WO2003000722A1 - Multi-copper oxidase protein enzymes for iron(ii) acquisition in prokaryotic cells - Google Patents

Abstract

The present invention relates generally to a class of enzymes involved in metal ion acquisition by cells and agents useful in the modulation of same. More particularly, the present invention is directed to novel mechanisms of ferrous ion (FeII) acquisition in prokaryotic organisms mediated through a member of the multi-copper oxidase family. Recognition of multi-copper oxidase-mediated (FeII) acquisition in bacteria permits the rationale design of agonists and antagonists with specific or broad spectrum activity amongst one or a number of multi-copper oxidases. The present invention further contemplates a genetic sequence encoding a multi-copper oxidase and the use of the enzyme and/or its genetic sequence in development of diagnostic or detection assays as well as recombinant organisms and plants.

Description

MULTI -COPPER OXIDASE PROTEIN ENZYMES FOR IRON (II) ACQUISITION IN PROKARYOTIC CELS

FIELD OF THE INVENTION

The present invention relates generally to a class of enzymes involved in metal ion acquisition by cells and agents useful in the modulation of same. More particularly, the present invention is directed to novel mechanisms of ferrous ion (Fe¹¹) acquisition in prokaryotic organisms mediated through a member of the multi-copper oxidase family. Recognition of multi-copper oxidase-mediated Fe¹¹ acquisition in bacteria permits the rationale design of agonists and antagonists with specific or broad spectrum activity amongst one or a number of multi-copper oxidases. The present invention further contemplates a genetic sequence encoding a multi-copper oxidase and the use of the enzyme and/or its genetic sequence in development of diagnostic or detection assays as well as recombinant organisms and plants.

BACKGROUND OF THE INVENTION

Bibliographic details of the publications referred to in this specification are collected at the end of the description.

Reference to any prior art in this specification is not, and should not be taken as, an acknowledgment or any form of suggestion that this prior art forms part of the common general knowledge in any country.

Copper-containing proteins occur in organisms from all three of the domains of life. Copper is recognized as a major prosthetic metal ion in the electron transfer proteins (Solomon, "Blue" copper-containing oxidases. Metal ions in biology, John Wiley and Sons, Inc., 1981) and it is also widely acknowledged to be an essential trace element for many processes such as amino acid metabolism and in anti-oxidants (hioue et al, J. Biol. Chem. 274: 27069-47075, 1999). Copper containing proteins are generally categorized on the basis of the number of copper centres. On this basis, the proteins are defined as being simple or complex copper proteins.

There are a variety of examples of simple copper proteins which have single or isolated copper centres. Azurin is the classic example of the simple copper protein (Fee, Structure and Bonding 23: 1-60, 1975). This protein has a single copper atom and is relatively small (16 kDa) (Fee, 1975, supra).

A group of blue copper proteins including mung bean protein, stellacyanin and umeyan has also been characterized as simple copper proteins but no known biological function has been described (Fee, 1975, supra). The protein involved in electron transfer in the chloroplast in plants and algae, known as plastocyanin, represents another simple copper containing protein (Fee, 1975, supra). These proteins are all able to be reduced by various electron donors (Fee, 1975, supra) and most likely have a function in electron transport.

There are a range of the complex copper containing proteins, including the multi-copper oxidases and the haem-copper oxidases. The super family of haem-copper oxidases represents a distinct family that includes bacterial respiratory oxidases and the mitochondrial cytochrome oxidase (Garcia-Horsman et al, J. Bacteriol 176: 5587-5600, 1994). The multi-copper oxidases and cytochrome c oxidase (haem-copper oxidase) have in common the ability to perform the four electron reduction of molecular oxygen (Fee, 1975, supra). Multi-copper oxidases are characterized by the presence of four or more copper ions in either mono- or binuclear configuration (Solomon, 1981, supra).

The most studied multi-copper oxidases are from eukaryotic organisms. Multi-copper oxidases are known to couple the one electron oxidation of a substrate to the four electron reduction of molecular oxygen to water (di Patti et al, Protein Eng. 12: 895-897, 1998). However, the reaction is not linked to energy conservation. The oxidizing activity of these enzymes is facilitated by three distinct types of copper prosthetic groups with different functional and spectroscopic properties (Hassett et al, J. Biol. Chem. 273: 7628-7638, 1998a). There are three enzymatic categories of eukaryotic multi-copper oxidases: laccases, ascorbate oxidases, and ceruloplasmins (Hassett et al, J. Biol. Chem. 273: 23274-23282, 1998b).

There are three types of copper Cu(LT) centres found in the multi-copper oxidases, and the interaction between these Cu (LT) atoms has been described in terms of the oxidation of the substrate and concomitant reduction of O₂ (Messerschmidt et al, J. Mol. Biol. 206: 513- 529, 1989). Multiple copper centres were initially detected in these enzymes through EPR spectroscopy, although not all of the copper centres can be detected by this spectroscopic method (Solomon, 1981, supra). These copper centres have been investigated and are highly conserved within this category of proteins. It is generally acknowledged that the type 1 copper centre receives electrons from the substrate, while the types 2 and 3 copper centres act as a tri-nuclear cluster, to reduce molecular oxygen (Hassett et al, 1998b, supra).

Laccases are blue copper oxidases and are also known as benzenediol-.oxygen oxidoreductases. These enzymes can oxidize aromatic amines and phenolic compounds (Hassett et al, 1998b, supra). Laccases are found in a number of ecosystems and have potential in a number of industrial processes. The term laccase was first assigned when the activity was identified in the latex of the lac tree Rhus succedanea (Fee, 1975, supra). The catalytic activity of the laccase is well understood and they are lαiown to have low specificity for the reducing substrate (Johannes and Majcherczyk, Appl Environ. Microbiol 66: 524-528, 2000). Substrates utilized by the laccases include mono-, di- and poly-paraphenols (which are most readily oxidized), aminophenols, diamines and inorganic substances such as hexacyanoferrocyanate (Johannes and Majcherczyk, 2000, supra). The biological role of laccase in fungi is known to include ligninolysis and degradation of xenobiotics, as extracellular enzymes, but the oxidation of manganese has also been identified as a role of some yeast laccase (Hofer and Schlosser, FEBS Lett. 451: 186-190, 1999; Archibald and Roy, Appl. Environ. Microbiol. 58: 1496-1499, 1992; Munoz et al, Appl. Environ. Microbiol 63: 2166-2174, 1997; Chefetz et al, Appl Environ. Microbiol 64: 3175-3179, 1998; Alexandre and Zhulin, Trends Biochem. Sci. 18: 41-42, 2000; Pickard et al, Appl. Environ. Microbiol 65: 3805-3809, 1999). Laccases are glycoproteins, although the role of the carbohydrate is not known (Johannes and Majcherczyk, 2000, supra), and can be found intracellularly and extracellularly (Johannes and Majcherczyk, 2000, supra). The structures of laccase and ascorbate oxidase (another multi-copper oxidase) are closely related (Gromov et al, Eur. J. Biochem. 266: 820-830, 1999).

The ascorbate oxidases are closely related to the laccase, and have also been found in a variety of organisms (Johannes and Majcherczyk, 2000, supra). The biological role of ascorbate oxidases is not known, but these enzymes are known to be highly substrate specific for ascorbate and other compounds containing a lactone ring (Johannes and Majcherczyk, 2000, supra). Ascorbate oxidase is thought to function as a dimer (Johannes and Majcherczyk, 2000, supra). The structure of the ascorbate oxidase found in zucchini, has been determined (Messerschmidt et al, 1989, supra) by X-ray crystallography.

Ceruloplasmin is a multi-copper oxidase found in the sera of all vertebrates (Sato and Gitlin, J. Biol Chem. 266: 5128-5134, 1991). It has been extensively studied and its structure determined by X-ray crystallography (Kaitseva et al, JBIC 1: 15-23, 1996). It is recognized as representing a unique class of multi-copper oxidase as it not only has the typel/type2-3 cluster of Cu(II) groups but is also noted to have two additional type 1 copper centres (Farver et al, J. Biol. Chem. 274: 26135-26140, 1999). There has been considerable speculation as to the physiological role ceruloplasmin plays in the human body. It was initially thought to act as an anti-oxidant by collecting free radicals in the bloodstream, and possibly a copper transporter in the blood (Fee, 1975, supra). The protein involved in copper loading of ceruloplasmin is known to be absent in patients suffering from Menkes/Wilson disorder (Sato and Gitlin, 1991, supra; Jensen et al, Biochim. Biophys. Acta 1434: 103-113, 1999).

Ceruloplasmin has been shown to have a number of enzymatic properties; including ferroxidase activity (oxidation of Fe¹¹ to Fe^ιπ with molecular oxygen), oxidation of organic and inorganic compounds like p-phenylenediamine, dopamines, serotonin, catechol derivatives, aminophenols (Messerschmidt and Huber, Eur. J. Biochem. 187: 341-352, 1990) and independent alkyl hydroperoxide peroxidase activity (Cha and Kim, Biochemistry 38: 12104-12110, 1999). The current opinion is that the enzyme has a ferroxidase role which facilitates high affinity iron uptake into cells (Farver et al, 1999, supra). Evidence for such a role has come from studies of the yeast homolog of ceruloplasmin, Fet3 (Hassett et al, 1998a, supra; Hassett et al, 1998b, supra).

Fet3 was initially characterized in Saccharomyces cerevisiae where its role in high affinity iron transport was proposed. Fet3 and Ceruloplasmin are proposed to facilitate iron uptake by catalyzing the oxidation of Fe¹¹ to Fe^πι with molecular oxygen (Hassett et al, 1998b, supra; Yuan et al, Proc. Natl. Acad. Sci. USA 92: 2632-2636, 1995). The ferric iron is then able to be transported by the high affinity iron transport systems, such as the Ftrl permease (Johannes and Majcherczyk, 2000, supra).

Fet3, also thought to be a glycoprotein, differs from ceruloplasmin as it has a trans- membrane region Hassett et al, 1998b, supra. Fet3 from S. cerevisiae has 633 amino acid residues Hassett et al, 1998a, supra. Homology modeling with ceruloplasmin has led to the proposal that the type 1 Cu¹¹ centre is essential for the its ability to oxidase iron

(Archibald and Roy, 1992, supra). Essential amino acid residues for the ferroxidase activity of the S. cerevisiae Fet3 have recently been shown (by site-directed mutagenesis) to be Glu 185 and Tyr 354 (Bonaccorsi di Patti et al, FEBS Lett. 472: 283-286, 2000). The iron transportation facilitated by Fet3 is thought to occur via the iron permease Ftrl (Eck et al, Microbiology 145(Pt 9): 2415-2422, 1999). The regulation of the expression of these genes in S. cerevisiae has also been demonstrated to be Fe dependent Hassett et al,

1998a, supra. Fet3 differs from ceruloplasmin as it does not have the additional two type 1 centres (Bonaccorsi di Patti et al, 2000, supra). In spite of the differences, it appears that the roles of Fet3 and ceruloplasmin are identical as components of high affinity iron uptake systems.

Copper uptake in bacteria has been characterized in only a few organisms and, hence, little is known about this transport process. It is crucial for the bacteria to maintain precise levels of copper in the cell since this ion can be toxic if levels are too high (Hung et al, J. Biol Chem. 273: 1749-1754, 1998). Copper is a transition metal with valences of Cu¹ and Cu¹¹, which makes it capable of participating in redox cycles. This has the potential to generate reactive oxygen species such as superoxide anion and hydroxyl radical (Cooksey, FEMS Micro. Revs. 14: 341-386, 1994), hence its potential toxicity. The sequestration of copper by periplasmic and outer membrane proteins has been described in Pseudomonas syringae (Cooksey, Mol. Micro. 7: 1-5, 1993). This organism is thought to also prevent copper from entering the cytoplasm utilising specific proteins, including the copper sequester CopA, while transport through the inner membrane involves the CopC/CopD transport system (Cooksey, 1993, supra). The other components of this copper homeostasis system, which has a homolog found in Enterococcus hirae (Wimrner et al, J. Biol. Chem. 274: 22597-22603, 1999), include a copper efflux protein, a copper import protein (CopB) and a related regulator (CopY).

Copper homeostasis in yeast has many similar components to those found in bacterial systems. Uptake proteins, such as Ctrl have been identified (Martins et al, J. Biol. Chem. 273: 23716-23721, 1998). Transport proteins have been such as Scol, which is involved in copper loading of the cytochrome c oxidase (Paret et al, FEBS Lett. 447: 65-70, 1999), Copper chaperones such as Atxlp and Ccc2p which are involved in copper transport for the loading of ceruloplasmin have also been identified in yeast (and their homologs in humans) (Larin et al, J. Biol. Chem. 274: 28497-28504, 1999). However, little is yet known about details of the sequestration and transport of copper in bacteria.

Iron is recognized as an essential element for the growth of many bacteria (Guerinot, Annu.

Rev. Microbiol 48: 743-772, 1994). Bacteria have developed a variety of mechanisms for the uptake and compartmentalization of iron, due to its low availability in the environment and potential toxicity (Braun and Killmann, Trends Biochem. Sci. 24: 104-109, 1999).

Under aerobic conditions at pH >2, iron exists in the insoluble ferric (Fe¹¹¹) state and, as a consequence, microbes have evolved a variety of mechanisms to acquire this form of iron

(Guerinot, 1994, supra). This is particularly important as iron levels present in the environment are usually low Braun and Killmann, 1999, supra). The uptake of iron is facilitated by bacteria in a number of ways. Common methods include production of iron (Fe¹¹) chelators (siderophores), uptake of iron from host chelators (e.g. lactoferrin), with both of these systems commonly found in pathogenic bacteria (Litwin and Calderwood, Clin. Microbiol. Rev. 6: 137-149, 1993), and finally uptake of the soluble ferrous iron (Fe¹¹).

In accordance with the present invention, the inventors have identified a multi-copper oxidase in a Pseudomonas species involved in Fe¹¹ acquisition. This represents a novel approach to Fe¹¹ acquisition and processing in prokaryotic organisms. The identification of this multi-copper oxidase permits screening for agonists and antagonists for this and functionally and/or structurally related enzymes in both prokaryotic and eukaryotic cells.

SUMMARY OF THE INVENTION

Throughout this specification, unless the context requires otherwise, the word "comprise", or variations such as "comprises" or "comprising", will be understood to imply the inclusion of a stated element or integer or group of elements or integers but not the exclusion of any other element or integer or group of elements or integers.

Nucleotide and amino acid sequences are referred to by a sequence identifier number (SEQ ID NO:). The SEQ ID NOs: correspond numerically to the sequence identifiers <400>1 (SEQ ID NO:l), <400>2 (SEQ ID NO:2), etc. A sequence listing is provided after the claims.

The present invention provides a multi-copper oxidase from Pseudomonas aeruginosa involved in Fe¹¹ acquisition. The ability to acquire Fe¹¹ permits its use in a range of metabolic and/or electron transport applications as well as providing a means for tolerance and/or resistance to this metal ion. Antagonists of the multi-copper oxidase identified in accordance with the present invention are useful not only in treating Pseudomonas infection but also infection by other microorganisms with structurally and functionally similar multi-copper oxidases. Furthermore, agonists are also useful for modulating metal ion acquisition in prokaryotic and eukaryotic organisms with similar multi-copper oxidases. This is particularly relevant for the treatment of a range of disease conditions.

The present invention provides, therefore, an isolated polypeptide or a derivative or chemical analog thereof wherein said polypeptide is characterized, when in active form, of having multi-copper oxidase activity, being capable of facilitating metal ion uptake into a cell and being isolatable from a prokaryotic organism.

More particularly, the present invention is directed to an isolated polypeptide or derivative or chemical analog thereof wherein said polypeptide is characterized, when in active form, of having multi-copper oxidase activity, being involved in Fe¹¹ acquisition, and being isolatable from a prokaryotic organism. Even more particularly, the present invention is directed to an isolated multi-copper oxidase or a derivative or chemical analog thereof wherein said multi-copper oxidase is isolatable from a prokaryotic organism and is capable or associated with, when in active form, of Fe¹¹ acquisition in said prokaryotic organism.

The present invention further contemplates a genetic sequence encoding the subject polypeptide and more particularly the subject multi-copper oxidase.

Still the present invention provides agonists and antagonists of the subject polypeptide and more particularly the subject multi-copper oxidase.

Another aspect of the present invention is directed to an isolated polypeptide or a derivative or chemical analog thereof wherein said polypeptide is characterized as having at least about 15% similarity at the amino acid level after optimal alignment to Fet3 from yeast and, when in active form, exhibits multi-copper oxidase activity including a capacity for facilitating the uptake of Fe¹¹ by a prokaryotic microorganism.

Yet another aspect of the present invention provides an isolated multi-copper oxidase from P. aeruginosa or a derivative, homolog or chemical analog of said multi-copper oxidase wherein said multi-copper oxidase is characterized as having at least about 15% similarity to Fet3 from yeast and facilitates Fe¹¹ acquisiton by said P. aeruginosa.

Still another aspect of the present invention contemplates a method for identifying a polypeptide potentially exhibiting multi-copper oxidase activity from a prokaryotic microorganism, said method comprising searching complete and/or incomplete microbial genomes for corresponding amino acid sequences having at least 15% homology to a multi-copper oxidase from a eukaryotic cell and selecting contigs with homologous regions for an open reading frame with at least about 15% similarity to the nucleotide sequence encoding said eukaryotic multi-copper oxidase. Still yet another aspect of the present invention provides an isolated multi-copper oxidase from a prokaryotic microorganism or a derivative or chemical analog of said multi-copper oxidase wherein said multi-copper oxidase comprises an amino acid sequence substantially set forth in one or more of SEQ ID NOS:l-12 or an amino acid sequence having at least about 15% similarity to one or more of SEQ ID NOS: 1-12 or SEQ ID NO:28 or SEQ ID NO:30.

Even yet another aspect of the present invention is directed to an isolated nucleic acid molecule comprising a sequence of nucleotides which encode or are complementary to a sequence which encodes a polypeptide or a derivative of said polypeptide wherein the polypeptide, when in active form, has multi-copper oxidase activity, is involved in metal ion uptake into a cell and is obtainable from a prokaryotic microorganism.

A further aspect of the present invention is directed to an isolated nucleic acid molecule or a genetic construct comprising said nucleic acid molecule wherein said nucleic acid molecule comprises a nucleotide sequence encoding or complementary to a sequence encoding an amino acid sequence substantially as set forth in one or more of SEQ D NOS-.1-12 or SEQ JD NO:28 or SEQ ID NO:30 or an amino acid sequence having at least 15% similarity to one or more of SEQ ID NOS:l-12 or SEQ ID NO:28 or SEQ ID NO:30 or a nucleotide sequence capable of hybridizing to said first mentioned nucleotide sequence under low stringency conditions.

Another aspect of the present invention comprises an amino acid sequence as set forth in SEQ ID NO:20 or an amino acid sequence having 15% similarity to SEQ ID NO:20 or to a sub-region thereof.

Yet another aspect of the present invention comprise a nucleotide sequence as set forth in SEQ ID NO: 19 or a nucleotide sequence having at least about 15% similarity to SEQ ID NO: 19 or a sub-region thereof or a nucleotide sequence capable of hybridizing to SEQ ID NO: 19 or a sub-region thereof or its complementary form under low stringency conditions. Still another aspect of the present invention contemplates a method for detecting a multi- copper oxidase in a biological sample from a subject said method comprising contacting said biological sample with an antibody specific for or immunologically cross-reactive with said multi-copper oxidase or its derivatives or homologs for a time and under conditions sufficient for an antibody-multi-copper oxidase complex to form, and then detecting said complex.

Still yet another aspect of the present invention contemplates a method for modulating metal ion and in particular Fe¹¹ acquisition by a cell, said method comprising administering to said cell or a higher organism comprising said cell an amount of an effector molecule capable of modulating the function of a multi-copper oxidase from a prokaryotic organism which multi-copper oxidate facilitates metal ion uptake in said prokaryotic organism.

Even yet another aspect of the present invention is encoded by a nucleotide sequence comprising a sequence of nucleotides which encodes a eukaryotic multi-copper oxidase signature sequence such as but not limited to amino acid sequences set forth in SEQ TD NO: 15 and SEQ ID NO: 16 or an amino acid sequence having 60% similarity thereto to either SEQ ID NO:15 or SEQ ID NO: 16.

A further aspect of the present invention is encoded by a nucleotide sequence comprising a sequence of nucleotides which encodes a eukaryotic multi-copper oxidase signature sequence such as but not limited to nucleotide sequences set forth in SEQ ID NO: 17 and SEQ ID NO: 18 or a nucleotide sequence having 60% similarity thereto or nucleotide sequences capable of hybridizing to the sequences set forth in SEQ ID NO: 17 and SEQ ID NO: 18 or their complementary forms under low stringency conditions.

Another aspect of the present invention provides a method for modulating metal ion uptake in a cell, said method comprising introducing to said cell or a parent of said cell a nucleic acid molecule encoding a polypeptide which functions as a multi-copper oxidase and is derivable from a prokaryotic microorganism. BRIEF DESCRIPTION OF THE FIGURES

Figure 1 is a representation showing alignment of bacterial multi-copper oxidase. The bacterial multi-copper oxidase in accordance with the present invention are aligned in the alignment with other previously characterized multi-copper oxidases. Highlighted in grey in the region of amino acid number 156 to amino acid number 194 is a region which has homology to the first signature sequence of eukaryotic multi-copper oxidases, and identifies copper binding histidines, thought to be part of the type 1 copper centre, this signature sequence also detects proteins which contain only a type 1 copper centre. The second signature sequence of the eucaryotic multi-copper oxidases includes the copper binding residues of the type 3 and type 1 copper centres. Homology to this signature sequence occurs in the amino acids of 644 to 686, highlighted in blue is a region which shows high homology to both the consensus signature sequences. The sequences highlighted in green, on the E. coli, Salmonella and Rhodobacter multi-copper oxidases have homology to only the second multi-copper oxidase signature sequence. KEY: Aeromonas - Aeromonas veronii, Bordetella - Bordetella pertussis this study, E. coli - YacK/CueO gene of Escherichia coli (Grass and Rensing, 2001, supra), Caulobacte - Caulobacter crescentus this study, coryne - Corynebacterium; Pseudomona - Pseudomonas aeruginosa PAO1 this study, Klebsiella - Klebsiella pneumonia this study, Mycobacter - Mycobacterium tuberculosis this study, Rhodobacte, Rhodobacter capsulatus this study; Salmonella - Salmonella typhimurium this study, Xanthomonas Xanthomonas campestris pv. Juglandis (Lee et al, J. Bacterio 176: 173-188, 1994) Consensus symbols: ! is anyone of TV; $ is anyone of LM; % is anyone of FY; # is anyone of NDQEBZ; Amino acids in blue are identical and those in red are similar.

Figure 2 is a diagrammatic representation showing a phylogenetic tree of bacterial multi- copper oxidase described during this investigation. Tree was constructed using the amino acid sequence of the proposed multi-copper oxidases using arb. Key: LEGIO- Legionella pneumophilia, CORYNE - Corynebacterium diptheriaei, RHODOC - Rhodobacger capsulatus, STYPHl - Salmonella typhi, E. COLI - Escherichia coli K-12 MG1655, CAULO - Caulobacter crescentus, MYCO33 - Mycobacterium tuberculosis CSU#93, BORDP - Bordetella pertussis, GENE1 - Pseudomonas aeruginosa PAO1, KLEBS - Klebsiella pneumoniae.

Figure 3 is a photographic representation showing Southern blots used to examine the genotype of P. aeruginosa multi-copper oxidase mutant. Blot 1 was conducted using a DIG- labeled probe generated from the suicide vector pJP5608. Lane 1 is the positive control pJP5608, Lane 2 is P. aeruginosa wild-type strain PAK genomic DNA, lane 3 is multi-copper oxidase mutant genomic DNA. DNA was digested by a double digest using Ncol and EcoRl (ΝΕ Biolabs). Blot 2 was conducted using a probe generated from the PCR product of the P. aeruginosa multi-copper gene. Lane 1 is the PCR product (positive control), lane 2 is PAK wild-type genomic DΝA, lane 3 is multi-copper oxidase mutant genomic DΝA. The genomic DΝA was digested using the restriction enzyme Ncol (ΝΕ Biolabs). This blot shows a different result of the digest between the multi-copper oxidase mutant and wild-type indicating that gene 1 has been disrupted in the mutant

Figure 4 is a graphical representation of the growth curve of P. aeruginosa wild-type and multi-copper oxidase mutant. Strains were examined during aerobic growth on minimal media and minimal media supplemented with FeSO₄.

Figure 5 is a graphical representation of the growth curve of P. aeruginosa wild-type and multi-copper oxidase mutant. The concentration of iron has been varied to show the iron dependent nature of aerobic growth of the multi-copper oxidase mutant.

Figure 6 is a representation showing the result of DΝA sequencing of PCR product from P. aeruginosa genomic DΝA to obtain multi-copper oxidase gene for complementation and overexpression of multi-copper oxidase gene. Sequence was obtained using the Ml 3 primer which is found adjacent to the multi-copper cloning site in pUCPSK (Watson et al, Gene 172: 163-164, 1996).

Figure 7 is a representation showing the nucleotide and protein sequence of the proposed P. aeruginosa multi-copper oxidase. Represented on the Figure in shaded area are nucleotides 395 to 466 which is a region with homology to eukaryotic multi-copper oxidase signature sequence 1 and nucleotides 1801 to 1890 which is a region homologous to eukaryotic multi-copper oxidase signature sequence 1 and 2.

Figure 8 is a representation showing ClustlW alignment of the copper binding segments of CueO from E. coli, with the homologous regions from the MCO (PcoA) protein from P. aeruginosa. The copper binding ligands identified in the CueO crystal structure (PDΕ TD :IKV7) and the homologous residues in the MCO protein are shown in shading. Amino acid residues are numbered accordingly with CueO numbers above and MCO numbers below the alignment (see-Roberts et al, Proc. Natl. Acad. Sci. USA 99: 2766-2771, 2002).

A summary of sequence identifiers used throughout the subject specification is provided below.

SUMMARY OF SEQUENCE IDENTIFIERS

Known as E. coli YacK or CueO

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

The present invention is predicated in part on the identification of an enzyme system useful for permitting metal ion acquisition by prokaryotic organisms. The enzyme system is a multi-copper oxidase system and generally involves the acquisition of Fe .

Accordingly, the present invention provides an isolated polypeptide or a derivative or chemical analog thereof wherein said polypeptide is characterized, when in active form, of having multi-copper oxidase activity, being capable of facilitating metal ion uptake into a cell and being isolatable from a prokaryotic organism.

Reference to "multi-copper oxidase activity" means in accordance with the present invention an enzyme or group of enzymes which catalyze the oxidation of a metal ion and in particular Fe¹¹. Although not intending to limit the present invention to any one theory or mode of action, it is proposed that Fe¹¹ is oxidized by the multi-copper oxidase and that Fe^ιπ is stored in the periplasm (in the case of a Gram-negative bacterium) or transported into the cytoplasm by a specific Fe^ιπ transporter. The term "uptake" may be considered synonymously with "acquisition". The terms "uptake" and "acquisition" also encompass tolerance.

Accordingly, another aspect of the present invention provides an isolated polypeptide or derivative or chemical analog thereof wherein said polypeptide is characterized, when in active form, of having multi-copper oxidase activity, being involved in Fe¹¹ acquisition, and being isolatable from a prokaryotic organism.

The preferred multi-copper oxidase of the present invention also exhibits laccase activity, i.e. a role in the oxidation of aromatic amines and phenolic compounds.

The term "polypeptide" is used in its broadest sense and includes a polypeptide or a fragment such as a peptide fragment having multi-copper oxidase activity. Multi-copper oxidase activity includes an ability to facilitate Fe¹¹ acquisition, and optionally, exhibiting laccase activity or, more preferably, exhibiting both properties. Preferably, the polypeptide is a multi-copper oxidase. A "polypeptide" also includes a derivative or homolog and which retains multi-copper oxidase activity and is still capable of facilitating Fe acquisition. A derivative also includes mutants which have lost, for example, laccase activity but return Fe¹¹ acquisition ability.

Accordingly, another aspect of the present invention is directed to an isolated multi-copper oxidase or a derivative or chemical analog thereof wherein said multi-copper oxidase is isolatable from a prokaryotic organism and is capable or associated with, when in active form, of Fe¹¹ acquisition in said prokaryotic organism.

A particularly preferred multi-copper oxidase of the present invention exhibits homology at the amino acid or corresponding nucleotide level to a eukaryotic multi-copper oxidase or to a region thereof comprising a conserved amino acid sequence such as but not limited to a copper binding site. A particularly useful reference to multi-copper oxidase is Fet3 from yeast (Hassett et al, 1998b, supra; Wimmer et al, 1999, supra) Conveniently, homology at the amino acid level to Fet3 of a prokaryotic multi-copper oxidase or a conserved region thereof such as a copper binding site is at least about 15%, preferably at least about 20%, preferably at least about 30%, preferably at least about 40%, preferably at least about 50%; preferably at least about 60%; preferably at least about 70%, preferably at least about 80%, preferably at least about 90% or above such as 95% or 96% or 97% or 98% or 99% or 100%. Similar percentage similarities apply at the genetic level with respect to nucleotide sequences which encode Fet3 or a conserved region thereof such as a copper binding site, i.e. from at least about 15-90% or above. Most preferably, multi-copper oxidases contemplated by the present invention have percentage similarity with respect to conserved regions such as copper binding sites.

Accordingly, another aspect of the present invention is directed to an isolated polypeptide or a derivative or chemical analog thereof wherein said polypeptide is characterized as having at least about 30% similarity at the amino acid level after optimal alignment to Fet3 from yeast and, when in active form, exhibits multi-copper oxidase activity including a capacity for facilitating the uptake of Fe¹¹ by a prokaryotic microorganism.

The term "similarity" as used herein includes exact identity between compared sequences at the nucleotide or amino acid level. Where there is non-identity at the nucleotide level, "similarity" includes differences between sequences which result in different amino acids that are nevertheless related to each other at the structural, functional, biochemical and/or conformational levels. Where there is non-identity at the amino acid level, "similarity" includes amino acids that are nevertheless related to each other at the structural, functional, biochemical and/or conformational levels. In a particularly preferred embodiment, nucleotide and sequence comparisons are made at the level of identity rather than similarity.

Terms used to describe sequence relationships between two or more polynucleotides or polypeptides include "reference sequence", "comparison window", "sequence similarity", "sequence identity", "percentage of sequence similarity", "percentage of sequence identity", "substantially similar" and "substantial identity". A "reference sequence" is at least 12 but frequently 15 to 18 and often at least 25 or above, such as 30 monomer units, inclusive of nucleotides and amino acid residues, in length. Because two polynucleotides may each comprise (1) a sequence (i.e. only a portion of the complete polynucleotide sequence) that is similar between the two polynucleotides, and (2) a sequence that is divergent between the two polynucleotides, sequence comparisons between two (or more) polynucleotides are typically performed by comparing sequences of the two polynucleotides over a "comparison window" to identify and compare local regions of sequence similarity. A "comparison window" refers to a conceptual segment of typically 12 contiguous residues that is compared to a reference sequence. The comparison window may comprise additions or deletions (i.e. gaps) of about 20% or less as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Optimal alignment of sequences for aligning a comparison window may be conducted by computerized implementations of algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Drive Madison, WI, USA) or by inspection and the best alignment (i.e. resulting in the highest percentage homology over the comparison window) generated by any of the various methods selected. Reference also may be made to the BLAST family of programs as, for example, disclosed by Altschul et al, Nucl. Acids Res. 25: 3389-3402,, 1997 . A detailed discussion of sequence analysis can be found in Unit 19.3 of Ausubel et al, "Current Protocols in Molecular Biology", John Wiley & Sons, Inc., Chapter 15, 1994-1998.

The terms "sequence similarity" and "sequence identity" as used herein refers to the extent that sequences are identical or functionally or structurally similar on a nucleotide-by- nucleotide basis or an amino acid-by-amino acid basis over a window of comparison. Thus, a "percentage of sequence identity", for example, is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g. A, T, C, G, I) or the identical amino acid residue (e.g. Ala, Pro, Ser, Thr, Gly, Val, Leu, He, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn, Gin, Cys and Met) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity. For the purposes of the present invention, "sequence identity" will be understood to mean the "match percentage" calculated by the DNASIS computer program (Version 2.5 for windows; available from Hitachi Software engineering Co., Ltd., South San Francisco, California, USA) using standard defaults as used in the reference manual accompanying the software. Similar comments apply in relation to sequence similarity.

The term "prokaryotic" microorganism is used in its broadest sense and includes any microorganism which is not a eukaryotic organism. A prokaryotic microorganism includes Gram positive, Gram negative and Gram variable microorganisms. Particular microorganisms include but are not limited to Pseudomonas sp., Sahnonella sp., Enterobacter sp., Escherichia coli sp., Klebsiella sp., Bordetella sp., Caulobacter sp., Aeromonas sp., Legionella sp., Pasteurella sp., Xanthomonas sp., Corynebacterium sp., Mycobacterium sp., Staphylococcus sp., Streptococcus sp. and Bacillus sp. amongst other microorganisms .

Particularly preferred microorganisms are Pseudomonas aeruginosa, Bordetella pertussis, Mycobacterium tuberculosis and Salmonella typhimurium.

hi another embodiment, the multi-copper oxidase is encoded by a nucleotide sequence comprising a sequence of nucleotides which encodes a eukaryotic multi-copper oxidase signature sequence such as but not limited to amino acid sequences set forth in SEQ TD NO: 15 and SEQ ID NO: 16 or an amino acid sequence having 60% similarity thereto to either SEQ ID NO: 15 or SEQ TD NO: 16.

Even more particularly, the multi-copper oxidase is encoded by a nucleotide sequence comprising a sequence of nucleotides which encodes a eukaryotic multi-copper oxidase signature sequence such as but not limited to nucleotide sequences set forth in SEQ ID NO:17 and SEQ ID NO:18 or a nucleotide sequence having 60% similarity thereto or nucleotide sequences capable of hybridizing to the sequences set forth in SEQ ID NO: 17 and SEQ ID NO: 18 or their complementary forms under low stringency conditions.

This aspect of the present invention is particularly directed to genes encoding multi-copper oxidases having eukaryotic signature sequences such as shown in Figure 7.

The present invention is particularly exemplified by a multi-copper oxidase from P. aeruginosa. This is done, however, with the understanding that the present invention extends to any novel multi-copper oxidase from any prokaryotic microorganism and in particular those having at least about 15% similarity to Fet3 from yeast and which, in bacteria, facilitate Fe¹¹ acquisition and optionally exhibit laccase activity.

Accordingly, another aspect of the present invention provides an isolated multi-copper oxidase from P. aeruginosa or a derivative, homolog or chemical analog of said multi- copper oxidase wherein said multi-copper oxidase is characterized as having at least about 15% similarity to Fet3 from yeast and facilitates Fe¹¹ acquisiton by said P. aeruginosa. By "homolog" is meant a multi-copper oxidase from another strain of P. aeruginosa or from another species of Pseudomonas or from another Gram negative microorganism or from another prokaryotic microorganism. A "homolog" may also be from a eukaryotic organism.

The term "multi-copper oxidase" includes a protein or polypeptide or a peptide having multi-copper oxidase activity or exhibiting a physical structure or amino acid sequence analogous or similar or homologous to a multi-copper oxidase. A multi-copper oxidase of the present invention is also involved in metal ion uptake and in particular Fe¹¹ acquisition in a prokaryotic organism. Such multi-copper oxidases may also be involved in the acquisition of other metal ions such as Cu¹¹. Copper acquisition as a detoxification mechanism is particularly encompassed by the present invention.

The present invention further contemplates a method for identifying a polypeptide potentially exhibiting multi-copper oxidase activity from a prokaryotic microorganism, said method comprising searching complete and/or incomplete microbial genomes for corresponding amino acid sequences having at least 15% homology to a multi-copper oxidase from a eukaryotic cell and selecting contigs with homologous regions for an open reading frame with at least about 15% similarity to the nucleotide sequence encoding said eukaryotic multi-copper oxidase.

Preferably, the eukaryotic multi-copper oxidase is from a yeast and is, for example, Fet3.

A "derivative" of the multi-copper oxidase or polypeptide having multi-copper oxidase activity includes a single or multiple amino acid substitution, deletion and/or addition to the naturally occurring molecule. A derivative may also be a polymorphism. The derivative may, therefore, be naturally occurring or induced by, for example, recombinant or mutagenesis techniques. A derivative further includes a hybrid or fusion protein suchas between two different multi-copper oxidases. This enables the development of broader spectrum enzymes involved in the acquisition or detoxification of a range of metal ions. Furthermore, a derivative includes a molecule capable of facilitating Fe¹¹ acquisition with a loss of laccase activity or vice versa.

Other derivatives of the subject multi-copper oxidase include chemical analogs. Analogs of the multi-copper oxidase contemplated herein include, but are not limited to, modifications of side chains, incorporation of unnatural amino acids and/or their derivatives during peptide, polypeptide or protein synthesis and the use of crosslinkers and other methods which impose conformational constraints on the proteinaceous molecule or their analogs. Such chemical analogs are particularly useful due to their stability and/or resistance to enzymatic degradation.

Examples of side chain modifications contemplated by the present invention include modifications of amino groups such as by reductive alkylation by reaction with an aldehyde followed by reduction with NaBH₄; amidination with methylacetimidate; acylation with acetic anhydride; carbamoylation of amino groups with cyanate; trinitrobenzylation of amino groups with 2, 4, 6-trinitrobenzene sulphonic acid (TNBS); acylation of amino groups with succinic anhydride and tetrahydrophthalic anhydride; and pyridoxylation of lysine with pyridoxal-5-phosphate followed by reduction with NaBH₄.

The guanidine group of arginine residues may be modified by the formation of heterocyclic condensation products with reagents such as 2,3-butanedione, phenylglyoxal and glyoxal.

The carboxyl group may be modified by carbodiimide activation via O-acylisourea formation followed by subsequent derivitization, for example, to a corresponding amide.

Sulphydryl groups may be modified by methods such as carboxymethylation with iodoacetic acid or iodoacetamide; performic acid oxidation to cysteic acid; formation of a mixed disulphides with other thiol compounds; reaction with maleimide, maleic anhydride or other substituted maleimide; formation of mercurial derivatives using 4- chloromercuribenzoate, 4-chloromercuriphenylsulphonic acid, phenylmercury chloride, 2- chloromercuri-4-nitrophenol and other mercurials; carbamoylation with cyanate at alkaline pH.

Tryptophan residues may be modified by, for example, oxidation with N- bromosuccinimide or alkylation of the indole ring with 2-hydroxy-5-nitrobenzyl bromide or sulphenyl halides. Tyrosine residues on the other hand, may be altered by nitration with tetranitromethane to form a 3-nitrotyrosine derivative.

Modification of the imidazole ring of a histidine residue may be accomplished by alkylation with iodoacetic acid derivatives or N-carbethoxylation with diethylpyrocarbonate.

Examples of incorporating unnatural amino acids and derivatives during peptide synthesis include, but are not limited to, use of norleucine, 4-amino butyric acid, 4-amino-3- hydroxy-5-phenylpentanoic acid, 6-aminohexanoic acid, t-butylglycine, norvaline, phenylglycine, ornithine, sarcosine, 4-amino-3-hydroxy-6-methylheptanoic acid, 2-thienyl alanine and/or D-isomers of amino acids. A list of unnatural amino acid, contemplated herein is shown in Table 1.

TABLE 1

Non-conventional Code Non-conventional Code amino acid amino acid

α-aminobutyric acid Abu L-N-methylalanine Nmala α-amino-α-methylbutyrate Mgabu L-N-methylarginine Nmarg aminocyclopropane- Cpro L-N-methylasparagine Nmasn carboxylate L-N-methylaspartic acid Nmasp aminoisobutyric acid Aib L-N-methylcysteine Nmcys aminonorbornyl- Norb L-N-methylglutamine Nmgln carboxylate L-N-methylglutamic acid Nmglu cyclohexylalanine Chexa L-Nmethylhistidine Nmhis cyclopentylalanine Cpen L-N-methylisolleucine Nmile D-alanine Dal L-N-methylleucine Nmleu

D-arginine Darg L-N-methyllysine Nmlys

D-aspartic acid Dasp L-N-methylmethionine Nmmet

D-cysteine Dcys L-N-methylnorleucine Nmnle

D-glutamine Dgln L-N-methylnorvaline Nmnva D-glutamic acid Dglu L-N-methylornithine Nmorn

D-histidine Dhis L-N-methylphenylalanine Nmphe

D-isoleucine Dile L-N-methylproline Nmpro

D-leucine Dleu L-N-methylserine Nmser

D-lysine Dlys L-N-methylthreonine Nmthr D-methionine Dmet L-N-methyltryptophan Nmtrp

D-ornithine Dorn L-N-methyltyrosine Nmtyr

D-phenylalanine Dphe L-N-methylvaline Nmval

D-proline Dpro L-N-methylethylglycine Nmetg

D-serine Dser L-N-methyl-t-butylglycine N tbug D-threonine Dthr L-norleucine Nle

D-tryptophan Dtrp L-norvaline Nva D-tyrosine Dtyr α-methyl-aminoisobutyrate Maib

D-valine Dval α-methyl-γ-aminobutyrate Mgabu

D-α-methylalanine Dmala α-methylcyclohexylalanine Mchexa

D-α-methylarginine Dmarg α-methylcylcopentylalanine Mcpen D-α-methylasparagine Dmasn α-methyl-α-napthylalanine Manap

D-α-methylaspartate Dmasp α-methylpenicillamine Mpen

D-α-methylcysteine Dmcys N-(4-aminobutyl)glycine Nglu

D-α-methylglutamine Dmgln N-(2-aminoethyl)glycine Naeg

D-α-methylhistidine Dmhis N-(3-aminopropyl)glycine Norn D-α-methylisoleucine Dmile N-amino-α-methylbutyrate Nmaabu

D-α-methylleucine Dmleu α-napthylalanine Anap

D-α-methyllysine Dmlys N-benzylglycine Nphe

D-α-methylmethionine Dmmet N-(2-carbamylethyl)glycine Ngln

D-α-methylornithine Dmorn N-(carbamylmethyl)glycine Nasn D-α-methylphenylalanine Dmphe N-(2-carboxyethyl)glycine Nglu

D-α-methylproline Dmpro N-(carboxymethyl)glycine Nasp

D-α-methylserine Dmser N-cyclobutylglycine Ncbut

D-α-methylthreonine Dmthr N-cycloheptylglycine Nchep

D-α-methyltryptophan Dmtrp N-cyclohexylglycine Nchex D-α-methyltyrosine Dmty N-cyclodecylglycine Ncdec

D-α-methylvaline Dmval N-cylcododecylglycine Ncdod

D-N-methylalanine Dnmala N-cyclooctylglycine Ncoct

D-N-methylarginine Dnmarg N-cyclopropylglycine Ncpro

D-N-methylasparagine Dnmasn N-cycloundecylglycine Ncund D-N-methylaspartate Dnmasp N-(2,2-diphenylethyl)glycine Nbhm

D-N-methylcysteine Dnmcys N-(3,3-diphenylpropyl)glycine Nbhe

D-N-methylglutamine Dnmgln N-(3-guanidinopropyl)glycine Narg

D-N-methylglutamate Dnmglu N-(l-hydroxyethyl)glycine Nthr

D-N-methylhistidine Dnmhis N-(hydroxyethyl))glycine Nser D-N-methylisoleucine Dnmile N-(imidazolylethyl))glycine Nhis D-N-methylleucine Dnmleu N-(3-indolylyethyl)glycine Nhtrp

D-N-methyllysine Dnmlys N-methyl-γ-aminobutyrate Nmgabu

N-methylcyclohexylalanine Nmchexa D-N-methylmethionine Dnmmet

D-N-methylornithine Dnmorn N-methylcyclopentylalanine Nmcpen N-methylglycine Nala D-N-methylphenylalanine Dnmphe

N-methylaminoisobutyrate Nmaib D-N-methylproline Dnmpro

N-(l-methylpropyl)glycine Nile D-N-methylserine Dnmser

N-(2-methylpropyl)glycine Nleu D-N-methylthreonine Dnmthr

D-N-methyltryptophan Dnmtrp N-(l-methylethyl)glycine Nval D-N-methyltyrosine Dnmtyr N-methyla-napthylalanine Nmanap

D-N-methylvaline Dnmval N-methylpenicillamine Nmpen γ-aminobutyric acid Gabu N-(p-hydroxyphenyl)glycine Nhtyr

L-t-butylglycine Tbug N-(thiomethyl)glycine Ncys

L-ethylglycine Etg penicillamine Pen L-homophenylalanine Hphe L-α-methylalanine Mala

L-α-methylarginine Marg L-α-methylasparagine Masn

L-α-methylaspartate Masp L-α-methyl-t-butylglycine Mtbug

L-α-methylcysteine Mcys L-methylethylglycine Metg

L-α-methylglutamine Mgln L-α-methylglutamate Mglu L-α-methylhistidine Mhis L-α-methylhomophenylalanine Mhphe

L-α-methylisoleucine Mile N-(2-methylthioethyl)glycine Nmet

L-α-methylleucine Mleu L-α-methyllysine Mlys

L-α-methylmethionine Mmet L-α-methylnorleucine Mnle

L-α-methylnorvaline Mnva L-α-methylornithine Morn L-α-methylphenylalanine Mphe L-α-methylproline Mpro

L-α-methylserine Mser L-α-methyltlireonine Mthr

L-α-methyltryptophan Mtrp L-α-methyltyrosine Mtyr

L-α-methylvaline Mval L-N-methylhomophenylalanine Nmhphe

N-(N-(2,2-diphenylethyl) Nnbhm N-(N-(3,3-diphenylpropyl) Nnbhe carbamylmethyl)glycine carbamylmethyl)glycine 1 -carboxy- l-(2,2-diphenyl- Nmbc ethylan ino)cyclopropane

Crosslinkers can be used, for example, to stabilize 3D conformations, using homo- bifunctional crosslinkers such as the bifunctional imido esters having (CH₂)_n spacer groups with n=l to n=6, glutaraldehyde, N-hydroxysuccinimide esters and hetero-bifunctional reagents which usually contain an amino-reactive moiety such as N-hydroxysuccinimide and another group specific-reactive moiety such as maleimido or dithio moiety (SH) or carbodumide (COOH). In addition, peptides can be conformationally constrained by, for example, incorporation of C_a and N _ormethylamino acids, introduction of double bonds between C_a and Cβ atoms of amino acids and the formation of cyclic peptides or analogs by introducing covalent bonds such as forming an amide bond between the N and C termini, between two side chains or between a side chain and the N or C terminus.

Particularly preferred prokaryotic multi-copper oxidases comprise an amino acid sequence set forth in one of SEQ ID NOS: 1-12 or SEQ ID NO:28 or SEQ ID NO:30 or an amino acid sequence having at least about 15% similarity to one or more of SEQ ID NOS:l-12 or SEQ ID NO:28 or SEQ TD NO:30.

Accordingly, another aspect of the present invention provides an isolated multi-copper oxidase from a prokaryotic microorganism or a derivative or chemical analog of said multi-copper oxidase wherein said multi-copper oxidase comprises an amino acid sequence substantially set forth in one or more of SEQ ID NOS: 1-12 or SEQ JD NO:28 or SEQ ID NO: 30 or an amino acid sequence having at least about 15% similarity to one or more of SEQ ID NOS: 1-12 or SEQ ID NO:28 or SEQ ID NO:30.

The present invention extends to genetic sequences encoding multi-copper oxidases of the present invention.

Accordingly, another aspect of the present invention is directed to an isolated nucleic acid molecule comprising a sequence of nucleotides which encode or are complementary to a sequence which encodes a polypeptide or a derivative of said polypeptide wherein the polypeptide, when in active form, has multi-copper oxidase activity, is involved in metal ion uptake into a cell and is obtainable from a prokaryotic microorganism.

In one embodiment, the multi-copper oxidase facilitates Fe¹¹ acquisition.

In another embodiment, the multi-copper oxidase comprises an amino acid sequence having at least about 15% similarity to a yeast multi-copper oxidase such as but not limited to Fet3.

In yet another embodiment, the multi-copper oxidase is from a Pseudomonas species such as but not limited to P. aeruginosa. The present invention, however, extends to a multi- copper oxidase from any microorganism.

A nucleic acid molecule may be a single or double stranded sequence of deoxyribonucleotides or ribonucleotides or a hybrid of both and be in linear or covalently closed circular form. The nucleic acid molecule is preferably in the form of DNA and may be cDNA or genomic DNA. The nucleic acid molecule may also comprise a vector or plasmid or other genetic construct. Such a genetic construct may be of bacterial or viral origin.

Yet another aspect of the present invention is directed to an isolated nucleic acid molecule or a genetic construct comprising said nucleic acid molecule wherein said nucleic acid molecule comprises a nucleotide sequence encoding or complementary to a sequence encoding an amino acid sequence substantially as set forth in one or more of SEQ TD NOS:l-12 or SEQ ID NO:28 or SEQ ID NO:30 or an amino acid sequence having at least 15% similarity to one or more of SEQ ID NOS.-1-12 or SEQ TD NO:28 or SEQ ID NO:30 or a nucleotide sequence capable of hybridizing to said first mentioned nucleotide sequence under low stringency conditions. In a preferred embodiment, the multi-copper oxidase comprises an amino acid sequence as set forth in SEQ ID NO:20 or an amino acid sequence having 15% similarity to SEQ ID NO:20 or to a sub-region thereof.

Preferably, the sub-region is a eukaryotic multi-copper oxidase signature sequence such as but not limited to the amino acid sequences set forth in SEQ ID NO: 15 and SEQ ID NO: 16.

In a particularly preferred embodiment, the multi-copper oxidase is encoded by a nucleotide sequence set forth in SEQ ID NO: 19 or a nucleotide sequence having at least about 15% similarity to SEQ ID NO:19 or a sub-region thereof or a nucleotide sequence capable of hybridizing to SEQ ID NO: 19 or a sub-region thereof or its complementary form under low stringency conditions.

Again, reference to sub-region refers to a nucleotide sequence encoding a eukaryotic multi- copper oxidase signature sequence such as but not limited to the nucleotide sequences set forth in SEQ ID NO: 17 and SEQ ID NO: 18.

Reference herein to a low stringency includes and encompasses from at least about 0 to at least about 15% v/v formamide and from at least about 1 M to at least about 2 M salt for hybridization, and at least about 1 M to at least about 2 M salt for washing conditions.

Generally, low stringency is at from about 25-30°C to about 42°C. The temperature may be altered and higher temperatures used to replace formamide and/or to give alternative stringency conditions. Alternative stringency conditions may be applied where necessary, such as medium stringency, which includes and encompasses from at least about 16% v/v to at least about 30% v/v formamide and from at least about 0.5 M to at least about 0.9 M salt for hybridization, and at least about 0.5 M to at least about 0.9 M salt for washing conditions, or high stringency, which includes and encompasses from at least about 31%) v/v to at least about 50%ι v/v formamide and from at least about 0.01 M to at least about 0.15 M salt for hybridization, and at least about 0.01 M to at least about 0.15 M salt for washing conditions. In general, washing is carried out T_m = 69.3 + 0.41 (G+C)% (Bonner and Laskey, Eur. J. Biochem. 46: 83, 1974). However, the T_m of a duplex DNA decreases by 1°C with every increase of 1% in the number of mismatch base pairs (Marmur and Doty, J. Mol. Biol. 5: 109, 1962). Formamide is optional in these hybridization conditions. Accordingly, particularly preferred levels of stringency are defined as follows: low stringency is 6 x SSC buffer, 0.1% w/v SDS at 25-42°C; a moderate stringency is 2 x SSC buffer, 0.1% w/v SDS at a temperature in the range 20°C to 65°C; high stringency is 0.1 x SSC buffer, 0.1% w/v SDS at a temperature of at least 65°C.

The term "construct" is used in its broadest sense and includes a genetic construct comprising a nucleic acid molecule, vector, plasmid or any other nucleotide sequence. The construct, therefore, is a recombinant molecule engineered to comprise a genetic sequence encoding all or part of a prokaryotic multi-copper oxidase. The genetic constructs of the present invention may be suitable for use in microorganisms or eukaryotic organisms including plants and animals, such as mammals including primates and humans. The use of the subject construct to genetic trans genie plants is particularly useful in order to grow plants in high iron containing regions and/or bioremediation. A plant construct generally comprises a promoter, the coding sequence and a terminator. In one embodiment, the construct is in an isolated form. The term "isolated" includes biologically pure, substantially pure or in another condition where at least one purification step has been performed on a sample comprising the construct. A "purification step" includes, for example, a precipitation, centrifugation and/or a chromatographic or electrophoretic separation. In another embodiment, the genetic construct or part thereof is integrated into the genome of a host cell. The construct may also comprise nucleotide sequences which are lost, removed or rearranged following integration.

The present invention is useful, therefore, to introduce a multi-copper oxidase in plants and other eukaryotic cells such as cells from insects, mammals or reptiles, insofar as the present invention relates to plants, the plants may be monocotyledonous or dicotyledonous plants.

Accordingly, another aspect of the present invention contemplates a method for modulating metal ion uptake in a cell, said method comprising introducing to said cell or a parent of said cell a nucleic acid molecule encoding a polypeptide which functions as a multi-copper oxidase and is derivable from a prokaryotic microorganism.

A plant cell includes protoplasts or other cells derived from plants, gamete-producing cells and cells which regenerate into whole plants. Plant cells include cells in plants as well as protoplasts or other cells in culture.

By "vector" is meant a nucleic acid molecule, preferably a DNA molecule derived, for example, from a plasmid, bacteriophage, or virus, into which a nucleic acid sequence may be inserted or cloned. A vector preferably contains one or more unique restriction sites and may be capable of autonomous replication in a defined host cell including a target cell or tissue or a progenitor cell or tissue thereof, or be integrable with the genome of the defined host such that the cloned sequence is reproducible. Accordingly, the vector may be an autonomously replicating vector, i.e., a vector that exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a linear or closed circular plasmid, an extrachromosomal element, a minichromosome, or an artificial chromosome. The vector may contain any means for assuring self-replication. Alternatively, the vector may be one which, when introduced into a cell, is integrated into the genome of the recipient cell and replicated together with the chromosome(s) into which it has been integrated. A vector system may comprise a single vector or plasmid, two or more vectors or plasmids, which together contain the total DNA to be introduced into the genome of the host cell, or a transposon. The choice of the vector will typically depend on the compatibility of the vector with the cell into which the vector is to be introduced. The vector may also include a selection marker such as an antibiotic resistance gene that can be used for selection of suitable transformants. Examples of such resistance genes are well known to those of skill in the art.

The term "gene" is used in its broadest sense and includes cDNA corresponding to the exons of a gene. Accordingly, reference herein to a "gene" is to be taken to include:- (i) a classical genomic gene consisting of transcriptional and/or translational regulatory sequences and or a coding region and/or non-translated sequences (i.e. introns, 5'- and 3'- untranslated sequences); or

(ii) mRNA or cDNA corresponding to the coding regions and 5'- and 3'- untranslated sequences of the gene; and/or

(iii) a structural region corresponding to the coding regions optionally further comprising untranslated sequences and/or a heterologous promoter sequence which consists of transcriptional and/or translational regulatory regions capable of conferring expression characteristics on said structural region.

The term "gene" is also used to describe synthetic or fusion molecules encoding all or part of a functional product, in particular, a sense or antisense mRNA product or a peptide, oligopeptide or polypeptide or a biologically-active protein. Reference to a "gene" also includes reference to a "synthetic gene".

The term "synthetic gene" refers to a non-naturally occurring gene such as hereinbefore defined which preferably comprises at least one or more transcriptional and/or translational regulatory sequences operably linked to a structural gene sequence.

The term "structural gene" shall be taken to refer to a nucleotide sequence which is capable of being transcribed to produce mRNA and then translated to a peptide, oligopeptide, polypeptide or protein having multi-copper oxidase activity when in active form.

The term "structural gene" also refers to that part of a gene or synthetic gene which is expressed in a cell under the control of a promoter sequence to which it is operably connected. A structural gene may be operably under the control of a single promoter sequence or multiple promoter sequences. Accordingly, the structural gene of a gene may comprise a nucleotide sequence which is capable of encoding an amino acid sequence or is complementary thereto. In this regard, a structural gene which is used in the performance of the instant invention may also comprise a nucleotide sequence which encodes an amino acid sequence yet lacks a functional translation initiation codon and/or a functional translation stop codon and, as a consequence, does not comprise a complete open reading frame. In the present context, the term "structural gene" also extends to a non-coding nucleotide sequences, such as 5'- upstream or 3 '-downstream sequences of a gene which would not normally be translated in a cell which expresses said gene.

Accordingly, in the context of the present invention, a structural gene may also comprise a fusion between two or more open reading frames of the same or different genes. In such embodiments, the invention may be used to modulate the expression of one gene, by targeting different non-contiguous regions thereof or alternatively, to simultaneously modulate the expression of several different genes, including different genes of a multigene family such as a family involved in iron acquisition. In the case of a fusion nucleic acid molecule which is non-endogenous to a particular cell and in particular comprises two or more nucleotide sequences derived from other metal ion acquisition genes, the fusion may provide the added advantage of conferring broad spectrum metal ion acquisition and/or tolerance.

Particularly preferred structural gene according to this aspect of the invention are those which include at least one translatable open reading frame, more preferably further including a translational start codon located at the 5 '-end of said open reading frame, albeit not necessarily at the 5 '-terminus of said structural gene.

For expression in cells, the construct generally comprises, in addition to the polynucleotide sequence, a promoter and optionally other regulatory sequences designed to facilitate expression of the polynucleotide sequence.

Reference herein to a "promoter" is to be taken in its broadest context and includes the transcriptional regulatory sequences of a classical genomic gene, including bacterial promoter elements which are required for accurate transcription initiationand optionally additional regulatory elements (e.g. upstream activating sequences, enhancers and silencers) which alter gene expression in response to particular stimuli. A promoter is usually, but not necessarily, positioned upstream or 5' of a structural gene, the expression of which it regulates.

In the present context, the term "promoter" is also used to describe a synthetic or fusion molecule, or derivative which confers, activates or enhances expression of a nucleic acid molecule in a cell.

Preferred promoters may contain additional copies of one or more specific regulatory elements, to further enhance expression of the sense molecule and/or to alter the spatial expression and/or temporal expression of said sense molecule.

Placing a nucleic acid molecule under the regulatory control of a promoter sequence means positioning the said molecule such that expression is controlled by the promoter sequence. Promoters are generally positioned 5' (upstream) to the genes that they control. In the construction of heterologous promoter/structural gene combinations, it is generally preferred to position the promoter at a distance from the gene transcription start site that is approximately the same as the distance between that promoter and the gene it controls in its natural setting, i.e. the gene from which the promoter is derived. As is known in the art, some variation in this distance can be accommodated without loss of promoter function. Similarly, the preferred positioning of a regulatory sequence element with respect to a heterologous gene to be placed under its control is defined by the positioning of the element in its natural setting, i.e. the genes from which it is derived. Again, as is known in the art, some variation in this distance can also occur.

Examples of promoters suitable for use in the synthetic genes of the present invention include viral, fungal, bacterial, animal and plant derived promoters capable of functioning in plant, animal, insect, fungal, yeast or bacterial cells. The promoter may regulate the expression of the structural gene component constitutively, or differentially with respect to cell, the tissue or organ in which expression occurs or, with respect to the developmental stage at which expression occurs, or in response to external stimuli such as physiological stresses, or pathogens, or metal ions, amongst others.

In the present context, the terms "in operable connection with" or "operably under the control" or similar shall be taken to indicate that expression of the structural gene or multiple structural genes is under the control of the promoter sequence with which it is spatially connected.

The term "terminator" refers to a DNA sequence at the end of a transcriptional unit which signals termination of transcription. Terminators are 3 '-non-translated DNA sequences generally containing a polyadenylation signal, which facilitates the addition of polyadenylate sequences to the 3 '-end of a primary transcript. Terminators are known and described in the literature and they may be isolated from bacteria, fungi, viruses, animals and/or plants or synthesized de novo.

Means for introducing (i.e. transfecting or transforming) cells with the constructs are well- known to those skilled in the art.

The constructs described supra are capable of being modified further, for example, by the inclusion of marker nucleotide sequences encoding a detectable marker enzyme or a functional analog or derivative thereof, to facilitate detection of the synthetic gene in a cell in which it is expressed. According to this embodiment, the marker nucleotide sequences will be present in a translatable format and expressed, for example, as a fusion polypeptide with the translation product(s) of any one or more of the structural genes or alternatively as a non-fusion polypeptide.

The constructs of the present invention may be introduced to a suitable cell without modification as linear DNA, optionally contained within a suitable carrier, such as a cell, virus particle or liposome, amongst others. To produce a genetic construct, the gene of the invention is inserted into a suitable vector or episome molecule, such as a bacteriophage vector, viral vector or a plasmid, cosmid or artificial chromosome vector which is capable of being maintained and/or replicated and/or expressed in the host cell, tissue or organ into which it is subsequently introduced.

The present invention extends to all genetic constructs which include further genetic sequences intended for the maintenance and/or replication of said genetic construct in prokaryotes or eukaryotes and/or the integration of said genetic constructs or a part thereof into the genome of a prokaryotic or eukaryotic cell.

The present invention further contemplates antibodies to the subject multi-copper oxidases of the present invention.

The use of monoclonal antibodies in an immunoassay is particularly preferred because of the ability to produce them in large quantities and the homogeneity of the product. The preparation of hybridoma cell lines for monoclonal antibody production derived by fusing an immortal cell line and lymphocytes sensitized against the immunogenic preparation can be done by techniques which are well known to those who are skilled in the art. (See, for example, Douillard and Hoffman, Basic Facts about Hybridomas, in Compendium of Immunology Vol. II, ed. by Schwartz, 1981; Kδhler and Milstein, Nature 256: 495-499, 1975; Kδhler and Milstein, European Journal of Immunology 6: 511-519, 1976).

Another aspect of the present invention contemplates a method for detecting a multi- copper oxidase in a biological sample from a subject said method comprising contacting said biological sample with an antibody specific for or immunologically cross-reactive with said multi-copper oxidase or its derivatives or homologs for a time and under conditions sufficient for an antibody-multi-copper oxidase complex to form, and then detecting said complex.

The antibodies may also be used as an antagonist of the multi-copper oxidase.

The presence of the multi-copper oxidase may be accomplished in a number of ways such as by Western blotting and ELISA procedures. A wide range of immunoassay techniques are available as can be seen by reference to U.S. Patent Nos. 4,016,043, 4,424,279 and 4,018,653. These, of course, includes both single-site and two-site or "sandwich" assays of the non-competitive types, as well as in the traditional competitive binding assays. These assays also include direct binding of a labeled antibody to a target.

Sandwich assays are among the most useful and commonly used assays and are favoured for use in the present invention. A number of variations of the sandwich assay technique exist, and all are intended to be encompassed by the present invention. Briefly, in a typical forward assay, an unlabeled antibody is immobilized on a solid substrate and the sample to be tested brought into contact with the bound molecule. After a suitable period of incubation, for a period of time sufficient to allow formation of an antibody-antigen complex, a second antibody specific to the antigen, labeled with a reporter molecule capable of producing a detectable signal is then added and incubated, allowing time sufficient for the formation of another complex of antibody-antigen-labeled antibody. The antigen, in this case, is a multi-copper oxidase. Any unreacted material is washed away, and the presence of the antigen is determined by observation of a signal produced by the reporter molecule. The results may either be qualitative, by simple observation of the visible signal, or may be quantitated by comparing with a control ample containing known amounts of hapten. Variations on the forward assay include a simultaneous assay, in which both sample and labeled antibody are added simultaneously to the bound antibody. These techniques are well known to those skilled in the art, including any minor variations as will be readily apparent. In accordance with the present invention, the sample is one which might contain multi-copper oxidase including cell extract, tissue biopsy or possibly serum, saliva, mucosal secretions, lymph, tissue fluid and respiratory fluid or a sample from an environmental location. The sample is, therefore, generally a biological sample comprising biological fluid but also extends to fermentation fluid and cell culture fluid.

In a typical forward sandwich assay, a first antibody having specificity for the multi- copper oxidase or antigenic parts thereof, is either covalently or passively bound to a solid surface. The solid surface is typically glass or a polymer, the most commonly used polymers being cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride or polypropylene. The solid supports maybe in the form of tubes, beads, discs of microplates, or any other surface suitable for conducting an immunoassay. The binding processes are well-known in the art and generally consist of cross-linking covalently binding or physically adsorbing, the polymer-antibody complex is washed in preparation for the test sample. An aliquot of the sample to be tested is then added to the solid phase complex and incubated for a period of time sufficient (e.g. 2-40 minutes or overnight if more convenient) and under suitable conditions (e.g. from room temperature to about 37°C including 25°C) to allow binding of any subunit present in the antibody. Following the incubation period, the antibody subunit solid phase is washed and dried and incubated with a second antibody specific for a portion of the hapten. The second antibody is linked to a reporter molecule which is used to indicate the binding of the second antibody to the antigen.

An alternative method involves immobilizing the target molecules in the biological sample and then exposing the immobilized target to specific antibody which may or may not be labeled with a reporter molecule. Depending on the amount of target and the strength of the reporter molecule signal, a bound target may be detectable by direct labelling with the antibody.

Alternatively, a second labeled antibody, specific to the first antibody is exposed to the target-first antibody complex to form a target-first antibody-second antibody tertiary complex. The complex is detected by the signal emitted by the reporter molecule.

By "reporter molecule", as used in the present specification, is meant a molecule which, by its chemical nature, provides an analytically identifiable signal which allows the detection of antigen-bound antibody. Detection may be either qualitative or quantitative. The most commonly used reporter molecules in this type of assay are either enzymes, fluorophores or radionuclide containing molecules (i.e. radioisotopes) and chemiluminescent molecules.

In the case of an enzyme immunoassay, an enzyme is conjugated to the second antibody, generally by means of glutaraldehyde or periodate. As will be readily recognized, however, a wide variety of different conjugation techniques exist, which are readily available to the skilled artisan. Commonly used enzymes include horseradish peroxidase, glucose oxidase, /3-galactosidase and alkaline phosphatase, amongst others. The substrates to be used with the specific enzymes are generally chosen for the production, upon hydrolysis by the corresponding enzyme, of a detectable color change. Examples of suitable enzymes include alkaline phosphatase and peroxidase. It is also possible to employ fluorogenic substrates, which yield a fluorescent product rather than the chromogenic substrates noted above, h all cases, the enzyme-labeled antibody is added to the first antibody hapten complex, allowed to bind, and then the excess reagent is washed away. A solution containing the appropriate substrate is then added to the complex of antibody-antigen- antibody. The substrate will react with the enzyme linked to the second antibody, giving a qualitative visual signal, which may be further quantitated, usually spectrophotometrically, to give an indication of the amount of hapten which was present in the sample. "Reporter molecule" also extends to use of cell agglutination or inhibition of agglutination such as red blood cells on latex beads, and the like.

Alternately, fluorescent compounds, such as fluorecein and rhodamine, may be chemically coupled to antibodies without altering their binding capacity. When activated by illumination with light of a particular wavelength, the fluorochrome-labeled antibody adsorbs the light energy, inducing a state to excitability in the molecule, followed by emission of the light at a characteristic color visually detectable with a light microscope. As in the EIA, the fluorescent labeled antibody is allowed to bind to the first antibody- hapten complex. After washing off the unbound reagent, the remaining tertiary complex is then exposed to the light of the appropriate wavelength, the fluorescence observed indicates the presence of the hapten of interest. Immunofluorescene and EIA techniques are both very well established in the art and are particularly preferred for the present method. However, other reporter molecules, such as radioisotope, chemiluminescent or bioluminescent molecules, may also be employed.

The present invention further contemplates agonists and antagonists of the subject multi- copper oxidases. As stated above, an example of an antagonist is an antibody. Accordingly, another aspect of the present invention contemplates a method for modulating metal ion and in particular Fe¹¹ acquisition by a cell, said method comprising administering to said cell or a higher organism comprising said cell an amount of an effector molecule capable of modulating the function of a multi-copper oxidase from a prokaryotic organism which multi-copper oxidate facilitates metal ion uptake in said prokaryotic organism.

Particularly, the multi-copper oxidase is from a Pseudomonas species such as P. aeruginosa.

Particularly, the metal ion is Fe¹¹.

Particularly, the target cell is a prokaryotic or eukaryotic cell.

The method of this aspect of the present invention is useful in controlling bacterial infection or facilitating Fe¹¹ uptake such as during bioremediation or in the treatment of disease conditions in higher amounts.

The effector molecules of the present invention may be protemaceous or may be chemical molecules identified from, for example, screening a chemical library or following natural product screening. The term "natural product screening" includes screening environmental and biological locations such as coral, river beds, plants, microorganisms, rock formations, antartic or artic regions or sea water or sea beds for chemical molecules which are capable of interacting with the multi-copper oxidase.

Accordingly, another aspect of the present invention provides an effector molecule capable of modulating the function of a multi-copper oxidase obtainable from P. aeruginosa and involved in Fe¹¹ uptake by said P. aeruginosa.

The effector molecule may be an agonist or an antagonist. Agonists and antagonists of the multi-copper oxidase are obtainable by a number of methods. For example, the agonist and antagonists may be immunologically derived molecules or agents identified through a combinatorial approach or through phage display libraries. Screening for the effects of these agonists and antagonists is conveniently via a ferroxidase and/or laccase assay and/or via effects on growth. These are described in the Examples.

The present invention provides, therefore, in one aspect a method of producing antibodies that specifically recognize a multi-copper oxidase useful as inhibitors of multi-copper oxidase activity. As indicated above, the invention permits the manufacture of, for example, monoclonal antibodies with such specificities.

The multi-copper oxidase can be separated from the biological fluid by any suitable means. For example, the separation may take advantage of any one or more of the multi-copper oxidase' s surface charge properties, size, density, biological activity and its affinity for another entity (e.g., another protein or chemical compound to which it binds or otherwise associates). Thus, for example, separation of the multi-copper oxidase from the biological fluid may be achieved by any one or more of ultra-centrifugation, ion-exchange chromatography (e.g., anion exchange chromatography, cation exchange chromatography), electrophoresis (e.g., polyacrylamide gel electrophoresis, isoelectric focussing), size separation (e.g., gel filtration, ultrafiltration) and affinity-mediated separation (e.g., immunoaffinity separation including, but not limited to, magnetic bead separation such as Dynabead™ separation, immunochromatography, immunoprecipitation).

Preferably, the separation of the multi-copper oxidase from the biological fluid preserves conformational epitopes present on the multi-copper oxidase surface and, thus, suitably avoids techniques that cause denaturation of the multi-copper oxidase. Persons of skill in the art will recognize the importance of maintaining or mimicking as close as possible physiological conditions peculiar to the multi-copper oxidase (e.g., the biological fluid from which it is obtained) to ensure that the antigenic determinants or active site/s on the multi-copper oxidase structurally identical to that of the native multi-copper oxidase. This would ensure the raising of appropriate antibodies in the immunized animal that would recognize the native multi-copper oxidase. hi a preferred embodiment of this type, the multi-copper oxidase is separated from the biological fluid using any one or more of affinity separation, gel filtration and ultra-filtration.

As stated above in relation to generating antibodies for diagnostics, immunization and subsequent production of monoclonal antibodies can be carried out using standard protocols as, for example, described by Kδhler and Milstein 1975, supra; Kδhler and Milstein, 1976, supra) or by more recent modifications thereof as described, for example, in Coligan et al. (Current Protocols in Immunology, John Wiley & Sons, Inc. 1991-1997) and in Toyama et al. (Shulman et al, Nature 276: 269-270, 1978). Essentially, an animal is immunized with an antigen-containing biological fluid or fraction thereof by standard methods to produce antibody-producing cells, particularly antibody-producing somatic cells (e.g. B lymphocytes). These cells can then be removed from the immunized animal for immortalization.

Immortalization of antibody-producing cells may be carried out using methods, which are well-known in the art. For example, the immortalization may be achieved by the transformation method using Epstein-Barr virus (EBV) (Kozbor et al, Methods in Enzymology 121: 140, 1986). In a preferred embodiment, antibody-producing cells are immortalized using the cell fusion method (described in Coligan et al, 1991-1997, supra), which is widely employed for the production of monoclonal antibodies. In this method, somatic antibody-producing cells with the potential to produce antibodies, particularly B cells, are fused with a myeloma cell line. These somatic cells may be derived from the lymph nodes, spleens and peripheral blood of primed animals, preferably rodent animals such as mice and rats. In the exemplary embodiment of this invention mice, spleen cells are used. It would be possible, however, to use rat, rabbit, sheep or goat cells, or cells from other animal species instead. Specialized myeloma cell lines have been developed from lymphocytic tumours for use in hybridoma-producing fusion procedures (Kδhler and Milstein, 1976, supra; Shulman, 1978, supra; Volk et al, J. Virol. 42(1): 220-227, 1982). These cell lines have been developed for at least three reasons. The first is to facilitate the selection of fused hybridomas from unfused and similarly indefinitely self-propagating myeloma cells. Usually, this is accomplished by using myelomas with enzyme deficiencies that render them incapable of growing in certain selective media that support the growth of hybridomas. The second reason arises from the inherent ability of lymphocytic tumour cells to produce their own antibodies. To eliminate the production of tumour cell antibodies by the hybridomas, myeloma cell lines incapable of producing endogenous light or heavy immunoglobulin chains are used. A third reason for selection of these cell lines is for their suitability and efficiency for fusion.

Many myeloma cell lines may be used for the production of fused cell hybrids, including, e.g. P3X63-Ag8, P3X63-AG8.653, P3/NSl-Ag4-l (NS-1), Sp2/0-Agl4 and S194/5.XXO.Bu.l. The P3X63-Ag8 and NS-1 cell lines have been described by Kδhler and Milstein (1976, supra). Shulman et al. (1978, supra) developed the Sp2/0-Agl4 myeloma line. The S194/5.XXO.Bu.l line was reported by Trowbridge (J Exp. Med. 148(1) 313-323, 1978).

Methods for generating hybrids of antibody-producing spleen or lymph node cells and myeloma cells usually involve mixing somatic cells with myeloma cells in a 10:1 proportion (although the proportion may vary from about 20:1 to about 1:1), respectively, in the presence of an agent or agents (chemical, viral or electrical) that promotes the fusion of cell membranes. Fusion methods have been described (Kδhler and Milstein, 1975, supra; Kδhler and Milstein, 1976, supra; Gefter et al. Somatic Cell Genet. 3: 231-236. 1977; Volk et al. 1982, supra). The fusion-promoting agents used by those investigators were Sendai virus and polyethylene glycol (PEG).

Because fusion procedures produce viable hybrids at very low frequency (e.g. when spleens are used as a source of somatic cells, only one hybrid is obtained for roughly every lxlO⁵ spleen cells), it is preferable to have a means of selecting the fused cell hybrids from the remaining unfused cells, particularly the unfused myeloma cells. A means of detecting the desired antibody-producing hybridomas among other resulting fused cell hybrids is also necessary. Generally, the selection of fused cell hybrids is accomplished by culturing the cells in media that support the growth of hybridomas but prevent the growth of the unfused myeloma cells, which normally would go on dividing indefinitely. The-somatic cells used in the fusion do not maintain long-term viability in in vitro culture and hence do not pose a problem. In the example of the present invention, myeloma cells lacking hypoxanthine phosphoribosyl transferase (HPRT-negative) were used. Selection against these cells is made in hypoxanthine/aminopterin/thymidine (HAT) medium, a medium in which the fused cell hybrids survive due to the HPRT-positive genotype of the spleen cells. The use of myeloma cells with different genetic deficiencies (drug sensitivities, etc.) that can be selected against in media supporting the growth of genotypically competent hybrids is also possible.

Several weeks are required to selectively culture the fused cell hybrids. Early in this time period, it is necessary to identify those hybrids which produce the desired antibody, so that they may subsequently be cloned and propagated. Generally, around 10% of the hybrids obtained produce the desired antibody, although a range of from about 1 to about 30% is not uncommon. The detection of antibody-producing hybrids can be achieved by any one of several standard assay methods, including enzyme-linked immunoassay and radioimmunoassay techniques as, for example, described in Kennet et al. ((eds), Monoclonal Antibodies and Hybridomas: A New Dimension in Biological Analyses, pp. 376-384, Plenum Press, New York, 1980).

Once the desired fused cell hybrids have been selected and cloned into individual antibody-producing cell lines, each cell line may be propagated in either of two standard ways. A suspension of the hybridoma cells can be injected into a histocompatible animal. The injected animal will then develop tumours that secrete the specific monoclonal antibody produced by the fused cell hybrid. The body fluids of the animal, such as serum or ascites fluid, can be tapped to provide monoclonal antibodies in high concentration. Alternatively, the individual cell lines may be propagated in vitro in laboratory culture vessels. The culture medium containing high concentrations of a single specific monoclonal antibody can be harvested by decantation, filtration or centrifugation, and subsequently purified.

The cell lines are tested for their specificity to detect the multi-copper oxidase of interest by any suitable immunodetection means. For example, cell lines can be aliquoted into a number of wells and incubated and the supernatant from each well is analyzed by enzyme- linked immunosorbent assay (ELISA), indirect fluorescent antibody technique or the like. The cell line(s) producing a monoclonal antibody capable of recognizing the multi-copper oxidase are directly cultured in vitro or injected into a histocompatible animal to form tumors and to produce, collect and purify the required antibodies.

Thus, the present invention further provides monoclonal antibodies which specifically detect multi-copper oxidase and which are produced by the method as broadly described above as well as hybridomas from which such monoclonal antibodies can be produced.

The invention also contemplates the use and generation of fragments of monoclonal antibodies produced by the method of the present invention including, for example, Fv, Fab, Fab' and F(ab')₂ fragments. Such fragments may be prepared by standard methods as for example described by Coligan et al. (1991-1997, supra).

The present invention also contemplates synthetic or recombinant antigen-binding molecules with the same or similar specificity as the monoclonal antibodies of the invention. Antigen binding molecules of this type may comprise a synthetic stabilized Fv fragment. Exemplary fragments of this type include single chain Fv fragments (sFv, frequently termed scFv) in which a peptide linker is used to bridge the N terminus or C terminus of a V# domain with the C terminus or N-terminus, respectively, of a V domain. ScFv lack all constant parts of whole antibodies and are not able to activate complement. Suitable peptide linkers for joining the V_# and V_t. domains are those which allow the V_# and Yι domains to fold into a single polypeptide chain having an antigen binding site with a three dimensional structure similar to that of the antigen binding site of a whole antibody from which the Fv fragment is derived. Linkers having the desired properties may be obtained by the method disclosed in U.S. Patent No 4,946,778. However, in some cases a linker is absent. ScFvs may be prepared, for example, in accordance with methods outlined in Krebber et al. (J. Immunol. Methods 201(1): 35-55, 1997). Alternatively, they may be prepared by methods described in U.S. Patent No 5,091,513, European Patent No 239,400 or the articles by Winter and Milstein (Nature 349: 293, 1991) and Plϋckthun et al. (In: Antibody engineering: A practical approach. 203-252, 1996).

Alternatively, the synthetic stabilized Fv fragment comprises a disulphide stabilized Fv (dsFv) in which cysteine residues are introduced into the V_# and Vz, domains such that in the fully folded Fv molecule the two residues will form a disulphide bond therebetween. Suitable methods of producing dsFv are described, for example, in (Glockshuber et al, Biochem. 29: 1363-1367, 1990; Reiter et al, J. Biol Chem. 269: 18327-18331, 1994; Reiter et al, Biochem. 33: 5451-5459, 1994; Reiter et al, Cancer Res. 54: 2714-2718, 1994; Webber et al, Mol Immunol. 32: 249-258, 1995).

Also contemplated as synthetic or recombinant antigen-binding molecules are single variable region domains (termed dAbs) as, for example, disclosed in (Ward et al, Nature 341: 544-546, 1989; Hamers-Casterman et al, Nature 363: 446-448, 1993; Davies & Riechmann, FEPSJett. 339: 285-290, 1994).

Alternatively, the synthetic or recombinant antigen-binding molecule may comprise a "minibody". In this regard, minibodies are small versions of whole antibodies, which encode in a single chain the essential elements of a whole antibody. Suitably, the minibody is comprised of the V_# and ^~V_L domains of a native antibody fused to the hinge region and CH3 domain of the immunoglobulin molecule as, for example, disclosed in U.S. Patent No 5,837,821.

In an alternate embodiment, the synthetic or recombinant antigen binding molecule may comprise non-immunoglobulin derived, protein frameworks. For example, reference may be made to Ku & Schultz (Proc. Natl. Acad. SCi. USA 92:6552-6556, 1995) which discloses a four-helix bundle protein cytochrome b562 having two loops randomized to create complementarity determining regions (CDRs), which have been selected for antigen binding.

The synthetic or recombinant antigen-binding molecule may be multivalent (i.e. having more than one antigen binding site). Such multivalent molecules may be specific for one or more antigens. Multivalent molecules of this type may be prepared by dimerization of two antibody fragments through a cysteinyl-containing peptide as, for example disclosed by (Adams et al, Cancer Res. 53: 4026-4034, 1993; Cumber et al, J. Immunol. 149: 120- 126, 1992). Alternatively, dimerization may be facilitated by fusion of the antibody fragments to amphiphilic helices that naturally dimerize (Plϋnckthun, Biochem. 31: 1579- 1584, 1992) or by use of domains (such as leucine zippers jun and fos) that preferentially heterodimerize (Kostelny et al, J. Immunol. 148: 1547-1553, 1992).

In an alternate embodiment, the multivalent molecule may comprise a multivalent single chain antibody (rnulti-scFv) comprising at least two scFvs linked together by a peptide linker. In this regard, non-covalently or covalently linked scFv dimers termed "diabodies" may be used. Multi-scFvs may be bispecific or greater depending on the number of scFvs employed having different antigen-binding specificities. Multi-scFvs may be prepared, for example, by methods disclosed in U.S. Patent No. 5,892,020.

The invention also encompasses chimeric antibodies having the same or similar specificity as the monoclonal antibodies prepared according to the invention. Chimeric antibodies are antibodies whose light and heavy chain genes have been constructed, typically by genetic engineering, from immunoglobulin variable and constant region genes belonging to different species. Thus, in accordance with the present invention, once a hybridoma producing the desired monoclonal antibody is obtained, techniques are used to produce interspecific monoclonal antibodies wherein the binding region of one species is combined with a non-binding region of the antibody of another species (Liu et al, Proc. Natl. Acad. Sci. USA 84: 3439-3443, 1987). For example, the CDRs from a non-human (e.g. murine) monoclonal antibody can be grafted onto a human antibody, thereby "humanizing" the murine antibody (European Patent Publication No. 0 239 400; Jones et al, Nature 321: 522-525, 1986; Verhoeyen et al, Science 239: 1534-1536, 1988; Reichmann et al, Nature 332: 323-327, 1988)). More particularly, the CDRs can be grafted onto a human antibody variable region with or without human constant regions. The non-human antibody providing the CDRs is typically referred to as the "donor" and the human antibody providing the framework is typically referred to as the "acceptor". Constant regions need not be present, but if they are, they must be substantially identical to human immunoglobulin constant regions, i.e. at least about 85-90%, preferably about 95% or more identical. Hence, all parts of a humanized antibody, except possibly the CDRs, are substantially identical to corresponding parts of natural human immunoglobulin sequences. Thus, a "humanized antibody" is an antibody comprising a humanized light chain and a humanized heavy chain immunoglobulin. A donor antibody is said to be "humanized", by the process of "humanization", because the resultant humanized antibody is expected to bind to the same antigen as the donor antibody that provides the CDRs.

It will be understood that the humanized antibodies may have additional conservative amino acid substitutions which have substantially no effect on antigen binding or other immunoglobulin functions. Exemplary conservative substitutions may be made according to Table 2.

TABLE 2

Exemplary methods which may be employed to produce humanized antibodies according to the present invention are described, for example, in Reichmann et al, 1988, supra; European Patent Publication No. 0 239 400 and U.S. Patent Nos. 6,056,957, 6,180,370, 6,180,378 and Chothia et al, J. Mol. Biol. 196:901, 1987. Humanized antibodies are a form of deimmunized antibody is particularly useful for use as an inhibitor in a particular animal.

Thus, in a preferred embodiment, the present invention contemplates a humanized antibody molecule having specificity for an epitope recognized by monoclonal antibody prepared according to the present invention, wherein at least one of the complementary determining regions (CDRs) of the variable domain is derived from said monoclonal antibody and the remaining immunoglobulin-derived parts of the humanized antibody molecule are derived from an immunoglobulin or an analog thereof from said humanized antibody molecule.

The identification of agonists and antagonists can also be facilitated through the use of a phage (or phagemid) display protein ligand screening system as, for example, described in Lowman et α/., Biochem. 30: 10832-10838, 1991; Markland et α/., Gene 109: 13-19, 1991; Roberts et al, Proc. Natl. Acad. Sci. USA 89: 2429-2433, 1992; Smith, Science 228: 1315- 1317, 1985; Smith et al, Science 248: 1126-1128, 1990 and U.S. Patent No. 5,223,409. In general, this method involves expressing a fusion protein in which the desired protein ligand is fused to the N-tenninus of a viral coat protein (such as the Ml 3 Gene III coat protein, or a lambda coat protein).

In one embodiment, a library of phage is engineered to display novel peptides within the phage coat protein sequences. Novel peptide sequences are generated by random mutagenesis of gene fragments encoding the multi-copper oxidase of the invention or biologically active fragment using error-prone PCR, or by in vivo mutation by E. coli mutator cells. The novel peptides displayed on the surface of the phage are placed in contact, with a multi-copper oxidase-specific binding partner molecule including a specific antibody as prepared above or enzyme substrate. Phage that display coat protein having peptides that are capable of binding to a binding partner are immobilized by such treatment, whereas all other phage can be washed away. After the removal of unbound phage, the bound phage can be amplified, and the DNA encoding their coat proteins can be sequenced. In this manner, the amino acid sequence of the embedded peptide or polypeptide can be deduced.

In more detail, the method involves (a) constructing a replicable expression vector comprising a first gene encoding a multi-copper oxidase of the invention, a second gene encoding at least a portion of a natural or wild-type phage coat protein wherein the first and second genes are heterologous, and a transcription regulatory element operably linked to the first and second genes, thereby forming a gene fusion encoding a fusion protein; (b) mutating the vector at one or more selected positions within the first gene thereby forming a family of related plasmids; (c) transforming suitable host cells with the plasmids; (d) infecting the transformed host cells with a helper phage having a gene encoding the phage coat protein; (e) culturing the transformed infected host cells under conditions suitable for forming recombinant phagemid particles containing at least a portion of the plasmid and capable of transforming the host, the conditions adjusted so that no more than a minor amount of phagemid particles display more than one copy of the fusion protein on the surface of the particle; (f) contacting the phagemid particles with a multi-copper oxidase- specific binding partner such as an antibody that binds to the parent multi-copper oxidase or fragment so that at least a portion of the phagemid particles bind to the binding partner; and (g) separating the phagemid particles that bind from those that do not. Preferably, the method further comprises transforming suitable host cells with recombinant phagemid particles that bind to the multi-copper oxidase-specific binding partner and repeating steps (d) through (g) one or more times.

Preferably in this method the plasmid is under tight control of the transcription regulatory element, and the culturing conditions are adjusted so that the amount or number of phagemid particles displaying more than one copy of the fusion protein on the surface of the particle is less than about 1%. Also, preferably, the amount of phagemid particles displaying more than one copy of the fusion protein is less than 10% of the amount of phagemid particles displaying a single copy of the fusion protein. Most preferably, the amount is less than 15%.

Typically in this method, the expression vector will further contain a secretory signal sequence fused to the DNA encoding each subunit of the polypeptide and the transcription regulatory element will be a promoter system. Preferred promoter systems are selected from lac Z, λp_L, tac, T7 polymerase, tryptophan, and alkaline phosphatase promoters and combinations thereof. Also, normally the method will employ a helper phage selected from M13K07, M13R408, M13-VCS, and Phi X 174. The preferred helper phage is M13K07, and the preferred coat protein is the Ml 3 Phage gene IH coat protein. The preferred host is E. coli, and protease-deficient strains of E. coli.

Repeated cycles of variant selection are used to select for higher and higher affinity binding by the phagemid selection of multiple amino acid changes that are selected by multiple selection cycles. Following a first round of phagemid selection, involving a first region or selection of amino acids in the ligand polypeptide, additional rounds of phagemid selection in other regions or amino acids of the ligand polypeptide are conducted. The cycles of phagemid selection are repeated until the desired affinity properties of the ligand polypeptide are achieved.

It will be appreciated that the amino acid residues that form the binding domain of the polypeptide or fragment may not be sequentially linked and may reside on different subunits of the polypeptide or fragment. That is, the binding domain tracks with the particular secondary structure at the binding site and not the primary structure. Thus, generally, mutations will be introduced into codons related to amino acids within a particular secondary structure at sites directed away from the interior of the polypeptide so that they will have the potential to interact with the multi-copper oxidase-specific binding partner.

The phagemid-display method herein contemplates fusing a polynucleotide encoding the polypeptide or fragment (polynucleotide 1) to a second polynucleotide (polynucleotide 2) such that a fusion protein is generated during transcription. Polynucleotide 2 is typically a coat protein gene of a phage, and preferably it is the phage Ml 3 gene III coat protein, or a fragment thereof. Fusion of polynucleotides 1 and 2 may be accomplished by inserting polynucleotide 2 into a particular site on a plasmid that contains polynucleotide 1, or by inserting polynucleotide 1 into a particular site on a plasmid that contains polynucleotide 2.

Between polynucleotide 1 and polynucleotide 2, DNA encoding a termination codon may be inserted, such termination codons being UAG (amber), UAA (ocher), and UGA (opel) (see for example, Davies et al, Microbiology, pp. 237, 245-247, 274, 1980). The termination codon expressed in a wild-type host cell results in the synthesis of the polynucleotide 1 protein product without the polynucleotide 2 protein attached. However, growth in a suppressor host cell results in the synthesis of detectable quantities of fused protein. Such suppressor host cells contain a tRNA modified to insert an amino acid in the termination codon position of the mRNA, thereby resulting in production of detectable amounts of the fusion protein. Suppressor host cells of this type are well known and described, such as E. coli suppressor strain (Bullock et al, BioTechniques 5: 376-379, 1987). Any acceptable method may be used to place such a termination codon into the mRNA encoding the fusion polypeptide.

The suppressible codon may be inserted between the polynucleotide encoding the polypeptide or fragment and a second polynucleotide encoding at least a portion of a phage coat protein. Alternatively, the suppressible termination codon may be inserted adjacent to the fusion site by replacing the last amino acid triplet in the polypeptide/fragment or the first amino acid in the phage coat protein. When the phagemid containing the suppressible codon is grown in a suppressor host cell, it results in the detectable production of a fusion polypeptide containing the polypeptide or fragment and the coat protein. When the phagemid is grown in a non-suppressor host cell the polypeptide or fragment is synthesized substantially without fusion to the phage coat protein due to termination at the inserted suppressible triplet encoding UAG, UAA, or UGA. hi the non-suppressor cell the polypeptide is synthesized and secreted from the host cell due to the absence of the fused phage coat protein which otherwise anchored it to the host cell.

The multi-copper polypeptide or fragment may be altered at one or more selected codons. An alteration is defined as a substitution, deletion, or insertion of one or more codons in the gene encoding the polypeptide or fragment that results in a change in the amino acid sequence as compared with the unaltered or native sequence of the said polypeptide or fragment. Preferably, the alterations will be by substitution of at least one amino acid with any other amino acid in one or more regions of the molecule. The alterations may be produced by a variety of methods known in the art, as for example above. These methods include, but are not limited to, oligonucleotide-mediated mutagenesis and cassette mutagenesis as described, for example, herein.

For preparing the multi-copper-specific binding partner molecule and binding it with the phagemid, the binding partner molecule is attached to a suitable matrix such as agarose beads, acrylamide beads, glass beads, cellulose, various acrylic copolymers, hydroxyalkyl methacrylate gels, polyacrylic acid, polymethacrylic copolymers, nylon, neutral and ionic carriers, and the like. Attachment of the binding partner molecule to the matrix may be accomplished by methods described (Methods Enzymol 44: 1916) or by other means known in the art.

After attachment of the specific binding partner molecule to the matrix, the immobilized binding partner is contacted with the library of phagemid particles under conditions suitable for binding of at least a portion of the phagemid particles with the immobilized binding partner or target. Normally, the conditions, including pH, ionic strength, temperature, and the like will mimic physiological conditions.

Bound phagemid particles ("binders") having high affinity for the immobilized target are separated from those having a low affinity (and thus do not bind to the target) by washing. Binders may be dissociated from the immobilized target by a variety of methods. These methods include competitive dissociation using the wild-type ligand, altering pH and/or ionic strength, and methods known in the art.

Suitable host cells are infected with the binders and helper phage, and the host cells are cultured under conditions suitable for amplification of the phagemid particles. The phagemid particles are then collected and the selection process is repeated one or more times until binders having the desired affinity for the target molecule are selected.

Agonists and antagonists of the multi-copper oxidase of the present invention may also be obtained using the principles of conventional or of rational drug design as, for example, described in Andrews et al, Munksgaard, Copenhagen 28: 145-165, 1990; McPherson, Eur. J. Biochem. 189: 1-24, 1990; Hoi et al, Royal Society of Chemistry, pp 84-93, 1989a, Robersts, S.M. (ed); Hoi, Agnew Chem. Int. Ed. Engl. 25:161-118, 1986 and Hoi, Arzneim- Forsch 39: 1016-1018, 1989b.

In accordance with the methods of conventional drug design, the desired variant molecules are obtained by randomly testing molecules whose structures have an attribute in common with the structure of a parent multi-copper oxidase or biologically active fragment thereof.

The quantitative contribution that results from a change in a particular group of a binding molecule can be determined by measuring the capacity of competition or cooperativity between the parent multi-copper oxidase polypeptide or polypeptide fragment and the candidate polypeptide variant.

In one embodiment of rational drug design, the multi-copper oxidase polypeptide variant is designed to share an attribute of the most stable three-dimensional conformation of a polypeptide or polypeptide fragment according to the invention. Thus, the variant may be designed to possess chemical groups that are oriented in a way sufficient to cause ionic, hydrophobic, or van der Waals interactions that are similar to those exhibited by the polypeptide or polypeptide fragment of the invention, hi a second method of rational design, the capacity of a particular polypeptide or polypeptide fragment to undergo conformational "breathing" is exploited. Such "breathing" - the transient and reversible assumption of a different molecular conformation - is a well-appreciated phenomenon, and results from temperature, thermodynamic factors, and from the catalytic activity of the molecule. Knowledge of the 3-dimensional structure of the polypeptide or polypeptide fragment facilitates such an evaluation. An evaluation of the natural conformational changes of a polypeptide or polypeptide fragment facilitates the recognition of potential hinge sites, potential sites at which hydrogen bonding, ionic bonds or van der Waals bonds might form or might be eliminated due to the breathing of the molecule, etc. Such recognition permits the identification of the additional conformations that the polypeptide or polypeptide fragment could assume, and enables the rational design and production of mimetic polypeptide variants that share such conformations.

The preferred method for performing rational mimetic design employs a computer system capable of forming a representation of the three-dimensional structure of the polypeptide or polypeptide fragment (such as those obtained using RIBBON (Grass and Rensing, 2001, supra), QUANTA (Polygen), INSIGHT 11 (MSI), or Nanovision (American Chemical Society)). Such analyses are exemplified by Hoi, et al. 1989, supra; Hoi, 1986, supra and Hoi, 1989, supra.

In lieu of such direct comparative evaluations of candidate polypeptide variants, screening assays may be used to identify such molecules. Such assays will preferably exploit the capacity of the variant to bind to a multi-copper oxidase and to promote multi-copper oxidase.

The present invention is further described by the following non-limiting Examples.

EXAMPLE 1 Bacterial strains and growth conditions

Strains used were; E. coli JM109 (Yanish-Perron et al, Gene 33: 103, 1985), E. coli S17-1 e pir (Penfold and Pemberton, Gene 118(1): 145-146, 1992), and P. aeruginosa PAK (Australian Culture Collection). All strains were routinely cultured on Luria-Bertani (LB) medium at 37°C. Antibiotics were used as follows: ampicillin, 100 μg/ml; kanamycin, 50 μg/ml; tetracycline, 25 μg/ml for E. coli and carbenicillin, 300 μg/ml; tetracycline, 250 μg/ml for P. aeruginosa. P. aeruginosa strains were grown on modified RCV minimal media (Weaver et al, Arch. Microbiol. 105: 1988-1998, 1975) at 37°C for all experiments involving physiological analysis and protein purification. This medium was prepared as described in the literature, except that FeSO was omitted. Iron assays revealed that the concentration in 'iron-free' RCV medium was less than 1 μM. RCV media, where specified, was also supplemented with filter-sterilized FeSO .7H₂O or FeCl₃. Aerobic growth of P. aeruginosa strains was conducted at 37°C, in 250 ml conical flasks shaking at 190 rpm. Anaerobic growth of P. aeruginosa using RCV media supplemented with 15 mM KNO₃ was conducted with standing cultures in completely filled 30 ml McCartney bottles. Copper tolerance experiments were conducted in RCV media containing 5 μM Fe(IH) aerobically, appropriate concentrations of copper were supplemented to the media in the form of cupric sulfate. The P. aeruginosa mco mutant, complemented with the mco gene was grown in the presence of 0.5 mM isopropyl-β-D-thiogalactoside (IPTG).

EXAMPLE 2 Genetic analysis

An mco mutation was created in P. aeruginosa PAK by single cross-over insertional mutagenesis. To achieve this a 380 nucleotide internal region of the mco gene (annotated inthe P. aeruginosa PAO1 genome sequencing project as PA2065 oxpcoP ) (Stover et al, Nature 406: 959-964, 2000) was generated by PCR amplification, using the primers GenelFl 5'-ggtgaacctcagcggctcg-3' [SEQ ID NO:21] and GenelRl 5'- gcggcttctcgtccgacc-3' [SEQ ID NO:22] and cloned into the suicide plasmid pJP5608 (P enfold and Pemberton, 1992, supra) to create plasmid pWHmco. The mutant was generated by conjugation of P. aeruginosa with E. coli SI 7-1 λ_pj_r (pWHmco) as described by Saunders and co-workers (In: Methods in Microbiology, Bennett, P.M. Grinstead, J. (eds), Academic Press, New York, 1984) with selection for colonies resistant to tetracycline at 250 μg/ml. The genotype of the Ps. aeruginosa mco mutant was confirmed by Southern blot and PCR analysis. The mco mutant was complemented by transformation with the plasmid pUCPSKmco using the method of Saunders et al. (1984, supra). This plasmid was generated by PCR amplification of the entire mco gene including its putative promoter region, using primers PseudoFl 5-cgggatcccgtccatgccattgtcctgcgc-3' [SΕQ ID NO:23] and PseudoRl 5'-gcgaattcgttcgtcaaaggcctcgccgc-3' [SΕQ ID NO:24] followed by directional cloning into pUCPSK, an IPTG inducible vector (Watson et al, Gene 172: 163-164, 1996), using the restriction enzymes ifømHI andEcoRI (underlined).

hi order to purify the MCO for antibody production the mco gene was cloned into plasmid expression vector pPROΕX-hta (GIBCO BRL). The mco gene was amplified using the primers geneltagf 5'-gtggatccgctcggcggactgggtctctgg-3' [SΕQ ID NO:25] and geneltag 5'-ggactagttcatgcgttgtctccttcgtctaccc-3' [SΕQ TD NO:26] and cloned into the vector using the restriction enzymes PαmHl and Spel (underlined) to create plasmid pPROΕXmco. The mco gene was sequenced from this construct using the ABI Big Dye Terminator System.

EXAMPLE 3 Cell Fractionation and Enzyme Activity Measurements

Cell pellets were obtained from cultures by centrifugation at 8 000 x g for 15 minutes, washed twice in 50 mM Tris pH 8.0 prior to resuspension in the same buffer. Total soluble cell-free extracts were prepared from cell suspensions by breakage in a French Press (18,000 psi). Periplasmic and cytoplasmic fractions were prepared essentially as described by Hanlon et al. (Eur. J. Biochem. 239: 391-396, 1996) except that the lysozyme concentration used was 10 μg/ml. Membranes were removed from total soluble, periplasmic and cytoplasmic fractions by ultracentrifugation at 105 600 x g for 90 minutes. Cell fractions from whole cell lysates or periplasmic fractions were assayed for laccase activity via an in-gel assay. Following separation of samples using non-denaturing PAGE, the gel was incubated in 50 mM sodium acetate pH 5.7 for 30 min. followed by 10 mM p- phenylenediamine, 50 mM sodium acetate pH 5.7 until activity was visible (Sato and Gitlin, 1991, supra). The oxidation of Fe¹¹ to Fe¹¹¹ by the purified MCO was measured spectrophotometrically by monitoring the production of Fe¹¹¹ at 315 nm in a Hitachi U- 3000 spectrophotometer. The assays were conducted using 5 mM ferrous ammonium sulfateas the substrate in 100 mM sodium acetate buffer (pH 5) at 30 o C (Hassett et al, 1998b, supra). Inhibition of ferroxidase activity was achieved by addition of NaF (Curzon, J Biochem. 77: 66-13, 1960).

EXAMPLE 4 Expression of the P. aeruginosa MCO in E. coli and generation of antibodies

P. aeruginosa MCO was expressed in E. coli JM109 (pPROEXmco) as a histidine-tagged protein according to the manufacturer's instructions. The histidine-tagged MCO (ht-MCO) protein was purified from inclusion bodies as previously described (Zaveckas et al, J. Chromatogr A 904: 145-169, 2000) followed by Ni-affinity chromatography under denaturing conditions as described by the manufacturer (QIAGEN). The purified protein was dialysed against 50 mM Tris-HCl (pH 8.0) prior to immunization. Lop rabbits were immunized with 200 μg pure protein in adjuvant (MPL + TDM + CWS) (Sigma) and boosted until a high titer response was achieved. The MCO protein was analyzed by Western blot using rabbit polyclonal sera. Soluble extracts were run on a 10% (w/v) SDS- polyacrylamide gel, transferred to nitrocellulose membrane using semi-dry transfer (Hoeffer semi-dry transfer cell) according to manufacturer's instructions. Polyclonal sera was used at a dilution of 1/4000 and secondary antibody at 1/10000 (Goat anti-rabbit IgG- AP conjugate, SIGMA). Activity of the Alkaline Phosphatase conjugate secondary antibody was detected by incubation with Nitro Blue Tetrazolium/5-Bromo-4-Chloro-3- Indolyl Phosphate with a development time of 20 minutes at room temperature. EXAMPLE 5 Purification of the MCO from P. aeruginosa PAK

The P. aeruginosa mco mutant complemented with plasmid pUCPSKmco was used for purification of the MCO. Periplasmic extracts from 3 litres of cells were prepared, as described above, and the MCO was precipitated in a 40-60% ammonium sulfate fraction. The precipitate was dialyzed in 50 mM Tris pH 8.0 at 4°C. The dialysed sample was fractionated by gel filtration (Pharmacia HiLoad, 16/60 Superdex 200). Fractions containing the MCO were identified by ferroxidase activity and Western blotting. The fractions containing MCO were further purified using anion exchange chromatography (Poros HQ, Boehringer Mannheim, Germany). The MCO eluted from the column at approximately 800 mM NaCl. The protein sample was then dialysed in 50 mM Tris pH 8.0.

EXAMPLE 6

Iron uptake analysis

The uptake of iron by P. aeruginosa strains was examined in CAA media (Cox, Infect. Immun. 52: 263-270, 1986). Cultures grown on LB media were harvested at late exponential phase of growth, washed three times in CAA media prior to resuspension in the media to a high cell density and storage on ice. For iron uptake assays all strains were resuspended in CAA medium to the same density (OD600 = 0.8). The iron uptake assay was conducted in 4 mis resuspended bacteria. The cell resuspension was incubated at 37°C, shaking at 190 rpm, and the assay was started by addition of ferrous sulfate or ferric chloride. Samples were taken from the assay at timed intervals to determine the amount of iron remaining in the supernatant. The supernatant was prepared from the samples collected by removal of the cells by centrifugation for 4 min. at 12000 rpm in the microfuge. The cell-free supernatant was then assayed for iron concentration using the ferrozine assay, as previously described by Stookey (Anal Chem. 42: 779-781, 1970). Standard curves were conducted using ferrous sulfate or ferric chloride prepared in CAA media. Media only control experiments showed that the levels of Fe¹¹ and Fe^m remained constant in CAA media for the duration of the experiment.

EXAMPLE 7 MCO sequence alignment and phylogenetic analysis

Sequences of the putative bacterial MCOs described in this paper were identified in public databases (NCBI) following a tBLASTx search (Altschul et al, 1997, supra) using the Saccharomyces cerevisiae Fet3 gene sequence (Genbank Accession Number 6323703) (Hassett et al, 1998b, supra). Sequences used in the tree and alignments were also obtained as described above from NCBI as well as the appropriate databases for completed genome sequences using the following gene names and Genbank Accession Numbers; P. aeruginosa PAO1: pcoA, (15597261) (Stover et al, 2000, supra) [SEQ TD NO:3], Mycobacterium tuberculosis H37Rv: (15607986) (Cole et al, Nature 393 537-544, 1998) [SEQ ID NO:8], Yersinia pestis: (16123558), Caulobacter crescentus: (16125216) [SEQ TD NO:6], Salmonella typhi LT2: (16418670) [SEQ TD NO:ll], Escherichia coli YacK: (2506227) [SEQ TD NO:10] and Legionella pneumophilia [SEQ TD NO:28]. Representative eukaryotic multi-copper oxidase sequences were also obtained from NCBI and are included in the phylogenetic tree. These include; an ascorbate oxidase: Cucumis sativus (cucumber) and laccase: Pycnoporus cinnabarinus (yeastj. A number of additional sequences used during the investigation are from contigs in early release data which remains to be annotated. These have been submitted to Genbank under the following Accession Numbers: Bordetella pertussis (AF455754) [SEQ ID NO:2] sequence data were produced by the Bordetella pertussis Sequencing Group at the Sanger Centre. Preliminary sequence data was obtained from The Institute for Genomic Research for the potential multi-copper oxidase of Corynebacterium diphtheria (AF455753) [SEQ ID NO:7] and from the Genome Sequencing Centre at Washington University for the potential multi- copper oxidase of Klebsiella pneumonia (AF455752) [SEQ ID NO:4]. The sequence of the mco from P. aeruginosa strain PAK is deposited under accession number (AF455751) [SEQ ID NO:30], this study. ClustlW alignment was used to compare amino acid level homology enabling identification of key residues in the protein sequences, including the proposed signal sequence and the comparison of CueO and MCO. The phylogenetic tree was constructed as a neighbour joining tree, using ARB sequence editor (http://www.mikro.biologie.tu-muenchen.de/) on the basis of amino acid similarity. The tree was generated on the basis of a ClustlW alignment of the protein sequences.

EXAMPLE 8 Identification of potential bacterial multi-copper oxidase

The proposed bacterial multi-copper oxidases were initially identified on the basis of sequence data using the NCBI database (BLAST program). The yeast multi-copper oxidase Fet3 (Hassett et al, 1998b, supra) which is known to have ferroxidase activity and a role in iron transport in yeast, was used as the model multi-copper oxidase to search for homologs in bacteria. The search was conducted using both complete and incomplete bacterial genome sequences and on the basis of amino acid level homology. The open reading frames (ORFs) and contigs containing regions of homology identified from this search were then downloaded to the ANGUS database for further analysis. The contigs with homologous regions found in the incomplete and unannotated bacterial genomes were then searched for the appropriate ORF with homology to the sequence of Fet3 (ANGIS).

The compilation of ORFs of potential bacterial MCOs was then further analyzed. Properties examined included regions homologous to known protein motifs (such as copper centers, secretory signals, transmembrane regions etc.) and similarity within the group including multiple sequence alignment of proposed amino acid sequence (ANGIS). This analysis was completed with the construction of phylogenetic trees (using amino acid level homology) and also homology to yeast multi-copper oxidases with known function (i.e. laccases, amine oxidase and ferroxidase) was examined by construction of a phylogenetic tree. A multi-copper oxidase was identified in a number of bacteria. A comparison of bacterial MCOs is given in Figure 1. A comparison of conserved copper binding ligands is shown in Figure 8. The motifs of the predicted multi-copper oxidase from a range of bacteria are shown in Table 3. TABLE 3 Motifs of predicted multi-copper oxidase (MCO) of bacteria

A phylogenetic tree of bacterial MCOs is shown in Figure 2.

EXAMPLE 9 Examination of the P. aeruginosa

The proposed multi-copper oxidase from P. aeruginosa was chosen for a number of reasons including the potential for P. aeruginosa being a convenient and well characterized model system. Furthermore, the genome sequence is closer to completion than many of the other bacterial genomes and, hence, sequence data are likely to be more reliable. The P. aeruginosa protein also appeared to be a reasonable representative of the potential bacterial multi-copper oxidases. The properties of the P. aeruginosa multi-copper oxidase are shown in Table 4. TABLE 4 Predicted properties of the P. aeruginosa multi-copper oxidase. These properties have been predicted on the basis of sequence data obtained from the Ps. aeruginosa genome project (htt ://www.pseudomonas.com/), and using the programs found on the ANGIS suite (http://www.angis.com.au).

EXAMPLE 10 Methods for investigation of the P. aeruginosa multi-copper oxidase

Growth of P. aeruginosa

P. aeruginosa was routinely grown on RCV media (Weaver et al, 1975, supra). The P. aeruginosa strain PAK was chosen to examine the proposed bacterial multi-copper oxidase. Modifications to RCV (when required for some experiments) included addition of FeSO₄7H₂O to appropriate concentrations when a variety of iron concentrations were required and the use of the divalent cation chelator 2,2'-dipyridyl (SIGMA) when iron-free media was required (Kim et al, Gene 239: 129-135, 1999). The copper chelator diethyldithiocarbamic acid (ICN) was used when copper-free media was required and CuSO₄ was added to provided desired concentrations of copper containing RCV media. P. aeruginosa strains were growth on LB media (Sambrook et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, NY, 1980) when required for experiments to manipulate the strains such as matings and transformations. Preparation of soluble and membrane fractions

The preparation of soluble and membrane fractions was performed on overnight cultures grown under the conditions described above. The cultures were initially centrifuged to obtain cell pellets at 7000 rpm for 20 mins. The pellet was then frozen overnight before being washed in 50 mM Tris pH 8.0 twice. The washed cell pellet was then resuspended in 5 ml of the same Tris buffer and were lysed using the French press at 800 psi. Unlysed cells and cell debris was removed from the solution by centrifugation at 7000 rpm for 20 mins. The supernatant was then ultracentrifuged at 40000 rpm for 90 mins to form a pellet of the membranes, with the soluble extract being the supernatant. The membranes were then resuspended in 0.5 ml of Tris buffer.

Preparation of periplasmic fractions

The method used to obtain periplasmic fractions was as described in (Hanlon et al, 1996, supra). Cultures grown as previously described were harvested by centrifugation prior to resuspension in sphearoplasting buffer. The resuspended cells were then incubated at 37°C prior to addition of lysozyme (500 mg/1 or 100 mg/1 as stated), then incubated for 30 mins at 37°C. The spheroplasts were then removed by centrifugation at 9000 rpm for 30 mins at 4°C. The spheroplasts were then lysed by French press in the manner described above to obtain the cytoplasmic fraction, whilst the periplasmic extract was ultracentrifuged at 30000 rpm for 90 mins to remove the outer membranes. The preparation resulted in a sample of periplasm, cytoplasm, outer membranes and cytoplasmic membranes.

Laccase and ferroxidase assays of P. aeruginosa cell fractions

The laccase and ferroxidase assays used during these experiments were both PAGE gel based and spectrophotometrically based, both methods had been previously described in the literature (Hanlon et al, 1996, supra). Ferroxidase assay - spectrophotometric method

The oxidation of Fe¹¹ to Fe^m is monitored in a spectrophotometer at 315 nm. The assay is conducted using 20-200 μM ferrous ammonium sulphate in a 100 mM acetate buffer at pH 5. The assay is performed at 30°C (Hassett et al, 1998b, supra; Johannes and Majcherczyk, 2000, supra).

Laccase assay - PAGE gel method

Cellular fractions (soluble and periplasmic) were assayed for laccase activity by two methods. The first assay aims to isolate activity, which can be attributed to a particular size on a protein gel. Samples were run on a non-dentauring SDS-PAGE gel and assayed by incubation in 10 mM sodium acetate pH 5.7 for 30 mins prior to incubation overnight (Hassett et al, 1998b, supra).

Laccase assay - spectrophotometric method

The laccase assay is the oxidation of a substrate which can be monitored at 540 nm. The assay is conducted at 30°C using 10 mM p-phenelyenediamine in 50 mM acetate pH 5. Water is used to set a baseline for the assay (Hassett et al, 1998b, supra).

Transformation of P. aeruginosa

The transformations of P. aeruginosa were conducted as previously described by Whiteley et al. (J. Bacteriol 182: 4356-4360, 2000).

DEAE- anion exchange chromotography — purification of protein

The further purification of the protein from the periplasmic extract used DEAE anion exchange chromotography. EXAMPLE 11

P. aeruginosa multi-copper oxidase

The properties of P. aeruginosa multi-copper oxidase are listed in Table 4. Assays were conducted to determine levels of ferroxidase and laccase activities in the various cellular fractions. The inventors then constructed a single crossover mutation in the gene encoding the multi-copper oxidase and examined the phenotype of the mutant. This experiment also included complementation of the mutant and phenotypic assessment of the mutant and wild type strains. A more highly purified extract of the protein was prepared by colurnn- chromotography using a DEAE-anion exchange column.

Laccase and ferroxidase activity

The cell fractions were then assayed using PAGE laccase and PAGE ferroxidase method. Laccase and ferroxidase activity was detected in both the periplasmic and soluble cell fractions.

Generation of P. aeruginosa multi-copper oxidase mutant

The P. aeruginosa PAK multi-copper oxidase mutant was successfully generated by conjugation utilizing a suicide vector. The suicide vector pJP5608 was used to generate a mutant of the gene of interest by single crossover causing interruption of the multi-copper oxidase gene (Penfold and Pemberton, 1992, supra). This was enabled by PCR generation of a 380 base pair internal fragment of the multi-copper oxidase gene, which was then cloned into pJP5608. The vector was then conjugated into P. aeruginosa strain PAK to generate the mutant, which could be selected for using tetracyclin resistance.

The construction of an unmarked deletion mutant of the P. aeruginosa multi-copper oxidase gene is also prepared. EXAMPLE 12 Genotypic and Phenotypic examination of P. aeruginosa MCO mutant

Genotype

The genotype of the mutant was confirmed using PCR and Southern blot analysis (Figure 3).

Southern blot

The genotype of the multi-copper oxidase mutant was compared with that of the wild-type by Southern blot analysis. This experiment was conducted in two ways. First, using a probe which was made from the suicide plasmid pJP5608 which is inserted into the chromosome of only the multi-copper oxidase mutant. Secondly, using a probe directed against the multi-copper oxidase gene which, due to the insertion of the suicide vector, will have a different result in the mutant and wild type strains. Figure 3 shows the successful results of these two southern blots.

PCR analysis

The second method of examining the P. aeruginosa multi-copper oxidase mutant was by PCR analysis. The PCR was conducted using primers aimed at the suicide vector and the multi-copper oxidase, and showed that products were amplified under the appropriate conditions.

Phenotype

Growth capabilities of P. aeruginosa multi-copper oxidase mutant and wild-type

The ability of the mutant to grow in comparison to the wild-type was also examined. This was compared under a variety of conditions using minimal media and varied Fe¹¹ and Cu¹¹ concentrations. The mutant showed distinctly impaired growth abilities when compared to that of the wild-type and this was consistently seen under a variety of iron (Fe¹¹) concentrations (see Figures 4 and 5).

EXAMPLE 13

Complementation of the P. aeruginosa multi-copper oxidase mutant

The complementation of the P. aeruginosa multi-copper oxidase mutant was conducted to confirm that the phenotype of the mutant was due to the absence of the multi-copper gene and to provide further evidence as to the proposed function of the multi-copper oxidase.

The experiment was conducted by PCR generation of the multi-copper oxidase gene from P. aeruginosa genomic DNA. The fragment of DNA containing the multi-copper oxidase ORF was then cloned into the Pseudomonas expression plasmid pUCPSK to allow IPTG inducible expression of the gene (Watson et al, 1996, supra) (Figure 6).

EXAMPLE 14 The mco mutant is defective in Fe¹¹ acquisition under aerobic conditions

If the MCO is essential for Fe¹¹ acquisition under aerobic conditions then this leads to the prediction that the rate of Fe¹¹ acquisition would be low in the mco mutant compared to wild-type P. aeruginosa. To test this we grew wild-type and mco mutant strains and ran a series of assays to measure iron uptake using the ferrozine assay to monitor depletion of Fe¹¹ or Fe¹¹¹ from the medium. As described in the Example above, cells of the two strains were first grown in LB medium supplemented with Fe¹¹¹ to attain a high cell density. Cells were then harvested by centrifugation and resuspended in the minimal CAA medium. Following addition of Fe¹¹, its removal from from CAA media by wild-type P. aeruginosa over a 60 minute period is shown in Table 5. In contrast, over the same time period the removal of Fe¹¹ by the mco mutant under identical conditions was four-fold lower. Fe¹¹¹ acquisition was similar in wild-type cells and the mco mutant, indicating that this iron uptake pathway was not affected by the mco mutation. TABLE 5 Comparison of iron uptake in P. aeruginosa PAK and mco mutant

Iron uptake by P. aeruginsoa PAK and P. aeruginosa mco. Iron uptake form CAA media is shown in nmol min^"1 mg prof¹. ± standard deviation is given in parentheses. A paired T- test confirmed the difference between the Fe¹¹ uptake of P. aeruginosa PAK and P. aeruginosa (P value of 0.0065).

EXAMPLE 15 The mco gene in P. aeruginosa does not appear to have a central role in copper tolerance

In E. coli, it has been suggested that the multi-copper oxidase, CueO, is a component of a system involved in tolerance to low levels of copper ions (Outten et al, Biol. Chem. 275: 31024-31029, 2001). This conclusion was based on the measurement of the final optical density reached by the aerobic cultures of E. coli wild-type and cueO mutant. It was observed that there was a slightly lower amount of biomass formed by the cueO mutant when the concentration of Cu(II) in the medium reached about 1 mM. To test whether the MCO of P. aeruginosa also had a role in resistance to copper ions, we carried out growth experiments at the critical concentration (1 mM Cu) where the difference was previously reported (Outten et al., 2001, supra), measuring final O.D. At this concentration no difference was observed between the wild-type and mco mutant. This leads to the conclusion that there is no immediate role for the MCO protein in copper tolerance in P. aeruginosa.

Those skilled in the art will appreciate that the invention described herein is susceptible to variations and modifications other than those specifically described. It is to be understood that the invention includes all such variations and modifications. The invention also includes all of the steps, features, compositions and compounds referred to or indicated in this specification, individually or collectively, and any and all combinations of any two or more of said steps or features.

BIBLIOGRAPHY

Adams et al, Cancer Res. 55: 4026-4034, 1993.

Alexandre, G. and Zhulin, I. G., (Trends Biochem. Sci. 18: 41-42, 2000.

Altschul et al., Nucl. Acids Res. 25: 3389-3402, 1997.

Andrews et al, Munksgaard, Copenhagen 28: 145-165, 1990.

Archibald, F. and Roy, B., Appl Environ. Microbiol 58: 1496-1499, 1992.

Ausubel et al., "Current Protocols in Molecular Biology" John Wiley & Sons hie, 1994- 1998, Chapter 15

Bonaccorsi di Patti, M. C, Felice, M. R., Camuti, A. P., Lania, A., and Musci, G., FEBS Lett. 472: 283-286, 2000.

Bonner and Laskey, Eur. J. Biochem. 46: 83, 1974.

Braun, V. and Killmann, H., Trends Biochem.Sci. 24: 104-109, 1999.

Bullock et al, BioTechniques 5: 376-379, 1987.

Cha, M. K. and Kim, I. H., Biochemistry 38: 12104-12110, 1999.

Chefetz, B., Chen, Y., and Hadar, Y., Appl. Environ. Microbiol 64: 3175-3179, 1998.

Chou et al (U.S. Patent No. 6,056,957).

Cole, S.T., Brosch, R., Parkhill, J., Gamier, T., Churcher, C, Harris, D., Gordon, S.V., Eiglmeier, K., Gas, S., Garry, C.E., III, Tekaia, F., Badcock, L., Basham, D., Brown, D., Chillingworth, T., Connor, R., Davies, R., Devlin, K., Feltwell, T., Gentles, S., Hamlin, N, Hohoyd, S., Hornsby, T., Jagels, K., and Bartrell, B.G., Nature 393: 537-544, 1998.

Coligan et al, Current Protocols in Immunology, John Wiley & Sons, Inc., 1991-1997. Cooksey, D. A., FEMS Micro. Revs. 14: 381-386, 1994.

Cooksey, D. A., Mol Micro. 7: 1-5, 1993.

Cox, CD., Infect. Immun. 52: 263-210, 1986.

Cumber et al, J. Immunol. 149: 120-126, 1992.

Curzon, G., J. Biochem. 77: 66-73, 1960.

Davies & Riechmann, FEBS Lett. 339: 285-290, 1994.

Davies et al, Microbiology (Harper and Row: New York, 1980), pp. 237,245-247 and 274.

di Patti, M. C, Pascarella, S., Catalucci, D., and Calabrese, L., Protein Eng 12: 895-897, 1999.

Douillard and Hoffman, Basic Facts about Hybridomas, in Compendium of Immunology Vol. II, ed. by Schwartz, 1981.

Eck, R., Hundt, S., Hartl, A., Roemer, E., and Kunkel, W., Microbiology 145 (Pt 9): 2415- 2422, 1999.

European Patent Publication No. 0 239 400.

Farver, O., Bendahl, L., Skov, L. K., and Pecht, I., J Biol Chem. 274: 26135-26140, 1999.

Fee, J. A., Structure and Bonding 23: 1-60, 1975.

Garcia-Horsman, J. A., Barquera, B., Rumbley, j., Ma, j., and Gennis, R. B., J. Bacteriol 176: 5587-5600, 1994.

Gefter et al, Somatic Cell Genet. 3: 231-236, 1977.

Glockshuber et al, Biochem. 29: 1363-1367, 1990.

Grass, G. and Rensing, C, J. Bacterial. 183: 2145-2147, 2001. Gromov, I., Marchesini, A., Farver, O., Pecht, I., and Goldfarb, D., Eur. J. Biochem. 266: 820-830, 1999.

Guerinot, M. L., Annu.Rev. Microbiol. 48: 743-772, 1994.

Hamers-Casterman et al, Nature 363: 446-448, 1993.

Hanlon et al, Eur. J. Biochem. 239: 391-396, 1996.

Hassett, R. F., Romeo, A. M., and Kosman, D. J., J. Biol. Chem. 273: 7628-7636, 1998a.

Hassett, R. F., Yuan, D. S., and Kosman, D. J., J. Biol. Chem. 273: 23274-23282, 1998b.

Hofer, C. and Schlosser, D., FEBS Lett. 451: 186-190, 1999.

Hoi et al, Royal Society of Chemistry, pp 84-93, 1989, Roberts, S.M. (ed).

Hoi, G.W. J. , Arzneim-Forsch 39: 1016-1018, 1989.

Hoi, W.G.J., Agnew Chem. Int. Ed. Engl. 25: 161-118, 1986.

Hung, I. H., Casareno, R. L., Labesse, G., Mathews, F. S., and Gitlin, J. D., J. Biol. Chem. 273: 1749-1754, 1998.

frioue, K., Akaike, T., Miyamoto, Y., Okamoto, T., Sawa, T., Otagiri, M., Suzuki, S., Yoshimura, T., and Maeda, H. J. Biol .Chem. 274: 27069-27075, 1999.

Jensen, P. Y., Bonander, N., Moller, L. B., and Farver, O., Biochim. Biophys. Ada 1434: 103-113, 1999.

Johannes, C. and Majcherczyk, A., Appl. Environ. Microbiol. 66: 524-528, 2000

Jones et al, Nature 321: 522-525, 1986.

Kaitseva, I., Zaitsev, V., Card, G., Moshkov, K., Bax, B., Ralph, A., and Lindley, P., JBIC 1: 15-23, 1996. Kennet et al. (eds) Monoclonal Antibodies and Hybridomas: A New Dimension in Biological Analyses, pp. 376-384, Plenum Press, New York, 1980.

Kim et /., Gene 239: 129-135, 1999.

Kohler and Milstein, European Journal of Immunolo y 6: 511-519, 1976.

Kohler and Milstein, Nature 256: 495-499, 1975.

Kostelny et al, J. Immunol 148: 1547-1553, 1992.

Kozbor et al, Methods in Enzymology 121: 140, 1986.

Krebber et al, J. Immunol. Methods 201(1): 35-55, 1997.

Ku & Schuxz, Proc. Natl. Acad. Sci. USA 92: 6552-6556, 1995.

Lardner et al, U.S. Patent No. 5,223,409.

Larin, D., Mekios, C, Das, K., Ross, B., Yang, A. S., and Gilliam, T. C, J.BiolChem. 274: 28497-28504, 1999.

Lee et al, J. Bacteriol 176: 173-188, 1994.

Litwin, C. M. and Calderwood, S. B., Clin.Microbiol.Rev. 6: 137-149, 1993.

Liu et al, Proc. Natl Acad. Sci. USA 84: 3439-3443, 1987.

Lowman et /., Biochem. 30: 10832-10838,1991.

Markland et al, Gene 109: 13-19, 1991.

Marmur and Doty, J Mol Biol. 5: 109, 1962.

Martins, L. J., Jensen, L. T., Simon, J. R., Keller, G. L., Winge, D. R., and Simons, J. R., J. Biol. Chem. 273: 23716-23721, 1998.

McPherson, A., Eur. J. Biochem. 189: 1-24, 1990. Messerschmidt, A. and Huber, R., Eur. J. Biochem. 187: 341-352, 1990.

Messerschmidt, A., Rossi, A., Ladenstein, R., Huber, R., Bolognesi, M., Gatti, G., Marchesini, A., Petruzzelli, R., and Finazzi-Agro, A., J. Mol Biol. 206: 513-529, 1989.

Methods Enzymol 44:, 1976.

Morgan et al. (U.S. Patent No. 6,180,377).

Munoz, C, Guillen, F., Martinez, A. T., and Martinez, M. J., Appl. Environ. Microbiol. 63: 2166-2174, 1997.

Outten, F.W., Outten, C.E., Hale, J and O'Halloran, T.V., J Biol. Chem. 275: 31024- 31029, 2000.

Paret, C, Ostermann, K., Krause-Buchholz, U., Rentzsch, A., and Rodel, G., FEBS Lett. 447: 65-70, 1999.

Penfold, R.J. and Pemberton, J.M, Gene 118(1): 145-146, 1992.

Pickard, M. A., Roman, R., Tinoco, R., and Vazquez-Duhalt, R., Appl Environ. Microbiol 65: 3805-3809, 1999.

Plϋckthun et al, In Antibody engineering: A practical approach 203-252, 1996.

Plunckthun, Biochem. 31: 1579-1584, 1992.

Queen et al. (U.S. Patent No. 6,180,370).

Reichmann et al, Nature 332: 323-327, 1988.

Reiter et al, Biochem. 33: 5451-5459, 1994.

Reiter et al, Cancer Res. 54: 2114-2118, 1994.

Reiter et al, J. Biol. Chem. 269: 18327-18331, 1994.

Roberts et al, Proc. Natl Acad. Sci USA 89: 2429-2433, 1992. Roberts et al, Proc. Natl. Acad. Sci. USA 99: 2166-2111, 2002.

Sambrook et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, NY, 1980.

Sato, M. and Gitlin, J. D., J. Biol. Chem. 266: 5128-5134, 1991.

Saunders, J.R., Docherty, A. and Humplirey, G.O., Transformation by bacteria by plasmid DNA. In Methods in Microbiology, Bennett, P.M., Grinstead, J. (eds). Academic Press, New York.

Shulman et al, Nature 276: 269-270, 1978;

Smith et al, Science 248: 1126-1128, 1990.

Smith, G.P., Science 228: 1315-1317, 1985.

Solomon, E. I. , "Blue" copper-containing oxidases. Metal ions in biology, John Wiley and Sons, hιc, 1981.

Stookey, L.L., Anal Chem. 42: 779-781, 1970.

Stover, C.K., Pham, X.Q., Erwin, A.L., Mizoguchi, S.D., Warrener, P., Hickey, M.J., Brinkman, F.S., Hufhagle, W.O., Kowalik, D.J., Lagrou, M., Garber, R.L., Goltry, L., Tolentino, E., Westbrook-Wadman, S., Yuan, Y., Brody, L.L., Coulter, S.N., Folger, K.R., Kas, A., Larbig, K., Lim, R., Smith, K., Spencer, D., Wong, G.K., Wu, Z. and Paulsen, I.T., Miol Microbiol. 39: 502-511, 2001

Toyama et al, "Monoclonal Antibody, Experiment Manual", published by Kodansha Scientific, 1987.

Trowbridge, J. Exp. Med. 148(1): 313-323, 1978.

Verhoeyen et al, Science 239: 1534-1536, 1988.

Volk et al, J. Virol. 42(1): 220-227, 1982. Ward et al, Nature 341: 544-546, 1989.

Watson et al, Gene 172: 163-164, 1996.

Weaver, P.F., Wall, J.D. and Gest, H., Arch. Microbial. 105: 188-198, 1975.

Webber et al, Mol. Immunol. 32: 249-258, 1995.

Whiteley et al, J. Bacteriol 182: 4356-4360, 2000.

Wimmer, R., Herrmann, T., Solioz, M., and Wuthrich, K., J. Biol. Chem. 274: 22597- 22603, 1999.

Winter and Milstein, Nature 349: 293, 1991.

Yannish-Perron, C.J., Vieiera, C.J. and Messing, J., Gene 33: 103, 1985.

Yuan, D. S., Stearman, R., Dancis, A., Dunn, T., Beeler, T., and Klausner, R. D., Proc. Natl. Acad. Sci. U.S.A 92: 2632-2636, 1995.

Zaveckas et al, J. Chromatogr. A 904: 145-169, 2000.

Claims

1. An isolated polypeptide or a derivative or chemical analog thereof wherein said polypeptide is characterized, when in active form, of having multi-copper oxidase activity, being capable of facilitating metal ion uptake into a cell and being isolatable from a prokaryotic organism.

2. The isolated polypeptide of Claim 1 wherein the metal ion taken up is Feⁿ.

3. The isolated polypeptide of Claim 1 or 2 wherein the polypeptide also exhibits laccase activity.

4. The isolated polypeptide of any one of Claims 1 to 3 wherein said polypeptide comprises an amino acid sequence having at least 30% similarity after optimal alignment to Fet from yeast.

5. The isolated polypeptide of Claim 1 wherein the prokaryotic microorganism is selected from Pseudomonas sp., Salmonella sp., Enterobacter sp., Escherichia coli sp., Klebsiella sp., Bordetella sp., Caulobacter sp., Aeromonas sp., Pasteurella sp., Xanthomonas sp., Corynebacterium sp., Legionella sp., Mycobacterium sp., Staphylococcus sp., Streptococcus sp. and Bacillus sp.

6. The isolated polypeptide of Claim 5 wherein the prokaryotic microorganism is Pseudomonas aeruginosa.

1. The isolated polypeptide of Claim 5 wherein the prokaryotic microorganism is

Bordetella pertussis.

8. The isolated polypeptide of Claim 5 wherein the prokaryotic microorganism is

Mycobacterium tuberculosis.

9. The isolated polypeptide of Claim 5 wherein the prokaryotic microorganism is Salmonella typhimurium.

10. The isolated polypeptide of Claim 6 wherein the polypeptide comprises a eukaryotic multi-copper oxidase signature sequence.

11. The isolated polypeptide of Claim 6 or 10 comprising an amino acid sequence encoded by a nucleotide sequence substantially as set forth in SEQ ID NO: 17 and/or SEQ ID NO:18 and/or SEQ ID NO:19 or a nucleotide sequence having at least about 60% similarity to SEQ ID NO: 17 and/or SEQ ID NO: 18 after optimal alignment or a nucleotide sequence capable of hybridizing to SEQ ID NO: 17 and/or SEQ ID NO: 18 and/or SEQ TD NO:19 or a complementary form thereof under low stringency conditions.

12. The isolated polypeptide of Claim 6 or 10 or 11 comprising an amino acid sequence substantially as set forth in SEQ ID NO: 15 and/or SEQ ID NO: 16 and/or SEQ ID NO:20 or an amino acid sequence having at least about 60% similarity to SEQ ID NO: 15 and/or SEQ ID NO:16 and/or SEQ ID NO:20 after optimal alignment.

13. A method for modulating metal ion by a cell, said method comprising administering to said cell or a higher organism comprising said cell an amount of an effector molecule capable of modulating the function of a multi-copper oxidase from a prokaryotic organism which multi-copper oxidate facilitates metal ion uptake in said prokaryotic organism.

14. The method of Claim 13 wherein the metal ion taken up is Fe¹¹.

15. The isolated polypeptide of Claim 13 or 14 wherein the polypeptide also exhibits laccase activity.

16. The isolated polypeptide of any one of Claims 13 to 15 wherein said polypeptide comprises an amino acid sequence having at least 30% similarity after optimal alignment to Fet from yeast.

17. The isolated polypeptide of Claim 13 wherein the prokaryotic microorganism is selected from Pseudomonas sp., Salmonella sp., Enterobacter sp., Escherichia coli sp., Klebsiella sp., Bordetella sp., Caulobacter sp., Aeromonas sp., Pasteurella sp., Xanthomonas sp., Corynebacterium sp., Legionella sp., Mycobacterium sp., Staphylococcus sp., Streptococcus sp. and Bacillus sp.

18. The isolated polypeptide of Claim 17 wherein the prokaryotic microorganism is Pseudomonas aeruginosa.

19. The isolated polypeptide of Claim 17 wherein the prokaryotic microorganism is Bordetella pertussis.

20. The isolated polypeptide of Claim 17 wherein the prokaryotic microorganism is Mycobacterium tuberculosis.

21. The isolated polypeptide of Claim 17 wherein the prokaryotic microorganism is Salmonella typhimurium.

22. The isolated polypeptide of Claim 18 wherein the polypeptide comprises a eukaryotic multi-copper oxidase signature sequence.

23. The isolated polypeptide of Claim 18 or 22 comprising an amino acid sequence encoded by a nucleotide sequence substantially as set forth in SEQ ID NO: 17 and/or SEQ ID NO: 18 and/or SEQ ID NO: 19 or a nucleotide sequence having at least about 60% similarity to SEQ ID NO: 17 and/or SEQ ID NO: 18 after optimal alignment or a nucleotide sequence capable of hybridizing to SEQ ID NO:17 and/or SEQ ID NO:18 and/or SEQ ID NO: 19 or a complementary form thereof under low stringency conditions.

24. The isolated polypeptide of Claim 18 or 22 or 23 comprising an amino acid sequence substantially as set forth in SEQ ID NO: 15 and/or SEQ ID NO: 16 and/or SEQ ID NO:20 or an amino acid sequence having at least about 60% similarity to SEQ TD NO: 15 and/or SEQ ID NO:16 and/or SEQ ID NO:20 after optimal alignment.

25. The method of Claim 13 wherein the cell is a prokaryotic microorganism.

26. The method of Claim 13 wherein the cell is a eukaryotic organism.

27. The method of Claim 13 wherein the effector molecule is an antagonist of the multi-copper oxidase.

28. The method of Claim 13 wherein the effector molecule is an agonist of the multi-copper oxidase.

29. A method for modulating metal ion uptake in a cell, said method comprising introducing to said cell or a parent of said cell a nucleic acid molecule encoding a polypeptide which functions as a multi-copper oxidase and is derivable from a prokaryotic microorganism.

30. The method of Claim 29 wherein the metal ion taken up is Fe¹¹.

31. The method of Claim 29 or 30 wherein the polypeptide also exhibits laccase activity.

32. The method of any one of Claims 29 to 31 wherein said polypeptide comprises an amino acid sequence having at least 30% similarity after optimal alignment to Fet from yeast.

33. The method of Claim 29 wherein the prokaryotic microorganism is selected from Pseudomonas sp., Salmonella sp., Enterobacter sp., Escherichia coli sp., Klebsiella sp., Bordetella sp., Caulobacter sp., Aeromonas sp., Pasteurella sp., Xanthomonas sp., Corynebacterium sp., Legionella sp., Mycobacterium sp., Staphylococcus sp., Streptococcus sp. and Bacillus sp.

34. The method of Claim 33 wherein the prokaryotic microorganism is Pseudomonas aeruginosa.

>

35. The method of Claim 33 wherein the prokaryotic microorganism is Bordetella pertussis.

36. The method of Claim 33 wherein the prokaryotic microorganism is Mycobacterium tuberculosis.

37. The method of Claim 33 wherein the prokaryotic microorganism is Salmonella typhimurium.

38. The method of Claim 34 wherein the polypeptide comprises a eukaryotic multi-copper oxidase signature sequence.

39. The method of Claim 34 or 38 comprising an amino acid sequence encoded by a nucleotide sequence substantially as set forth in SEQ ID NO:17 and/or SEQ ID NO:18 and/or SEQ ID NO: 19 or a nucleotide sequence having at least about 60% similarity to SEQ ID NO: 17 and/or SEQ ID NO: 18 after optimal alignment or a nucleotide sequence capable of hybridizing to SEQ ID NO:17 and/or SEQ ID NO:18 and/or SEQ ID NO:19 or a complementary form thereof under low stringency conditions.

40. The method of Claim 34 or 38 or 39 comprising an amino acid sequence substantially as set forth in SEQ ID NO:15 and/or SEQ ID NO:16 and/or SEQ ID NO:20 or an amino acid sequence having at least about 60% similarity to SEQ ID NO: 15 and/or SEQ ID NO: 16 and/or SEQ ID NO:20 after optimal alignment.

41. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO:l or an amino acid sequence having at least about 60% similarity thereto.

42. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO:2 or an amino acid sequence having at least about 60% similarity thereto.

43. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO:3 or an amino acid sequence having at least about 60% similarity thereto.

44. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO:4 or an amino acid sequence having at least about 60% similarity thereto.

45. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO:5 or an amino acid sequence having at least about 60% similarity thereto.

46. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO:6 or an amino acid sequence having at least about 60% similarity thereto.

47. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO:7 or an amino acid sequence having at least about 60% similarity thereto.

48. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO:8 or an amino acid sequence having at least about 60% similarity thereto.

49. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO:9 or an amino acid sequence having at least about 60% similarity thereto.

50. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO: 10 or an amino acid sequence having at least about 60% similarity thereto.

51. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO:l 1 or an amino acid sequence having at least about 60% similarity thereto.

52. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO: 12 or an amino acid sequence having at least about 60% similarity thereto.

53. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO:28 or an amino acid sequence having at least about 60% similarity thereto.

54. The method of Claim 29 wherein the multi-copper oxidase comprises the amino acid sequence substantially as set forth in SEQ ID NO:30 or an amino acid sequence having at least about 60% similarity thereto.

55. An isolated antibody capable of binding to a multi-copper oxidase from a prokaryotic microorganism.

56. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO:l.

57. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO:2.

58. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO:3.

59. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO:4.

60. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO:5.

61. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO:6.

62. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO:7.

63. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO:8.

64. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO: 9.

65. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO: 10.

66. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO: 11.

67. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO: 12.

68. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO: 20.

69. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO:28.

70. The antibody of Claim 55 wherein the multi-copper oxidase comprises the amino acid sequence set forth in SEQ ID NO:30.

71. The antibody of any one of Claims 55 to 70 wherein the antibody is a monoclonal antibody.

72. The antibody of any one of Claims 55 to 70 wherein the antibody is a deimmunized antibody.