greatly affected (Table 1).

The main effect of the L244A mutation was to increase the coupling efficiency of PeCB oxidation. This was consistent with this mutation creating the space required for PeCB to bind in an orientation similar to that observed for 1 ,3,5- TCB. The contrast with the V247L mutation may be important. The 247 side-chain was located high up in the active site. Bulky substitutions here would tend to force the substrate to bind closer to the heme, facilitating the displacement of the water molecule bound at the heme sixth coordination site and therefore increase the ΝADH turnover activity. However, the high location of 247 side-chain meant that it cannot effectively promote the binding of the planar chlorinated benzenes in the parallel orientation to maximise the coupling efficiency. The role of the 244 side-chain appeared to be exactly the reverse. Changes such as the L244A mutation could create the space necessary for the parallel binding orientation for PeCB but they were not sufficient to force this substrate to bind exclusively in this orientation. It is very gratifying that combining the L244A and V247L mutations has such a spectacular effect of enabling the enzyme to have the best of both worlds.

In general terms the activity trends for HCB mirrored those for PeCB. The F87W/Y96F/L244A/N247L mutant was again the most active but the rates and coupling were lower. HCB was much less soluble and less reactive than PeCB. In addition, PCP formation by oxidative dechlorination required 4 electrons from two molecules of ΝADH, most likely occurred via an arene oxide or a ketone intermediate generated by an ΝIH-shift involving chlorine. Such a shift has been observed recently in a flavin monoxygenase-mediated oxidation of a chlorinated benzene derivative. Reduction by two electrons, loss of chloride and protonation gives the PCP product. References

Jones, J. P., O'Hare, E. J., and Wong, L. L. (2000) Chem. Commun. 247-248. Jones, J. P., O'Hare, E. J., and Wong, L. L. (2001) Eur. J. Biochem. 268, 1460-1467. Manchester, J. I., and Ornstein, R. L. (1995) Prot. Engng. 8, 801-807. Nickerson, D. P., and Wong, L.-L. (1997) Prot. Engng. 10, 1357-1361.

Peterson, J. A., Lorence, M. C, and Amarneh, B. (1990) J. Biol. Chem. 265, 6066- 6073.

Poulos, T. L., Finzel, B. C, and Howard, A. J. (1987) J. Mol. Biol. 195, 687-700.

Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2^nd Ed., Cold Spring Harbor Laboratory Press, New York.

Schlichting, I., Berendzen, J., Chu, K., Stock, A. M., Maves, S. A., Benson, D. E., Sweet, R. M., Ringe, D., Petsko, G. A., and Sligar, S. G. (2000) Science 287, 1615- 1622.

Stevenson, J.-A., Westlake, A. C. G., Whittock, C, and Wong, L.-L. (1996) J. Am. Chem. Soc. 118, 12846-12847.

Westlake, A. C, Harford-Cross, C. F., Donovan, J., and Wong, L. L. (1999) Eur. J. Biochem. 265, 929-935.

Yasukochi, T., Okada, O., Hara, T., Sagara, Y., Sekimizu, K., and Horiuchi, T. (1994) Biochim. Biophys. Ada 1204, 84-90.

Claims

I. A monoxygenase comprising: (a) CYPIOI having the mutations L244A and V247L;

(b) a homologue thereof in which the equivalent amino acids to L244 and V247 have been substituted to increase the coupling efficiency or oxidation rate of pentachlorobenzene compared to the unmodified homologue.

2. A monoxygenase according to claim 1 further comprising the mutation Y96F, or a homologue thereof having an equivalent mutation.

3. A monoxygenase according to claim 1 or claim 2 further comprising the mutuation F87W or a homologue thereof having an equivalent mutation.

4. A monoxygenase according to claim 1, 2 or 3 further comprising the mutation T101 A or a homologue thereof having an equivalent mutation.

5. A polynucleotide comprising a sequence encoding a monoxygenase according to any one of the preceding claims.

6. A cell capable of expressing a monoxygenase according to any one of claims 1 to 4.

7. A cell according to claim 6, which further expresses an electron transfer reductase and an electron transfer redoxin.

8. A process for oxidising a substrate which is a halo aromatic compound, which process comprises oxidising said substrate with a monoxygenase enzyme according to any one of claims 1 to 4.

9. A process according to claim 8 in which the halogen is chlorine.

10. A process according to claim 8 or claim 9 in which the aromatic compound is a benzene or biphenyl.

I I. Process according to any one of claims 8 to 10 in which the substrate has more than one halogen atom.

12. A process according to claim 11 in which the substrate is pentachlorobenzene or hexachlorobenzene.

13. A process according to any one of claims 8 to 12 which is carried out in a cell according to claim 6 or 7.

14. A transgenic animal or plant whose cells are as defined in claims 6 or 7.

15. A method of treating a locus contaminated with a substrate as defined in any one of claims 8 to 11 comprising contacting the locus with an enzyme as defined in any one of claims 1 to 4 or a cell as defined in claim 6 to 7, or an animal or plant as defined in claim 14.