SELF-SECRETING PROTEASES

Abstract: A method for engineering a protease, wherein said protease is able to cleave a user defined target amino acid sequence. The method includes the steps of incorporating a target DNA sequence which encodes a target amino acid sequence into a gene DNA sequence for a self-secreting protease in the alpha region. The cleavage region of the protease DNA sequence incorporating the target DNA sequence is then modified and an engineered protease is selected which is encoded by a DNA sequence produced by said modifying step which has been modified in the cleavage region to be able to cleave an amino acid sequence encoded by the target DNA sequence.

Description: SELF-SECRETING PROTEASES BACKGROUND OF THE INVENTION 1. Technical Field of the Tnvention The present invention relates to means and methods for producing modified self- secreting endoproteases which can cleave targeted sequences and such proteases produced by the method. 2. Background of the Invention Proteases (peptidases) are proteins which cleave other proteins and have been useful, for example, in the isolation of recombinant proteins. Sec, for example, United States Patent Nos. 5,387,518, 5,391,490 and 5,427,927 (see particularly columns 1-3 of the '927 patent) which describe various proteases and their use in the isolation of desired components from fusion proteins. Self-secreting extracellular proteases, such as IgΛ proteases have substrate specificity for IgA and are produced by bacteria in the genera Streptococcus, Neisseria, Haemiophilas, Ureuplasma, Clostridium, Copaocytophags ωid Bacteroid.es [Meyer et al. , 1987; Klauser et al., 1993, Pohlner et al. , 1987; Morton et al. , 1993; US patent 5,427,927; Canadian patent application 2,058,872]. The enzymes are secreted to the extracellular environment. The bacterial IgA proteases are characteristic of the self- secreting endoproteases. AU have substrate specificity for human IgA immunoglobulins, generally for IgAl . IgAl is one of the two IgA isotypes, the dominant form of antibody in human secretion. For IgAl, each protease attacks a single, specific peptide bond in the heavy chain hinge region resulting in formation of hydrolysis products consisting of the intact antigen- binding Fab and the Fc region of these antibody proteins. The various proteases can have different catalytic mechanisms. The synthesis and secretion of IgAl protease is a fairly well understood process. The information for the enzyme activity and secretion in gram-negative bacteria is in a single polypeptide chain with 4 domains: 1) a signal peptide sequence; 2) a carboxy-terminal domain; 3) an intervening or α region; and 4) the IgA protease enzyme [Klauser et al. , 1993; Koomey et al. , 1992; Miller et al. , 1992; Pohlcr et al. , 1987]. The signal sequence directs the enzyme precursor to the periplasm, and is proteolytically removed during transport across the cytoplasmic membrane (inner membrane). The remainder of the polypeptide is then determined by the carboxy terminal domain which has eight transmembrane β-sheets, typical of this class of membrane proteins [reviewed in Klauser et al. , 1993], The carboxy terminal domain forms a channel rough which the amino-proximal end is threaded. The amino-proximal end including the catalyticaly active part of the protein (protease and a region) is long and is initially exposed on the outside of the outer membrane before it is cleaved and released. Autoproteolytic processing at typical cleavage site in and around the α region results in the release of the protease from the cell membrane. The cleavage sites contain proline-rich sequences similar to the cleavage site of IgA protease in human IgAl. The sole secretion factor specifically required by IgA protease secretion is an integral part of the protease precursor. There is no need for receptors that specifically select proteins from periplasmic pools for secretion across the outer membrane. In fact, the IgA protease secretion pathway may facilitate the outer membrane translocation of virtually any polypeptide that is fused to its amino terminus provided that all other conditions for efficient secretion are met [Pohlner et al. , 1993]. The IgA proteases are extensively used as a proteolytic enzyme for cleavage of fusion proteins produced by genetic engineering [US Patent No. 5,427,927], There has been extensive investigation of these proteases and other proteases to improve their activity and to extend the substrate specificity [Canadian patent application 2,058,872, Pohlner et al. , 1987; Morton et al., 1993; Gilbert et al. , 1988; Koomey et al. , 1982, Pohlner et al., 1992, Pohlner et al. , 1993; Walker et al. , 1994, Pompejus et al. , 1993; Wong et al., 1994; Pohlner et al., 1993, Pohler et al. , 1992, US patent 5,427,927; US patent 5,252, 478; Miller et al. , 1992]. However, the method of choice for extending the targets of the proteases has been to insert into the target protein the cleavage sequence that is required by the protease. Alternatively, many proteases may be screened until one is found that will cleave at the requisite sequence. Methods of rapidly and efficiently engineering or designing an existing protease to cleave a new sequence specifically have not heretofore been available. SUMMARY OF THE INVENTION According to the present invention, a method for making (engineering) and selecting a site-specific protease able to cleave a user defined recognition sequence is disclosed. The method includes the steps of incorporating a DNA sequence encoding the target amino acid sequence to be cleaved (recognition sequence) into a tolerant region of a self-secreting protease gene, thereby replacing the natural cleavage site for autoproteolysis. Expression of this gene leads to accumulation of a surface-bound protease that has the user defined recognition site incorporated into the portion of the molecule that links the protease to the cell surface. The coding region of the active domain of the protease is then subjected to extensive mutagenesis. From among the pool of modified proteases some will be able to recognize the user defined recognition sequence and will cleave that site, thereby releasing the active protease from the cell surface. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT The present invention is a method for making (engineering) a site-specific protease that is able to cleave a user defined target amino acid sequence (recognition sequence). That is, a self-secreting protease, such as an IgA protease, is modified to cleave a target amino acid sequence that is not its natural target. The self-secreting protease to be modified is selected from proteases that are secreted from a cell and in the process of secretion are attached externally on the cell membrane. To be released from the membrane the protease autocleaves at the α region of the molecule, thereby being released from the membrane. The user defined toget amino acid sequence can be from any protein or peptide for which a protease is needed. The amino acid sequence that is the target must be expressed in the protein or peptide molecule in a position that is accessible to the designed protease. The first step of the process incorporates a DNA sequence for a user defined target amino acid sequence into the gene sequence for the protease between the protease coding domain and the autotranslocator coding domain of the protease DNA sequence. That is, the target sequence is inserted into a tolerant region of a self-secreting protease gene, thereby replacing the natural cleavage site for autoproteolysis. Any method known in the art may be used to incorporate the target DNA sequence into the DNA sequence of the protease. Standard methods such as site-directed insertion mutagenesis (Sayer et al., 1992) or the introduction of point mutations to alter the coding region while maintaining the reading frame may be used. The catalytic domain of the protease sequence with the incorporated target DNA sequence is then modified at the cleavage region of the protease DNA sequence. That is, the DNA is subjected to in vitro mutagenesis which alters the DNA sequence of the protease. Any method known in the art can be used to modify the sequence. In particular, methods which can be directed to alter a specific region as in the present invention, i.e. the cleavage region, are used [Eglinton et al., Zoller and Smith, 1982; Wong et al. , 1994; Pompejus et al. , 1993; Mildner et al. , 1994] as for example, site direct mutagenesis and/or gene shuffling [Stemmer, 1994]. A protease encoded by a modified cleavage DNA sequence that is able to autoclave the target amino acid sequence is then selected and isolated. Because of the nature of the protease employed, only those proteases carrying the desired cleavage mutation will be soluble, i.e. will be released from the cell membrane. For example, single or multiple rounds of gene shuffling can be undertaken. The protease gene sequence is first amplified by PCR and then the PCR products are randomly cut into fragments by DNAasel. Gel purification of small fragments and reassembly of the fragments in a PCR-like reaction without primers is undertaken. Amplification of the reassembled product can be undertaken by PCR followed by cloning into a vector such as a plasmid. Up to 10 9 mutant clones can be generated from each round of gene shuffling. This library of-modified clones can then be transferred to a host cell which will express the fusion product, i.e. mutant protein from the mutated gene sequence. In general, a bacterial host such as E. coli is used. Clones from cells in which the mutant protease fails to cleave (hydrolyze) the target sequence in the α region of the protease will have protease bound on the cell membrane and can be depleted using standard methods known in the art, i.e. negative selection. For example, antibodies directed against an unmodified region of the protease can be mixed with the cells and complement mediated lysis can be used. Alternatively, antibodies immobilized on a sold support could be used to selectively remove the cells with surface bound protease, or cell sorting could be used to remove cells tagged with labeled antibodies. Positive selection could also be used. That is, enrichment can be based on selecting cells which do not have proteases bound to the cell membrane surface. For„ example, the cell media for a clone can be assayed using an immunoassay for the presence of soluble protease in the media. Alternatively, a functional assay for the presence of the protease could be undertaken. In a preferred embodiment, a combination of negative and positive selection is used. As an exemplar throughout the application, the IgA proteases may be used, but the invention is not limited to the IgA proteases; any self-secreting protease may be used. IgA proteases (IgAses) are naturally exported by some Gram negative bacteria [Meyer et al. , 1987]. These bacteria include but are not limited to Streptococcus sanguis, Streptococcus oralis [Gilbert et al. , 1988, Morton et al., 1993], Neisseήa gonorrhoeae, Neisseria meningitidis, and Haemophilus influence [Klauser et al., 1993; Koomey et al., 1982, Miller et al., 1992; Pohler et al. , 1987]. The IgA proteases are a group of highly homologous proteins each with its own unique cleavage specificity directed at specific sites on an IgA molecule. As discussed herein above, the protein is synthesized as a fusion of protease, alpha peptide and autotranslocator domains [Klauser et al., 1993; Meyer et al. , 1987; Pohler et al. , 1987]. The preprotein is transported to the cell surface where it folds and undergoes autocleavage at internal recognition sites to produce free mature protease. Once translocated to the outside of the cell, the protease domain folds into its active conformation. It then cleaves itself from the autotranslocator by cutting its specific recognition sequence present in the peptide region. Mutants which lack the protease' s recognition site are known to remain tethered to the outer membrane. An embodiment of the present invention will now be described, by way of example alone, with reference to the accompanying flow diagram. The flow diagram represents the main sequence of steps, according to one embodiment of the present invention, for engineering a protease. Firstly, the target coding region is cloned into a protease vector as represented by step A, this is followed by subjecting the protease coding domain to mutagenesis techniques as represented by step B. Step C involves transforming the bacteria and amplifying the library, this is followed by step D which is a negative selection step involving depleting clones from cells in which the mutant protease fails to cleave the target sequence in the alpha region of the protease, i.e. depleting clones from cells carrying surface bound protease. Step D may be carried out by affinity chromatography. Step D may then be followed either by a positive selection stage, step E, or by amplifying the library enriched for bacteria expressing active autocleavers, step F. The clones are then screened (in step G) for active protease-producing clones, by using, for example, an ELISA. The desired clones are then amplified (step H) or the plasmid DNA from the library is isolated and the protease coding domain subjected to mutagenesis techniques, as represented by step B. Steps B to H are then repeated, as described above. A protein for which a protease is needed is identified. For example, in one embodiment, certain proteases (i.e. the target protein in this embodiment) are known to be critical to cancer cell growth and it is therapeutically useful to have anti-pro teases available. The target protein is analyzed chemically and stnjcturally to determine if there are unique amino acid sequences that can be used as a target of the designer protease of the present invention. The DNA coding for this unique sequence is then determined and is used to replace the sequence in the region of the IgA protease gene. A recombinant plasmid is prepared carrying the alpha peptide replaced by the target sequence. The construct lacks the cleavage site of the natural protease and thus, a fusion protein would be expressed on the cell surface and would not be released. However, the protease (cleavage) coding region is then subjected to mutagenesis techniques as are known in the art. A combination of the highly efficient Stemmer [1994] mutagenesis and more classical site-directed protocols may be used, but other techniques known to those skilled in the art may likewise be employed. This procedure generates large numbers of combinatorially mutated plasmids (up to 10 9 different clones per library). The library is then expressed in a host cell. Suitable host cells include, but are not limited to E. coli and other host cells known to those skilled in the art. Clones expressing mutant proteases which fail to hydrolyze the target sequence would have protease bound on their surfaces. However, cells which carry active mutant protease genes capable of cleaving somewhere in the user defined target sequence expressing soluble, rather than surface-bound protease. Given that natural variants of the IgA proteases have different sequence specificities, the above system will be capable of generating huge numbers of mutant proteases, some of which will have novel sequence specificities. The next step is to select the mutants which can cleave the protein target of interest. This can be done by a number of different approaches known to those skilled in the art, including, but not limited to a combination of positive and negative selection steps. The first step uses a negative selection procedure to remove cells which have large amounts of surface bound protease. Cells are washed to remove soluble protease and then subjected to negative selection using immobilized polyclonal antibodies. These can be directed against a recombinant sequence tag expressed on the protease N-terminal, or alternatively polyclonal anti-protease antibodies could be used (as mutant proteases are still likely to be recognized by a proportion of polyclonals). Thus, cell suspensions are depleted of bacteria carrying surface bound protease. The resultant cells, enriched for cells lacking surface bound protease, are amplified/cloned and then subjected to a positive screening step. This involves screening individual clones for production of soluble protease. This can be done either with polyclonal antibodies directed to the protease (to detect clones which do produce soluble protein) in an i munoassay or by using a functional assay which utilizes a peptide containing the target sequence. Such screening procedures are carried out on many thousands of clones selected from the primary negative screen. This procedure leads to the isolation of proteases able to cleave somewhere within the target sequence and the procedure produces at least one, but generally several, clones with a number of different cleavage specificities for any given polypeptide target sequence. The process can be made iterative at either stage leading to the isolation of more proteases with improved catalytic activities/ specificities. The designer proteases are used in a variety of applications. In principle, any protein could be targeted for cleavage. The natural IgAses have low immunogenicity and so designer proteases will be best utilized to target important mediators of inflammatory processes, hormones, viral proteins, microbial proteins, proteins that regulate cell cycle, oncogene products, enzymes etc. Sequence specific endoproteases such as wild-type IgA protease, thrombin, and factor Xa have been used in the processing of fusion proteins for protein engineering work and in biotransformations. However, the number of sequence specific proteases is very limited at present and often produce fusions with undesired additional amino acid residues. In this context a designer protease could be engineered for accurate processing of a particular fusion or preprotein. The above procedure can also be modified to use other proteases, e.g. , of human origin, by replacing the IgAse domain with the protease of interest. A system based on the above outline can also select for chemical synthesis of proteins from peptide (or even non-peptide) precursors which could have uses in the synthesis of biologically active molecules. In general, this approach allows negative manipulation of proteins through cleavage at sites necessary for defined biological activity and also positive biological regulation by, for example, increasing rates of processing of bio-active materials from endogenous precursor molecules that is an improvement over the methods of the prior art [Walker et al., 1994; Pompejus et al. 1993; Wong et al. , 1994; Pohlner et al., 1993; Pohler et al., 1992; US Patent No. 5,427,927]. The present invention also discloses a site-specific protease (designer protease) produced by the method of the present invention that is able to cleave a user defined target amino acid sequence. Preferably, the protease is an IgA protease. The designer protease produced by the present invention when used as a medicament is administered and dosed in accordance with good medical practice, taking into account the clinical condition of the individual patient, the site and method of administration, scheduling of administration, patient age, sex, body weight and other factors known to medical practitioners. The pharmaceutically "effective amount" for purposes herein is thus determined by such considerations as are known in the art. The amount must be effective to achieve improvement including, but not limited to, improved survival rate or more rapid recovery, or improvement or elimination of symptoms and other indicators as are selected as appropriate measures by those skilled in the art. In a preferred embodiment delivery of the designer protease is by methods known in the art to deliver large molecules into the body and cells, such as liposome technology, mucoadhesives or gene therapy as described herein below. The designer protease or therapeutically active peptide fragments of the protease are administered and dosed in accordance with good medical practice, taking into account the clinical condition of the individual patient, the site and method of administration, scheduling of administration, and other factors known to medical practitioners. The "effective amount" for purposes herein is thus determined by such considerations as are known in the art. The amount must be effective to achieve improvement including, but not limited to, a reduction in infection and other indicators as are selected as appropriate measures by those skilled in the art. In the method of the present invention, the designer protease can be administered in various ways. It should be noted that it can be administered as the compound or as pharmaceutically acceptable salt and can be administered alone or in combination with pharmaceutically acceptable carriers designed to maintain the integrity of the compound, as for example in protecting against proteolysis of the anti-protease. The compounds will generally be administered intravenously due to the size of the molecule. However, as other methods become available it is contemplated that it can be administered orally, subcutaneously or parenterally. Additional administration routes include intraarterial, intramuscular, intraperitoneal, and intranasal administration. Implants of the compounds are also useful. Treatment may be administered to a human or to a warm-blooded animal, such as a mammal. The doses may be single doses or multiple doses over a period of several days. The treatment generally has a length proportional to the length of the disease process and drug effectiveness and the species being treated. When administering the protease or active peptide parenterally, the protease will generally be formulated in a unit dosage injectable form (solution, suspension, emulsion). The pharmaceutical formulations suitable for injection include sterile aqueous solutions or dispersions and sterile powders for reconstitution into sterile injectable solutions or dispersions. The carrier can be a solvent or dispersing medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils. Proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Nonaqueous vehicles such as cottonseed oil, sesame oil, olive oil, soybean oil, corn oil, sunflower oil, or peanut oil and esters, such as isopropyl myristate, ay also be used in solvent systems for compound compositions. Additionally, various additives which enhance the stability, sterility, and isotonicity of the compositions, including antimicrobial preservatives, antioxidants, chelating agents, and buffers, can be added. Prevention of the action of microorganisms can be ensured by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, and the like. In many cases, it will be desirable to include isotonic agents, for example, sugars, sodium chloride, and the like. Prolonged absorption of the injectable pharmaceutical form can be brought about by the use of agents delaying absorption, for example, aluminum ministered and gelatin. According to the present invention, however, any vehicle, diluent, or additive used would have to be compatible with the protease and delivery system. Sterile injectable solutions can be prepared by incorporating the compounds utilized in practicing the present invention in the required amount of the appropriate solvent with various of the other ingredients, as desired. A pharmacological formulation of the designer protease can be administered to the patient in an injectable formulation containing any compatible carrier, such as various vehicle, adjuvants, additives, diluents and antiproteolytic agents; or the compounds utilized in the present invention can be administered parenterally to the patient in the form of slow-release subcutaneous implants or targeted delivery systems such as monoclonal antibodies, vectored delivery, iontophoretic, polymer matrices, liposomes, and microspheres. Examples of delivery systems useful in the present invention include U.S. Patent No. 5,225, 182; U.S. Patent No. 5, 169,383; U.S. Patent No. 5, 167,616; U.S. Patent No. 4,959,217; U.S. Patent No. 4,487,603; U.S. Patent No. 4,486, 194; U. S. Patent No. 4,447,233; U.S. Patent No. 4,447,224; U.S. Patent No. 4,439, 196; and U.S. Patent No. 4,475, 196. Many other such implants, delivery systems, and modules are well known to those skilled in the art. A pharmacological formulation of the protease as developed by the method of the present invention can be administered orally to the patient. Conventional methods such as administering the compounds in tablets, suspensions, solutions, emulsions, capsules, powders, syrups and the like are usable. Known techniques which deliver the peptide orally or intravenously and reώn the biological activity are preferred. Other designer proteases developed as drugs would be administered as described herein above. For example, the HTV-l protease is preceived as a target for development of drugs against AIDS [Mildner et al. , 1994; Tomasselli et al., 1990]. Standard methods in immunology known in the art and not specifically described may be generally followed as in Stites et al. (eds), Basic and Clinical Immunology (8th Edition), Appleton & Lange, Norwalk, CT (1994) and Mishell and Shiigi (eds), Selected Methods in Cellular Immunology, W.H. Freeman and Co. , New York (1980). If needed, ELISAs and RIAs are in general the immunoassays that can be employed. ELIS A assays are well known to those skilled in the art. Both polyclonal and monoclonal antibodies can be used in the assays. Where appropriate other immunoassays, can be used as are known to those in the art. Available immunoassays are extensively described in the patent and scientific literature. See, for example, United States patents 3,791 ,932; 3,839, 153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901 ,654, 3,935,074; 3,984,533; 3,996,345; 4.034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281 ,521 as well as Sambrook et al. , Molecular Cloning: A Laboratory Manual, Cold Springs Harbor, New York, 1989. Standard molecular biology techniques known in the art and not specifically described are generally followed as in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), and in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Maryland (1989). Polymerase chain reaction (PCR) can be carried out generally as in PCR Protocols: A Guide to Methods and Applications, Academic Press, San Diego, CA (1990).] Reactions and manipulations involving nucleic acid techniques, unless stated otherwise, may be performed as generally described in Sambrook et al. , 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press; and methodology as set forth in United States patents 4,666,828; 4,683,202; 4,801 ,531 ; 5, 192,659 and 5,272,057 and incorporated herein by reference. The gene shuffling protocol can be conducted by any shuffling protocol known to those skilled in the art, including, but not limited to, the protocol according to Stemper, 1994, incorporated by reference herein. Site directed mutagenesis may be conducted according to the technique described in Sayer et al., 1992, incorporated by reference herein. Vectors can be constructed containing the cDNA of the present invention and should contain all expression elements necessary to achieve the desired transcription of the sequences. Other beneficial characteristics can also be contained within the vectors such as mechanisms for recovery of the nucleic acids in a different form. Phagemids are a specific example of such beneficial vectors because they can be used either as plasmids or as bacteriophage vectors. Examples of other vectors include viruses such as bacteriophages, baculoviruses and retroviruses, DNA viruses, cosmids, plasmids, liposomes and other recombination vectors. The vectors can also contain elements for use in either procaryotic or eucaryotic host systems. One of ordinary skill in the art will know which host systems are compatible with a particular vector. The vectors can be introduced into cells by any one of a variety of known methods within the art. The host cell can be any eucaryotic and procaryotic cells, which an be transformed with the vector and which will support the production of the enzyme. E. coli and Pichia pastoris are host cells in bacterial and yeast (Cregg et al., 1993) preferred embodiments, respectively. Methods for transformation can be found generally described in Sambrook et al. , Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1992), in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Maryland (1989), Chang et al. , Somatic Gene Therapy, CRC Press, Ann Arbor, MI (1995), Vega et al. , Gene Targeting, CRC Press, Ann Arbor, MI (1995) and Gilboa, et al. (1986), all incorporated by reference herein, and include, for example, stable or transient transfection, lipofection, electroporation and infection with recombinant viral vectors. In addition, see United States patents 5,464,764 and 5,487,992 for positive-negative selection methods. Antibodies used for selection may be either monoclonal or polyclonal. Conveniently, the anitbodies may be prepared against a synthetic peptide based on the sequence, or prepared recombinantly by cloning techniques or the natural gene product and/or portions thereof may be isolated and used as the immunogen. Such proteins or peptides can be used to produce antibodies by standard antibody production technology well known to those skilled in the art as described generally in Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1988 and Borrebaeck, Antibody Engineering - A Practical Guide, W.H. Freeman and Co. , 1992. For producing polyclonal antibodies a host, such as a rabbit or goat, is immunized with the protein or peptide, generally with an adjuvant and, if necessary, coupled to a carrier; antibodies to the protein are collected from the area. For producing monoclonal antibodies the technique involves hyperimmunization of an appropriate donor with the protein or peptide fragment, generally a mouse, and isolation of splenic antibody producing cells. These cells are fused to a cell having immortality, such as a myeloma cell, to provide a fused cell hybrid which has immortality and secretes the required antibody. The cells are then cultured, in bulk, and the monoclonal antibodies harvested from the culture media for use. The antibody can be bound to a solid support substrate or conjugated with a detectable moiety or toxin or be both bound and conjugated as is well known in the art. (For a general discussion of conjugation of fluorescent or enzymatic moieties see Johnstone & Thorpe, Immunochemistry in Practice, Blackwell Scientific Publications, Oxford, 1982). The binding of antibodies to a solid support substrate is also well known in the art. (see for a general discussion Harlow & Lane Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Publications, New York, 1988 and Borrebaeck, Antibody Engineering - A Practical Guide, W.H. Freeman and Co. , 1992). The detectable moieties contemplated with the present invention can include, but are not limited to, fluorescent, metallic, enzymatic and radioactive markers such as biotin, gold, ferritin, alkaline phosphatase, β-galactosidase, peroxidase, urease, fluorescein, rhodamine, tritium, I4 C and iodination. The toxins can include plant toxins such as ricin, bacterial toxins such as diphtheria toxin. Throughout tlύs application, various publications, including United States patents, are referenced by citation or number. Full citations for the cited publications are listed below. The disclosures of these publications and patents in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this invention pertains. The invention has been described in an illustrative manner, and it is to be understood that the terminology which has been used is intended to be in the nature of woods of description rather than of limitation. Obviously, many modifications and variations of the present invention are possible in light of the above teachings. It is, therefore, to be understood that within the scope of the appended claims, the invention may be practiced otherwise than as specifically described. REFERENCES Eglinton et al. , "Site-directed mutagenesis to study protein structure and function" in Laboratory Methods in Immunology, editor, Zola, H., CRC Press, Inc., Boca Raton, Florida, Vol. 1, Chapter 16, p. 195-206. Gilbert et al., "Cloning of the gene encoding streptococcal immunoglobulin A protease and its expression in Escherichia coli" Infect Immun, 56(8) : 1961-6 (1988). Klauser et al., "The secretion pathway of IgA protease-type proteins in gram-negative bacteria" Bώ≤ssays, 15(12):799-805 (1993). Koomey et al. , "Genetic and biochemical analysis of gonococcal IgA l protease: cloning in Escherichia coli and construction of mutants of gonococci that fail to produce the activity" ENΔS_ iSΔ}, 79(24):7881-5 (1982). Meyer et al., "Mechanism of extracellular secretion of an IgA protease by gram-negative host cells" Adv Exp Med Biol. 216B.1271-81 (1987) Mildner et al., "The HIV-1 protease as enzyme and substrate: mutagenesis of autolysis sites and generation of a stable mutant with retained kinetic properties" Biochemistry, 33:9405-9413 (1994). MUler et al., "Endoglucanase A from Cellulomonas fimi in which the hinge sequence of human IgAl is substituted for the linker connecting its two domains is hydrolyzed by IgA proteases from Neisseria gonorrhoeae" FEMS Microbiol Lett 71(2): 199-203 (1992). Morton et al. , "Purification and characterization of chimeric human IgAl and IgA2 expressed in COS and Chinese hamster ovary cells" J Immunol, 151(9): 4743-52 (1993). Pohlner et al. , "Neisseria gonorrhoease IgA protease. Secretion and implications for pathogenesis" Antonie Van Leeuwenhoek. 53(6):479-84 (1987). Pohlner et al., "Sequence-specific cleavage of protein fusions using a recbinant Neisseria type 2 igA protease" Biotechnology CNY), 10(7): 799-804 (1992). Pohlner et al., "A plasmid system for high-level expression and in vitro processing of recombinant proteins" Gj£ne, 130(1): 121-6 (1993). Pompejus et al., "High-yield production of bacteriorhodopsin via expression of a synthetic gene in Escherichia coli" Fur J Biochem. 211 :(l-2):27-35 (1993). Sayer, et al, "Rapid high efficiency site-directed mutagenesis by the phophorthioate approach. BioTechniques 13:592-596 (1992). Stem er, "Rapid evolution of a protein in vitro by DNA shuffling", Ji lius 370:389-391 (1994). Tomasselli et al., "Substrate analogue inhibition and active site titration of purified recombinant HIV-1 protease" Biochemistry, 29:264-269 (1990). Walker et al., "Efficient and rapid affinity purification of proteins using recombinant fusion proteases" Biotechnology (NY). 12(6):601-5 (1994). Wong and Nathoo, "Engineering and production of streptokinase in a Bacillus subtilis expression-secretion system" Appl Environ Microbiol, 60(2):517-23 (1994). Zoller and Smith, "Oligonucleotide-directed mutagenesis using M1 -derived vectors: an efficient and general procedure for the production of point mutations in any fragment of DNA" Nucleic Acids Research. 10(20):6487-6500 (1982). Cregg JM, Vedvick TS, Raschke WC: Recent Advances in the Expression of Foreign Genes in Pichia pastoris, Bio/Technology 11 : 905-910, 1993. Gilboa, E, Eglitis, MA, Kantoff, PW, Anderson, WF: Transfer and expression of cloned genes using retroviral vectors. BioTechniques 4(6): 504- 12, 1986.

Claims: What is claimed is: 1. A method for engineering a protease, said protease having the ability to cleave a user defined target amino acid sequence, comprising the steps of: (a) incorporating a target DNA sequence encoding a target amino acid sequence into the gene sequence of a self-secreting protease, wherein said gene sequence encodes the α region of said self-secreting protease; and (b) modifying the cleavage region of said self-secreting protease gene sequence, and selecting an engineered protease encoded by a DNA sequence produced by said modifying step which has been modified in the cleavage region to be able to cleave an amino acid sequence encoded by the target DNA sequence. 2. A method according to claim 1 , wherein said modifying step is further characterised by site directed mutagenesis and Stemmer gene shuffling to produce a modified protease sequence. 3. A method according to claim 1 or 2, wherein said self-secreting protease is an IgA protease. 4. A method according to any of claims 1 to 3, wherein said modifying step includes the further steps of cloning the modified protease sequence generated into a vector; generating a library of modified clones after each gene shuffling; and transferring the library to a bacterial host cell which will express a fusion product. 5. A method according to any of claims 1 to 4, wherein said selecting step is further characterised by being a negative selecting step wherein a cell expressing a non-soluble IgA protease on its surface is depleted. 6. A method according to claim 5, wherein said selecting step is further characterised by being a positive selecting step comprising the further steps of assaying for released protease, and isolating cells which released the protease. 7. A protease which has been engineered to cleave a user defined amino acid sequence, said protease being produced by the method of claim 1. 8. A protease according to claim 7, which is an IgA protease. 9. A protease according to claim 7 or 8, wherein said user defined sequence comprises an amino acid sequence in the a region of said protease, said amino acid sequence having been defined by a target nucleotide sequence.

Inventors: DUFF GORDON, SAYER JON, DUFF, GORDON, SAYER, JON
Applicants: DUFF GORDON, SAYER JON, DUFF, GORDON, SAYER, JON
Application year: 1997
Main classification: C12N15
IPC codes: C12N9, C12N15