# Patent

## Title
Methods for isolating novel antimicrobial agents from hypermutable mammalian cells

## Abstract

Dominant-negative alleles of human mismatch repair genes can be used to generate hypermutable cells and organisms. By introducing these genes into mammalian cells new cell lines with novel and useful properties can be prepared more efficiently than by relying on the natural rate of mutation or introduction of mutations by chemical mutagens. These methods are useful for generating novel and highly active antimicrobial molecules as well as superior antimicrobial agents from pre-existing chemicals. These methods are also useful for generating cell lines expressing novel antimicrobials that are useful for pharmaceutical manufacturing.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This is a divisional of U.S. application Ser. No. 10/369,845, filed Feb. 19, 2003 now abandoned, which is a continuation of U.S. application Ser. No. 09/708,200 filed Nov. 7, 2000, now U.S. Pat. No. 6,576,468, issued Jun. 10, 2003, both of which are incorporated by reference herein in their entireties.


FIELD OF THE INVENTION
The present invention is related to the area of antimicrobial agents and cellular production of those agents. In particular, it is related to the field of identification of novel antimicrobial agents by placing mammalian cells under selection in the presence of the microbe.
BACKGROUND OF THE INVENTION
For as long as man has shared the planet with microorganisms there have been widespread outbreaks of infectious disease and subsequent widespread mortality associated with it. Although microorganisms and man frequently share a symbiotic relationship, microorganisms can, under some conditions, lead to sickness and death. The discovery, wide use and dissemination of antibiotics to treat microbial infection in both human and animal populations over the last one hundred or so years has done much to control, and in some instances, eradicate some microbes and associated infectious disease. However, microbes have a strong propensity to evolve and alter their genetic makeup when confronted with toxic substances that place them under life and death selective pressures. Therefore, emerging infectious diseases currently pose an important public health problem in both developed as well as developing countries. Not only have microbes evolved to evade and defeat current antibiotic therapeutics, but also there are novel and previously unrecognized and/or characterized bacterial fungal, viral, and parasitic diseases that have emerged within the past two decades. Sass, Curr. Opin. in Drug Discov. & Develop. 2000, 3(5):646–654.
Since the accidental discovery of a penicillin-producing mold by Fleming there has been steady progress in synthesizing, isolating and characterizing new and more effective beta-lactam antibiotics. In addition to the great success of the beta-lactam family of antibiotics, the newer fluoroquinolones have a broad-spectrum of bactericidal activity as well as excellent oral bio-availability, tissue penetration and favorable safety and tolerability profiles. King et al., Am. Fam. Physician, 2000, 61, 2741–2748. A newly devised four-generation classification of the quinolone drugs accounts for the expanded antimicrobial spectrum of the more recently introduced fluoroquinolones and their clinical indications. The so-called first generation drugs, which include nalidixic acid, are capable of achieving minimal serum levels. The second-generation quinolones, such as ciprofloxacin, have an increased gram-negative and systemic activity. The third-generation drugs comprise pharmaceuticals such as levofloxacin and are have significant and expanded action against gram-positive bacteria and atypical pathogens. Finally, the fourth-generation quinolone drugs, which, to date, only includes trovofloxacin, are highly active against anaerobes in addition to the activity described for the third-generation drugs. Furthermore, the quinolone class of anti-microbial drugs can be divided based on their pharmacokinetic properties and bioavailability.
Mammalian epithelial surfaces are remarkable for their ability to provide critical physiologic functions in the face of frequent microbial challenges. The fact that these mucosal surfaces remain infection-free in the normal host suggests that highly effective mechanisms of host defense have evolved to protect these environmentally exposed tissues. Throughout the animal and plant kingdoms, endogenous genetically encoded antimicrobial peptides have been shown to be key elements in the response to epithelial compromise and microbial invasion. Zasloff, Curr. Opin. Immunol., 1992, 4, 3–7; and Bevins, Ciba Found. Symp., 1994, 186, 250–69. In mammals, a variety of such peptides have been identified, including the well-characterized defensins and cathelicidins and others (andropin, magainin, tracheal antimicrobial peptide, and PR-39; see Bevins, Ciba Found. Symp., 1994, 186, 250–69 and references therein). A major source of these host defense molecules is circulating phagocytic leukocytes. However, more recently, it has been shown that resident epithelial cells of the skin and respiratory, alimentary, and genitourinary tracts also synthesize and release antimicrobial peptides. Both in vitro and in vivo data support the hypothesis that these molecules are important contributors to intrinsic mucosal immunity. Alterations in their level of expression or biologic activity can predispose the organism to microbial infection. Huttner et al., Pediatr. Res., 1999, 45, 785–94.
Across the evolutionary scale species from insects to mammals to plants defend themselves against invading pathogenic microorganisms by utilizing cationic antimicrobial peptides that rapidly kill microbes without exerting toxicity to the host. Physicochemical peptide-lipid interactions provide attractive mechanisms for innate immunity as discussed below. Many of these peptides form cationic amphipathic secondary structures, typically alpha-helices and beta-sheets, which can selectively interact with anionic bacterial membranes via electrostatic interactions. Rapid, peptide-induced membrane permeabilization and subsequent cellular lysis is the result. Matsuzaki, Biochim. Biophys. Acta, 1999, 1462, 1–10.
The primary structures of a large number of these host-defense peptides have been determined. While there is no primary structure homology, the peptides are characterized by a preponderance of cationic and hydrophobic amino acids. The secondary structures of many of the host-defense peptides have been determined by a variety of techniques. Sitaram et al., Biochim, Biophys. Acta, 1999, 1462, 29–54. The acyclic peptides tend to adopt helical conformation, especially in media of low dielectric constant, whereas peptides with more than one disulfide bridge adopt beta-structures.
As described above, one reason for the rise in microbial drug resistance to the first line antimicrobial therapies in standard use today is the inappropriate and over-use of prescription antibiotics. Although bacteria are the most common organisms to develop drug-resistance, there are numerous examples of demonstrated resistance in fungi, viruses, and parasites. The development of a resistant phenotype is a complex phenomenon that involves an interaction of the microorganism, the environment, and the patient, separately as well as in combination. Sitaram et al., Biochim. Biophys. Acta, 1999, 1462, 29–54. The microorganism in question may develop resistance while under antibiotic selection or it may be a characteristic of the microbe prior to exposure to a given agent. There are a number of mechanisms of resistance to antibiotics that have been described, including genes that encode antibiotic resistance enzymes that are harbored on extrachromosomal plasmids as well as DNA elements (e.g. transposable elements) that can reside either extra-chromosomally or within the host genome.
Due to the ability of microorganisms to acquire the ability to develop resistance to antibiotics there is a need to continually develop novel antibiotics. Traditional methods to develop novel antibiotics have included medicinal chemistry approaches to modify existing antibiotics (Kang et al., Bioorg. Med. Chem. Lett., 2000, 10, 95–99) as well as isolation of antibiotics from new organisms (Alderson et al., Res. Microbiol., 1993, 144, 665–72). Each of these methods, however, has limitations. The traditional medicinal chemistry approach entails modification of an existing molecule to impart a more effective activity. The chemist makes a “best guess” as to which parts of the molecule to alter, must then devise a synthetic strategy, synthesize the molecule, and then have it tested. This approach is laborious, requires large numbers of medicinal chemists and frequently results in a molecule that is lower in activity than the original antibiotic. The second approach, isolation of novel antimicrobial agents, requires screening large numbers of diverse organisms for novel antimicrobial activity. Then, the activity must be isolated from the microorganism. This is not a small task, and frequently takes many years of hard work to isolate the active molecule. Even after the molecule is identified, it may not be possible for medicinal chemists to effectively devise a synthetic strategy due to the complexity of the molecule. Furthermore, the synthetic strategy must allow for a cost-effective synthesis. Therefore, a method that would allow for creation of more effective antibiotics from existing molecules or allow rapid isolation of novel antimicrobial agents is needed to combat the ever-growing list of antibiotic resistant organisms. The present invention described herein is directed to the use of random genetic mutation of a cell to produce novel antibiotics by blocking the endogenous mismatch repair activity of a host cell. The cell can be a mammalian cell that produces an antimicrobial agent naturally, or a cell that is placed under selective pressure to obtain a novel antimicrobial molecule that attacks a specific microbe. Moreover, the invention describes methods for obtaining enhanced antimicrobial activity of a cell line that produces an antimicrobial activity due to recombinant expression or as part of the innate capacity of the cell to harbor such activity.
In addition, the generation of genetically altered host cells that are capable of secreting an antimicrobial activity, which can be protein or non-protein based, will be valuable reagents for manufacturing the entity for clinical studies. An embodiment of the invention described herein is directed to the creation of genetically altered host cells with novel and/or increased antimicrobial production that are generated by a method that interferes with the highly ubiquitous and phylogenetically conserved process of mismatch repair.
The present invention facilitates the generation of novel antimicrobial agents and the production of cell lines that express elevated levels of antimicrobial activity. Advantages of the present invention are further described in the examples and figures described herein.
SUMMARY OF THE INVENTION
One embodiment of the present invention provides a method for generating genetically altered mammalian cells and placing the cells under direct microbial selection as a means to isolate novel antimicrobial agents. Another embodiment provides a method for identifying novel microbe-specific toxic molecules by altering the ability of the cell to correct natural defects that occur in the DNA during the process of DNA replication. Interference with this process, called mismatch repair, leads to genetically dissimilar sibling cells. These genetically dissimilar cells contain mutations, ranging from one mutation/genome to two or more mutations/genome, offer a rich population of cells from which to select for specific output traits, such as the novel ability to resist microbial insult. The genetically altered cell generated by manipulation of the mismatch repair process is then incubated with a microbe that is normally toxic to cells. Most of the cells will rapidly lose viability and die; however, a subset of resistant cells will have the capacity to resist the microbial insult. These cells express a molecule, protein or non-protein in structure, that imbues an antimicrobial activity to the newly selected mammalian clones. These newly created cells can be expanded in vitro and the new molecule isolated and characterized by standard methods that are well described it the art. The novel molecule(s) are then tested for their ability to kill or inhibit the growth of the microbe by standard microbial assays that are well described in the art. Finally, the novel cell line generated serves as an additional resource for large-scale production of the novel antimicrobial agent for use in clinical studies. The processes described herein are applicable to any mammalian cell and any microbe for which an antibiotic agent is sought.
The invention provides methods for rendering mammalian cells hypermutable as a means to generate antimicrobial agents.
The invention also provides methods for generating genetically altered cell lines that secrete enhanced amounts of a known or novel antimicrobial polypeptide.
The invention also provides methods for generating genetically altered cell lines that secrete enhanced amounts of a known or novel antimicrobial non-polypeptide based molecule.
The invention also provides methods for generating genetically altered cell lines that do not secrete enhanced amounts of an antimicrobial peptide or non-peptide molecule but rather have a cell-surface active molecule that detoxifies the microbe under test.
The invention also provides methods for producing an enhanced rate of genetic hypermutation in a mammalian cell and use of this as the basis to select for microbial-resistant cell lines.
The invention also provides methods of mutating a known antimicrobial encoding gene of interest in a mammalian cell as a means to obtain a molecule with enhanced bactericidal activity.
The invention also provides methods for creating genetically altered antimicrobial molecules in vivo.
The invention also provides methods for creating novel antimicrobial molecules from pre-existing antimicrobial molecules by altering the innate enzymatic or binding ability of the molecules by altering the mismatch repair system within the host mammalian cell.
The invention also provides methods for creating a novel anti-microbial polypeptide or non-polypeptide based molecule that has the capacity to bind in an irreversible manner to a microbe and thereby block binding of the pathogenic microbe to a host target organism and result in loss of viability of the microbe.
The invention also provides methods for creating a novel antimicrobial polypeptide or non-polypeptide based small molecule that can block microbial cell growth and/or survival.
The invention also provides methods for creating a novel antimicrobial polypeptide or non-polypeptide based biochemical that are able to irreversibly bind to toxic chemicals produced by pathogenic microbes.
The invention also provides methods for creating genetically altered antimicrobial molecules, either peptide of non-peptide based, that have enhanced pharmacokinetic properties in host organisms.
The invention also provides methods for creating genetically altered cell lines that manufacture an antimicrobial molecules, either peptide of non-peptide based, for use in large-scale production of the antimicrobial agent for clinical studies.
These and other aspects of the invention are described in the embodiments below. In one embodiment of the invention described, a method for making a microbial-sensitive mammalian cell microbe resistant by rendering the cell line hypermutable is provided. A polynucleotide encoding a dominant negative allele of a mismatch repair gene is introduced into an mammalian cell. The cell becomes hypermutable as a result of the introduction of the gene.
In another embodiment of the invention, an isolated hypermutable cell is provided. The cell comprises a dominant negative allele of a mismatch repair gene. The cell exhibits an enhanced rate of hypermutation.
In another embodiment of the invention, an isolated hypermutable cell is provided. The cell comprises a dominant negative allele of a mismatch repair gene. The cell exhibits an enhanced rate of hypermutation. The populations of cells generated by introduction of the mismatch repair gene are grown in the presence of microbes that are toxic to the wild type non-mutant cells. Cells are selected that are resistant to the microbe and the novel molecule(s) isolated and characterized for antimicrobial activity by standard methods well described in the art.
In another embodiment of the invention, an isolated hypermutable cell is described to create a novel antimicrobial molecule from a pre-existing antimicrobial molecule by altering the innate enzymatic or binding ability of the molecule.
In another embodiment of the invention, a method of creating a novel antimicrobial polypeptide or non-polypeptide based molecule that has the capacity to bind in an irreversible manner to a microbe and thereby block binding of the pathogenic microbe to a host target organism and result in loss of viability of the microbe.
In another embodiment of the invention, a method of creating a novel antimicrobial polypeptide or non-polypeptide based small molecule that can block microbial cell growth and/or survival is described.
In another embodiment of the invention, a method of creating a novel antimicrobial polypeptide or non-polypeptide based biochemical that are able to irreversibly bind to toxic chemicals produced by pathogenic microbes is described.
In another embodiment of the invention, a method is provided for introducing a mutation into a known endogenous gene encoding for an antimicrobial polypeptide or a non-protein based antimicrobial molecule as a means to create a more efficacious antimicrobial. A polynucleotide encoding a dominant negative allele of a mismatch repair gene is introduced into a cell. The cell becomes hypermutable as a result of the introduction of the gene. The cell further comprises an antimicrobial gene(s) of interest. The cell is grown and tested to determine whether the gene encoding for an antimicrobial is altered and whether the novel molecule is more active by standard microbiology assays well known in the art.
In another embodiment of the invention, a gene or genes encoding for an antimicrobial molecule is introduced into a mammalian cell host that is mismatch repair defective. The cell is grown, and then clones are analyzed for enhanced antimicrobial characteristics.
In another embodiment of the invention, a method is provided for producing new phenotypes of a cell. A polynucleotide encoding a dominant negative allele of a mismatch repair gene is introduced into a cell. The cell becomes hypermutable as a result of the introduction of the gene. The cell is grown and tested for the expression of new phenotypes where the phenotype is enhanced secretion of a novel or known antimicrobial polypeptide.
In another embodiment of the invention, a method is provided for producing new phenotypes of a cell. A polynucleotide encoding a dominant negative allele of a mismatch repair gene is introduced into a cell. The cell becomes hypermutable as a result of the introduction of the gene. The cell is grown and tested for the expression of new phenotypes where the phenotype is enhanced secretion of a novel or known antimicrobial non-polypeptide based molecule.
In another embodiment of the invention, a method is provided for producing new phenotypes of a cell. A polynucleotide encoding a dominant negative allele of a mismatch repair gene is introduced into a cell. The cell becomes hypermutable as a result of the introduction of the gene. The cell is grown and tested for the expression of new phenotypes where the phenotype is enhanced antimicrobial activity of a novel or known antimicrobial polypeptide that is not secreted.
In another embodiment of the invention, a method is provided for producing new phenotypes of a cell. A polynucleotide encoding a dominant negative allele of a mismatch repair gene is introduced into a cell. The cell becomes hypermutable as a result of the introduction of the gene. The cell is grown and tested for the expression of new phenotypes where the phenotype is enhanced antimicrobial activity of a novel or known antimicrobial non-polypeptide based molecule that is not secreted.
In another embodiment of the invention, a method is provided for restoring genetic stability in a cell containing a polynucleotide encoding a dominant negative allele of a mismatch repair gene. The expression of the dominant negative mismatch repair gene is suppressed and the cell is restored to its former genetic stability.
In another embodiment of the invention, a method is provided for restoring genetic stability in a cell containing a polynucleotide encoding a dominant negative allele of a mismatch repair gene and a newly selected phenotype. The expression of the dominant negative mismatch repair gene is suppressed and the cell restores its genetic stability and the new phenotype is stable.
These and other embodiments of the invention provide the art with methods that generate enhanced mutability in cells and animals as well as providing cells and animals harboring potentially useful mutations and novel protein and non-protein based molecules.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a representative in situ β-galactosidase staining of TK-hPMS2-134 or TKvect cells to measure for cells containing genetically altered β-galactosidase genes; arrows indicate Blue (β-galactosidase positive) cells.
FIG. 2 is a schematic representation of sequence of alterations of the β-galactosidase gene produced by expression of TK-hPMS2-134 host cells in TK cells.
FIGS. 3A, 3B and 3C show a representative immunoprecipitation of in vitro translated hPMS2 and hMLH1 proteins.
FIG. 4 shows representative complementation of MMR activity in transduced SH cells.
FIG. 5 is a representative photograph of Syrian hamster TK-ts13 cells transfected with a eukaryotic expression vector that produces a novel anti-microbial polypeptide.
FIG. 6 is a representative graph showing TK-hPMS-134 transfected TK cells can suppress the growth of bacteria in vitro.



The presented invention is directed to, in part, methods for developing hypermutable mammalian cells by taking advantage of the conserved mismatch repair process of host cells. Mismatched repair process is described in several references. Baker et al., Cell, 1995, 82, 309 319; Bronner et al., Nature, 1994, 368, 258 261; de Wind et al., Cell, 1995, 82, 321 330; and Drummond et al., Science, 1995, 268, 1909 1912. Dominant negative alleles of such genes, when introduced into cells or transgenic animals, increase the rate of spontaneous mutations by reducing the effectiveness of DNA repair and thereby render the cells or animals hypermutable. Hypermutable cells or animals can then be utilized to develop new mutations in a gene of interest or in a gene whose function has not been previously described. Blocking mismatch repair in cells such as, for example, mammalian cells or mammalian cells transfected with genes encoding for specific antimicrobial peptides or non-peptide based antimicrobials, can enhance the rate of mutation within these cells leading to clones that have novel or enhanced antimicrobial activity or production and/or cells that contain genetically altered antimicrobials with enhanced biochemical activity against a range of opportunistic microbes.
The process of mismatch repair, also called mismatch proofreading, is carried out by protein complexes in cells ranging from bacteria to mammalian cells. Modrich, Science, 1994, 266, 1959 1960. A mismatch repair gene is a gene that encodes for one of the proteins of such a mismatch repair complex. Baker et. al., Cell, 1995, 82, 309 319; Bronner et al., Nature, 1994, 368, 258 261; de Wind et al., Cell, 1995, 82, 321 330; Drummond et al., Science, 1995, 268, 1909 1912; and Modrich, Science, 1994, 266, 1959 1960. Although not wanting to be bound by any particular theory of mechanism of action, a mismatch repair complex is believed to detect distortions of the DNA helix resulting from non-complementary pairing of nucleotide bases. The non-complementary base on the newer DNA strand is excised, and the excised base is replaced with the appropriate base that is complementary to the older DNA strand. In this way, cells eliminate many mutations, which occur as a result of mistakes in DNA replication.
Dominant negative alleles cause a mismatch repair defective phenotype even in the presence of a wild-type allele in the same cell. An example of a dominant negative allele of a mismatch repair gene is the human gene hPMS2-134, which carries a truncation mutation at codon 134. Nicolaides et al., Mol. Cell. Biol., 1998, 18, 1635–1641. The mutation causes the product of this gene to abnormally terminate at the position of the 134th amino acid, resulting in a shortened polypeptide containing the N-terminal 133 amino acids. Such a mutation causes an increase in the rate of mutations that accumulate in cells after DNA replication. Expression of a dominant negative allele of a mismatch repair gene results in impairment of mismatch repair activity, even in the presence of the wild-type allele. Any allele, which produces such effect, can be used in this invention.
Dominant negative alleles of a mismatch repair gene can be obtained from the ells of humans, animals, yeast, bacteria, or other organisms. Prolla et al., Science, 1994, 264, 1091 1093; Strand et al., Nature, 1993, 365, 274 276; and Su et al., J. Biol. Chem., 1988, 263, 6829 6835. Screening cells for defective mismatch repair activity can identify such alleles. Cells from animals or humans with cancer can be screened for defective mismatch repair. Cells from colon cancer patients may be particularly useful. Parsons et al., Cell, 1993, 75, 1227 1236; and Papadopoulos et al., Science, 1993, 263, 1625 1629. Genomic DNA, cDNA, or mRNA from any cell encoding a mismatch repair protein can be analyzed for variations from the wild type sequence. Perucho, Biol. Chem., 1996, 377, 675 684. Dominant negative alleles of a mismatch repair gene can also be created artificially, for example, by producing variants of the hPMS2-134 allele or other mismatch repair genes. Various techniques of site-directed mutagenesis can be used. The suitability of such alleles, whether natural or artificial, for use in generating hypermutable cells or animals can be evaluated by testing the mismatch repair activity caused by the allele in the presence of one or more wild-type alleles, to determine if it is a dominant negative allele.
A cell or an animal into which a dominant negative allele of a mismatch repair gene has been introduced will become hypermutable. This means that the spontaneous mutation rate of such cells or animals is elevated compared to cells or animals without such alleles. The degree of elevation of the spontaneous mutation rate can be at least 2-fold, 5-fold, 10-fold, 20-fold, 50-fold, 100-fold, 200-fold, 500-fold, or 1000-fold that of the normal cell or animal.
According to one aspect of the invention, a polynucleotide encoding a dominant negative form of a mismatch repair protein is introduced into a cell. The gene can be any dominant negative allele encoding a protein that is part of a mismatch repair complex, for example, PMS2, PMS1, MLH1, or MSH2. The dominant negative allele can be naturally occurring or made in the laboratory. The polynucleotide can be in the form of genomic DNA, cDNA, RNA, or a chemically synthesized polynucleotide.
The polynucleotide can be cloned into an expression vector containing a constitutively active promoter segment (such as but not limited to CMV, SV40, Elongation Factor or LTR sequences) or to inducible promoter sequences such as the steroid inducible pIND vector (InVitrogen), where the expression of the dominant negative mismatch repair gene can be regulated. The polynucleotide can be introduced into the cell by transfection.
Transfection is any process whereby a polynucleotide is introduced into a cell. The process of transfection can be carried out in a living animal, e.g., using a vector for gene therapy, or it can be carried out in vitro, e.g., using a suspension of one or more isolated cells in culture. The cell can be any type of eukaryotic cell, including, for example, cells isolated from humans or other primates, mammals or other vertebrates, invertebrates, and single celled organisms such as protozoa, yeast, or bacteria.
In general, transfection will be carried out using a suspension of cells, or a single cell, but other methods can also be applied as long as a sufficient fraction of the treated cells or tissue incorporates the polynucleotide so as to allow transfected cells to be grown and utilized. The protein product of the polynucleotide may be transiently or stably expressed in the cell. Techniques for transfection are well known and available techniques for introducing polynucleotides include but are not limited to electroporation, transduction, cell fusion, the use of calcium chloride, and packaging of the polynucleotide together with lipid for fusion with the cells of interest. Once a cell has been transfected with the mismatch repair gene, the cell can be grown and reproduced in culture. If the transfection is stable, such that the gene is expressed at a consistent level for many cell generations, then a cell line results.
An isolated cell is a cell obtained from a tissue of humans or animals by mechanically separating out individual cells and transferring them to a suitable cell culture medium, either with or without pretreatment of the tissue with enzymes, e.g., collagenase or trypsin. Such isolated cells are typically cultured in the absence of other types of cells. Cells selected for the introduction of a dominant negative allele of a mismatch repair gene may be derived from a eukaryotic organism in the form of a primary cell culture or an immortalized cell line, or may be derived from suspensions of single-celled organisms.
The invention described herein is useful for creating microbial-resistant mammalian cells that secrete new antimicrobial biochemical agents, either protein or non-protein in nature. Furthermore, the invention can be applied to cell lines that express known antimicrobial agents as a means to enhance the biochemical activity of the antimicrobial agent.
Once a transfected cell line has been produced, it can be used to generate new mutations in one or more gene(s) of interest or in genes that have not been previously described. A gene of interest can be any gene naturally possessed by the cell line or introduced into the cell line by standard methods known in the art. An advantage of using transfected cells or to induce mutation(s) in a gene or genes of interest that encode antimicrobial activity is that the cell need not be exposed to mutagenic chemicals or radiation, which may have secondary harmful effects, both on the object of the exposure and on the workers. Furthermore, it has been demonstrated that chemical and physical mutagens are base pair specific in the way they alter the structure of DNA; the invention described herein results in mutations that are not dependent upon the specific nucleotide or a specific string of nucleotides and is a truly random genetic approach. Therefore, use of the present invention to obtain mutations in novel or known antimicrobial genes will be much more efficient and have a higher likelihood of success in contrast to conventional mutagenesis with chemical or irradiation. Once a new antimicrobial trait is identified in a sibling cell, the dominant negative allele can be removed from the cell by a variety of standard methods known in the art. For example, the gene can be directly knocked out the allele by technologies used by those skilled in the art or use of a inducible expression system; the dominant-negative allele is driven by a standard promoter that is regulated by inclusion of an inducer, withdrawal of the inducer results in attenuation of the expression of the dominant negative mismatch repair mutant and a normal DNA repair process will ensue.
New antimicrobial agents are selected from cells that have been exposed to the dominant negative mismatch repair process followed by incubating the mutant cells in the presence of the microbe for which an novel antimicrobial agent is sought. The novel antimicrobial agent is purified by standard methods known to those skilled in the art and characterized. The antimicrobial agents are re-screened to determine the specific activity of the novel antimicrobial as well as tested against a broad range of microbes to determine spectrum of activity. The gene(s) that encode the novel antimicrobial are isolated by standard well known methods to those in the art. The mutations can be detected by analyzing for alterations in the genotype of the cells by examining the sequence of genomic DNA, cDNA, messenger RNA, or amino acids associated with the gene of interest. A mutant polypeptide can be detected by identifying alterations in electrophoretic mobility, spectroscopic properties, or other physical or structural characteristics of a protein encoded by a mutant gene when the cell that has undergone alteration encodes a known antimicrobial that is altered by the means described in the current invention to obtain a more efficacious antimicrobial.
Examples of Mismatch Repair Proteins and Nucleic Acid Sequences Include the Following:









PMS2 (mouse)
(SEQ ID NO:7)



MEQTEGVSTE CAKAIKPIDG KSVHQICSGQ VILSLSTAVK ELIENSVDAG ATTIDLRLKD
 60


 


YGVDLIEVSD NGCGVEEENF EGLALKHHTS KIQEFADLTQ VETFGFRGEA LSSLCALSDV
 120


 


TISTCHGSAS VGTRLVFDHN GKITQKTPYP RPKGTTVSVQ HLFYTLPVRY KEFQRNIKKE
 180


 


YSKMVQVLQA YCIISAGVRV SCTNQLGQGK RHAVVCTSGT SGMKENIGSV FGQKQLQSLI
 240


 


PFVQLPPSDA VCEEYGLSTS GRHKTFSTFR ASFHSARTAP GGVQQTGSFS SSIRGPVTQQ
 300


 


RSLSLSMRFY HMYNRHQYPF VVLNVSVDSE CVDINVTPDK RQILLQEEKL LLAVLKTSLI
 360


 


GMFDSDANKL NVNQQPLLDV EGNLVKLHTA ELEKPVPGKQ DNSPSLKSTA DEKRVASISR
 420


 


LREAFSLHPT KEIKSRGPET AELTRSFPSE KRGVLSSYPS DVISYRGLRG SQDKLVSPTD
 480


 


SPGDCMDREK IEKDSGLSST SAGSEEEFST PEVASSFSSD YNVSSLEDRP SQETINCGDL
 540


 


DCRPPGTGQS LKPEDHGYQC KALPLARLSP TNAKRFKTEE RPSNVNISQR LPGPQSTSAA
 600


 


EVDVAIKMNK RIVLLEFSLS SLAKRMKQLQ HLKAQNKHEL SYRKFRAKIC PGENQAAEDE
 660


 


LRKEISKSMF AEMEILGQFN LGFIVTKLKE DLFLVDQHAA DEKYNFEMLQ QHTVLQAQRL
 720


 


ITPQTLNLTA VNEAVLIENL EIFRKNGFDF VIDEDAPVTE RAKLISLPTS KNWTFGPQDI
 780


 


DELIFMLSDS PGVMCRPSRV RQMFASRACR KSVMIGTALN ASEMKKLITH MGEMDHPWNC
 840


 


PHGRPTMRHV ANLDVISQN
 859


 


PMS2 (mouse cDNA)
(SEQ ID NO:8)


gaattccggt gaaggtcctg aagaatttcc agattcctga gtatcattgg aggagacaga
 60


 


taacctgtcg tcaggtaacg atggtgtata tgcaacagaa atgggtgttc ctggagacgc
 120


 


gtcttttccc gagagcggca ccgcaactct cccgcggtga ctgtgactgg aggagtcctg
 180


 


catccatgga gcaaaccgaa ggcgtgagta cagaatgtgc taaggccatc aagcctattg
 240


 


atgggaagtc agtccatcaa atttgttctg ggcaggtgat actcagttta agcaccgctg
 300


 


tgaaggagtt gatagaaaat agtgtagatg ctggtgctac tactattgat ctaaggctta
 360


 


aagactatgg ggtggacctc attgaagttt cagacaatgg atgtggggta gaagaagaaa
 420


 


actttgaagg tctagctctg aaacatcaca catctaagat tcaagagttt gccgacctca
 480


 


cgcaggttga aactttcggc tttcgggggg aagctctgag ctctctgtgt gcactaagtg
 540


 


atgtcactat atctacctgc cacgggtctg caagcgttgg gactcgactg gtgtttgacc
 600


 


ataatgggaa aatcacccag aaaactccct acccccgacc taaaggaacc acagtcagtg
 660


 


tgcagcactt attttataca ctacccgtgc gttacaaaga gtttcagagg aacattaaaa
 720


 


aggagtattc caaaatggtg caggtcttac aggcgtactg tatcatctca gcaggcgtcc
 780


 


gtgtaagctg cactaatcag ctcggacagg ggaagcggca cgctgtggtg tgcacaagcg
 840


 


gcacgtctgg catgaaggaa aatatcgggt ctgtgtttgg ccagaagcag ttgcaaagcc
 900


 


tcattccttt tgttcagctg ccccctagtg acgctgtgtg tgaagagtac ggcctgagca
 960


 


cttcaggacg ccacaaaacc ttttctacgt ttcgggcttc atttcacagt gcacgcacgg
1020


 


cgccgggagg agtgcaacag acaggcagtt tttcttcatc aatcagaggc cctgtgaccc
1080


 


agcaaaggtc tctaagcttg tcaatgaggt tttatcacat gtataaccgg catcagtacc
1140


 


catttgtcgt ccttaacgtt tccgttgact cagaatgtgt ggatattaat gtaactccag
1200


 


ataaaaggca aattctacta caagaagaga agctattgct ggccgtttta aagacctcct
1260


 


tgataggaat gtttgacagt gatgcaaaca agcttaatgt caaccagcag ccactgctag
1320


 


atgttgaagg taacttagta aagctgcata ctgcagaact agaaaagcct gtgccaggaa
1380


 


agcaagataa ctctccttca ctgaagagca cagcagacga gaaaagggta gcatccatct
1440


 


ccaggctgag agaggccttt tctcttcatc ctactaaaga gatcaagtct aggggtccag
1500


 


agactgctga actgacacgg agttttccaa gtgagaaaag gggcgtgtta tcctcttatc
1560


 


cttcagacgt catctcttac agaggcctcc gtggctcgca ggacaaattg gtgagtccca
1620


 


cggacagccc tggtgactgt atggacagag agaaaataga aaaagactca gggctcagca
1680


 


gcacctcagc tggctctgag gaagagttca gcaccccaga agtggccagt agctttagca
1740


 


gtgactataa cgtgagctcc ctagaagaca gaccttctca ggaaaccata aactgtggtg
1800


 


acctggactg ccgtcctcca ggtacaggac agtccttgaa gccagaagac catggatatc
1860


 


aatgcaaagc tctacctcta gctcgtctgt cacccacaaa tgccaagcgc ttcaagacag
1920


 


aggaaagacc ctcaaatgtc aacatttctc aaagattgcc tggtcctcag agcacctcag
1980


 


cagctgaggt cgatgtagcc ataaaaatga ataagagaat cgtgctcctc gagttctctc
2040


 


tgagttctct agctaagcga atgaagcagt tacagcacct aaaggcgcag aacaaacatg
2100


 


aactgagtta cagaaaattt agggccaaga tttgccctgg agaaaaccaa gcagcagaag
2160


 


atgaactcag aaaagagatt agtaaatcga tgtttgcaga gatggagatc ttgggtcagt
2220


 


ttaacctggg atttatagta accaaactga aagaggacct cttcctggtg gaccagcatg
2280


 


ctgcggatga gaagtacaac tttgagatgc tgcagcagca cacggtgctc caggcgcaga
2340


 


ggctcatcac accccagact ctgaacttaa ctgctgtcaa tgaagctgta ctgatagaaa
2400


 


atctggaaat attcagaaag aatggctttg actttgtcat tgatgaggat gctccagtca
2460


 


ctgaaagggc taaattgatt tccttaccaa ctagtaaaaa ctggaccttt ggaccccaag
2520


 


atatagatga actgatcttt atgttaagtg acagccctgg ggtcatgtgc cggccctcac
2580


 


gagtcagaca gatgtttgct tccagagcct gtcggaagtc agtgatgatt ggaacggcgc
2640


 


tcaatgcgag cgagatgaag aagctcatca cccacatggg tgagatggac cacccctgga
2700


 


actgccccca cggcaggcca accatgaggc acgttgccaa tctggatgtc atctctcaga
2760


 


actgacacac cccttgtagc atagagttta ttacagattg ttcggtttgc aaagagaagg
2820


 


ttttaagtaa tctgattatc gttgtacaaa aattagcatg ctgctttaat gtactggatc
2880


 


catttaaaag cagtgttaag gcaggcatga tggagtgttc ctctagctca gctacttggg
2940


 


tgatccggtg ggagctcatg tgagcccagg actttgagac cactccgagc cacattcatg
3000


 


agactcaatt caaggacaaa aaaaaaaaga tatttttgaa gccttttaaa aaaaaa
3056


 


PMS2 (human)
(SEQ ID NO:9)


MERAESSSTE PAKAIKPIDR KSVHQICSGQ VVLSLSTAVK ELVENSLDAG ATNIDLKLKD
 60


 


YGVDLIEVSD NGCGVEEENF EGLTLKHHTS KIQEFADLTQ VETFGFRGEA LSSLCALSDV
 120


 


TISTCHASAK VGTRLMFDHN GKIIQKTPYP RPRGTTVSVQ QLFSTLPVRH KEFQRNIKKE
 180


 


YAKMVQVLHA YCIISAGIRV SCTNQLGQGK RQPVVCTGGS PSIKENIGSV FGQKQLQSLI
 240


 


PFVQLPPSDS VCEEYGLSCS DALHNLFYIS GFISQCTHGV GRSSTDRQFF FINRRPCDPA
 300


 


KVCRLVNEVY HMYNRHQYPF VVLNISVDSE CVDINVTPDK RQILLQEEKL LLAVLKTSLI
 360


 


GMFDSDVNKL NVSQQPLLDV EGNLIKMHAA DLEKPMVEKQ DQSPSLRTGE EKKDVSISRL
 420


 


REAFSLRHTT ENKPHSPKTP EPRRSPLGQK RGMLSSSTSG AISDKGVLRP QKEAVSSSHG
 480


 


PSDPTDRAEV EKDSGHGSTS VDSEGFSIPD TGSHCSSEYA ASSPGDRGSQ EHVDSQEKAP
 540


 


ETDDSFSDVD CHSNQEDTGC KFRVLPQPTN LATPNTKRFK KEEILSSSDI CQKLVNTQDM
 600


 


SASQVDVAVK INKKVVPLDF SMSSLAKRIK QLHHFAQQSE GEQNYRKFRA KICPGENQAA
 660


 


EDELRKEISK TMFAEMEIIG QFNLGFIITK LNEDIFIVDQ HATDEKYNFE MLQQHTVLQG
 720


 


QRLIAPQTLN LTAVNEAVLI ENLEIFRKNG FDFVIDENAP VTERAKLISL PTSKNWTFGP
 780


 


QDVDELIFML SDSPGVMCRP SRVKQMFASR ACRKSVMIGT ALNTSEMKKL ITHMGEMDHP
 840


 


WNCPHGRPTM RHIANLGVIS QN
 862


 


PMS2 (human cDNA)
(SEQ ID NO:10)


cgaggcggat cgggtgttgc atccatggag cgagctgaga gctcgagtac agaacctgct
 60


 


aaggccatca aacctattga tcggaagtca gtccatcaga tttgctctgg gcaggtggta
 120


 


ctgagtctaa gcactgcggt aaaggagtta gtagaaaaca gtctggatgc tggtgccact
 180


 


aatattgatc taaagcttaa ggactatgga gtggatctta ttgaagtttc agacaatgga
 240


 


tgtggggtag aagaagaaaa cttcgaaggc ttaactctga aacatcacac atctaagatt
 300


 


caagagtttg ccgacctaac tcaggttgaa acttttggct ttcgggggga agctctgagc
 360


 


tcactttgtg cactgagcga tgtcaccatt tctacctgcc acgcatcggc gaaggttgga
 420


 


actcgactga tgtttgatca caatgggaaa attatccaga aaacccccta cccccgcccc
 480


 


agagggacca cagtcagcgt gcagcagtta ttttccacac tacctgtgcg ccataaggaa
 540


 


tttcaaagga atattaagaa ggagtatgcc aaaatggtcc aggtcttaca tgcatactgt
 600


 


atcatttcag caggcatccg tgtaagttgc accaatcagc ttggacaagg aaaacgacag
 660


 


cctgtggtat gcacaggtgg aagccccagc ataaaggaaa atatcggctc tgtgtttggg
 720


 


cagaagcagt tgcaaagcct cattcctttt gttcagctgc cccctagtga ctccgtgtgt
 780


 


gaagagtacg gtttgagctg ttcggatgct ctgcataatc ttttttacat ctcaggtttc
 840


 


atttcacaat gcacgcatgg agttggaagg agttcaacag acagacagtt tttctttatc
 900


 


aaccggcggc cttgtgaccc agcaaaggtc tgcagactcg tgaatgaggt ctaccacatg
 960


 


tataatcgac accagtatcc atttgttgtt cttaacattt ctgttgattc agaatgcgtt
1020


 


gatatcaatg ttactccaga taaaaggcaa attttgctac aagaggaaaa gcttttgttg
1080


 


gcagttttaa agacctcttt gataggaatg tttgatagtg atgtcaacaa gctaaatgtc
1140


 


agtcagcagc cactgctgga tgttgaaggt aacttaataa aaatgcatgc agcggatttg
1200


 


gaaaagccca tggtagaaaa gcaggatcaa tccccttcat taaggactgg agaagaaaaa
1260


 


aaagacgtgt ccatttccag actgcgagag gccttttctc ttcgtcacac aacagagaac
1320


 


aagcctcaca gcccaaagac tccagaacca agaaggagcc ctctaggaca gaaaaggggt
1380


 


atgctgtctt ctagcacttc aggtgccatc tctgacaaag gcgtcctgag acctcagaaa
1440


 


gaggcagtga gttccagtca cggacccagc gaccctacgg acagagcgga ggtggagaag
1500


 


gactcggggc acggcagcac ttccgtggat tctgaggggt tcagcatccc agacacgggc
1560


 


agtcactgca gcagcgagta tgcggccagc tccccagggg acaggggctc gcaggaacat
1620


 


gtggactctc aggagaaagc gcctgaaact gacgactctt tttcagatgt ggactgccat
1680


 


tcaaaccagg aagataccgg atgtaaattt cgagttttgc ctcagccaac taatctcgca
1740


 


accccaaaca caaagcgttt taaaaaagaa gaaattcttt ccagttctga catttgtcaa
1800


 


aagttagtaa atactcagga catgtcagcc tctcaggttg atgtagctgt gaaaattaat
1860


 


aagaaagttg tgcccctgga cttttctatg agttctttag ctaaacgaat aaagcagtta
1920


 


catcatgaag cacagcaaag tgaaggggaa cagaattaca ggaagtttag ggcaaagatt
1980


 


tgtcctggag aaaatcaagc agccgaagat gaactaagaa aagagataag taaaacgatg
2040


 


tttgcagaaa tggaaatcat tggtcagttt aacctgggat ttataataac caaactgaat
2100


 


gaggatatct tcatagtgga ccagcatgcc acggacgaga agtataactt cgagatgctg
2160


 


cagcagcaca ccgtgctcca ggggcagagg ctcatagcac ctcagactct caacttaact
2220


 


gctgttaatg aagctgttct gatagaaaat ctggaaatat ttagaaagaa tggctttgat
2280


 


tttgttatcg atgaaaatgc tccagtcact gaaagggcta aactgatttc cttgccaact
2340


 


agtaaaaact ggaccttcgg accccaggac gtcgatgaac tgatcttcat gctgagcgac
2400


 


agccctgggg tcatgtgccg gccttcccga gtcaagcaga tgtttgcctc cagagcctgc
2460


 


cggaagtcgg tgatgattgg gactgctctt aacacaagcg agatgaagaa actgatcacc
2520


 


cacatggggg agatggacca cccctggaac tgtccccatg gaaggccaac catgagacac
2580


 


atcgccaacc tgggtgtcat ttctcagaac tgaccgtagt cactgtatgg aataattggt
2640


 


tttatcgcag atttttatgt tttgaaagac agagtcttca ctaacctttt ttgttttaaa
2700


 


atgaaacctg ctacttaaaa aaaatacaca tcacacccat ttaaaagtga tcttgagaac
2760


 


cttttcaaac c
2771


 


PMS1 (human)
(SEQ ID NO:11)


MKQLPAATVR LLSSSQIITS VVSVVKELIE NSLDAGATSV DVKLENYGFD KIEVRDNGEG
 60


 


IKAVDAPVMA MKYYTSKINS HEDLENLTTY GFRGEALGSI CCIAEVLITT RTAADNFSTQ
 120


 


YVLDGSGHIL SQKPSHLGQG TTVTALRLFK NLPVRKQFYS TAKKCKDEIK KIQDLLMSFG
 180


 


ILKPDLRIVF VHNKAVIWQK SRVSDHKMAL MSVLGTAVMN NNESFQYHSE ESQIYLSGFL
 240


 


PKCDADHSFT SLSTPERSFI FINSRPVHQK DILKLIRHHY NLKCLKESTR LYPVFFLKID
 300


 


VPTADVDVNL TPDKSQVLLQ NKESVLIALE NLMTTCYGPL PSTNSYENNK TDVSAADIVL
 360


 


SKTAETDVLF NKVESSGKNY SNVDTSVIPF QNDMHNDESG KNTDDCLNHQ ISIGDFGYGH
 420


 


CSSEISNIDK NTKNAFQDIS MSNVSWENSQ TEYSKTCFIS SVKHTQSENG NKDHIDESGE
 480


 


NEEEAGLENS SEISADEWSR GNILKNSVGE NIEPVKILVP EKSLPCKVSN NNYPIPEQMN
 540


 


LNEDSCNKKS NVIDNKSGKV TAYDLLSNRV IKKPMSASAL FVQDHRPQFL IENPKTSLED
 600


 


ATLQIEELWK TLSEEEKLKY EEKATKDLER YNSQMKRAIE QESQMSLKDG RKKIKPTSAW
 660


 


NLAQKHKLKT SLSNQPKLDE LLQSQIEKRR SQNIKMVQIP FSMKNLKINF KKQNKVDLEE
 720


 


KDEPCLIHNL RFPDAWLMTS KTEVMLLNPY RVEEALLFKR LLENHKLPAE PLEKPIMLTE
 780


 


SLFNGSHYLD VLYKMTADDQ RYSGSTYLSD PRLTANGFKI KLIPGVSITE NYLEIEGMAN
 840


 


CLPFYGVADL KEILNAILNR NAKEVYECRP RKVISYLEGE AVRLSRQLPM YLSKEDIQDI
 900


 


IYRMKHQFGN EIKECVHGRP FFHHLTYLPE TT
 932


 


PMS1 (human)
(SEQ ID NO:12)


ggcacgagtg gctgcttgcg gctagtggat ggtaattgcc tgcctcgcgc tagcagcaag
 60


 


ctgctctgtt aaaagcgaaa atgaaacaat tgcctgcggc aacagttcga ctcctttcaa
 120


 


gttctcagat catcacttcg gtggtcagtg ttgtaaaaga gcttattgaa aactccttgg
 180


 


atgctggtgc cacaagcgta gatgttaaac tggagaacta tggatttgat aaaattgagg
 240


 


tgcgagataa cggggagggt atcaaggctg ttgatgcacc tgtaatggca atgaagtact
 300


 


acacctcaaa aataaatagt catgaagatc ttgaaaattt gacaacttac ggttttcgtg
 360


 


gagaagcctt ggggtcaatt tgttgtatag ctgaggtttt aattacaaca agaacggctg
 420


 


ctgataattt tagcacccag tatgttttag atggcagtgg ccacatactt tctcagaaac
 480


 


cttcacatct tggtcaaggt acaactgtaa ctgctttaag attatttaag aatctacctg
 540


 


taagaaagca gttttactca actgcaaaaa aatgtaaaga tgaaataaaa aagatccaag
 600


 


atctcctcat gagctttggt atccttaaac ctgacttaag gattgtcttt gtacataaca
 660


 


aggcagttat ttggcagaaa agcagagtat cagatcacaa gatggctctc atgtcagttc
 720


 


tggggactgc tgttatgaac aatatggaat cctttcagta ccactctgaa gaatctcaga
 780


 


tttatctcag tggatttctt ccaaagtgtg atgcagacca ctctttcact agtctttcaa
 840


 


caccagaaag aagtttcatc ttcataaaca gtcgaccagt acatcaaaaa gatatcttaa
 900


 


agttaatccg acatcattac aatctgaaat gcctaaagga atctactcgt ttgtatcctg
 960


 


ttttctttct gaaaatcgat gttcctacag ctgatgttga tgtaaattta acaccagata
1020


 


aaagccaagt attattacaa aataaggaat ctgttttaat tgctcttgaa aatctgatga
1080


 


cgacttgtta tggaccatta cctagtacaa attcttatga aaataataaa acagatgttt
1140


 


ccgcagctga catcgttctt agtaaaacag cagaaacaga tgtgcttttt aataaagtgg
1200


 


aatcatctgg aaagaattat tcaaatgttg atacttcagt cattccattc caaaatgata
1260


 


tgcataatga tgaatctgga aaaaacactg atgattgttt aaatcaccag ataagtattg
1320


 


gtgactttgg ttatggtcat tgtagtagtg aaatttctaa cattgataaa aacactaaga
1380


 


atgcatttca ggacatttca atgagtaatg tatcatggga gaactctcag acggaatata
1440


 


gtaaaacttg ttttataagt tccgttaagc acacccagtc agaaaatggc aataaagacc
1500


 


atatagatga gagtggggaa aatgaggaag aagcaggtct tgaaaactct tcggaaattt
1560


 


ctgcagatga gtggagcagg ggaaatatac ttaaaaattc agtgggagag aatattgaac
1620


 


ctgtgaaaat tttagtgcct gaaaaaagtt taccatgtaa agtaagtaat aataattatc
1680


 


caatccctga acaaatgaat cttaatgaag attcatgtaa caaaaaatca aatgtaatag
1740


 


ataataaatc tggaaaagtt acagcttatg atttacttag caatcgagta atcaagaaac
1800


 


ccatgtcagc aagtgctctt tttgttcaag atcatcgtcc tcagtttctc atagaaaatc
1860


 


ctaagactag tttagaggat gcaacactac aaattgaaga actgtggaag acattgagtg
1920


 


aagaggaaaa actgaaatat gaagagaagg ctactaaaga cttggaacga tacaatagtc
1980


 


aaatgaagag agccattgaa caggagtcac aaatgtcact aaaagatggc agaaaaaaga
2040


 


taaaacccac cagcgcatgg aatttggccc agaagcacaa gttaaaaacc tcattatcta
2100


 


atcaaccaaa acttgatgaa ctccttcagt cccaaattga aaaaagaagg agtcaaaata
2160


 


ttaaaatggt acagatcccc ttttctatga aaaacttaaa aataaatttt aagaaacaaa
2220


 


acaaagttga cttagaagag aaggatgaac cttgcttgat ccacaatctc aggtttcctg
2280


 


atgcatggct aatgacatcc aaaacagagg taatgttatt aaatccatat agagtagaag
2340


 


aagccctgct atttaaaaga cttcttgaga atcataaact tcctgcagag ccactggaaa
2400


 


agccaattat gttaacagag agtcttttta atggatctca ttatttagac gttttatata
2460


 


aaatgacagc agatgaccaa agatacagtg gatcaactta cctgtctgat cctcgtctta
2520


 


cagcgaatgg tttcaagata aaattgatac caggagtttc aattactgaa aattacttgg
2580


 


aaatagaagg aatggctaat tgtctcccat tctatggagt agcagattta aaagaaattc
2640


 


ttaatgctat attaaacaga aatgcaaagg aagtttatga atgtagacct cgcaaagtga
2700


 


taagttattt agagggagaa gcagtgcgtc tatccagaca attacccatg tacttatcaa
2760


 


aagaggacat ccaagacatt atctacagaa tgaagcacca gtttggaaat gaaattaaag
2820


 


agtgtgttca tggtcgccca ttttttcatc atttaaccta tcttccagaa actacatgat
2880


 


taaatatgtt taagaagatt agttaccatt gaaattggtt ctgtcataaa acagcatgag
2940


 


tctggtttta aattatcttt gtattatgtg tcacatggtt attttttaaa tgaggattca
3000


 


ctgacttgtt tttatattga aaaaagttcc acgtattgta gaaaacgtaa ataaactaat
3060


 


aac
3063


 


MSH2 (human)
(SEQ ID NO:13)


MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT
 60


 


QGVIKYMGPA GAKNLQSVVL SKMNFESFVK DLLLVRQYRV EVYKNRAGNK ASKENDWYLA
 120


 


YKASPGNLSQ FEDILFGNND MSASIGVVGV KMSAVDGQRQ VGVGYVDSIQ RKLGLCEFPD
 180


 


NDQFSNLEAL LIQIGPKECV LPGGETAGDM GKLRQIIQRG GILITERKKA DFSTKDIYQD
 240


 


LNRLLKGKKG EQMNSAVLPE MENQVAVSSL SAVIKFLELL SDDSNFGQFE LTTFDFSQYM
 300


 


KLDIAAVRAL NLFQGSVEDT TGSQSLAALL NKCKTPQGQR LVNQWIKQPL MDKNRIEERL
 360


 


NLVEAFVEDA ELRQTLQEDL LRRFPDLNRL AKKFQRQAAN LQDCYRLYQG INQLPNVIQA
 420


 


LEKHEGKHQK LLLAVFVTPL TDLRSDFSKF QEMIETTLDM DQVENHEFLV KPSFDPNLSE
 480


 


LREIMNDLEK KMQSTLISAA RDLGLDPGKQ IKLDSSAQFG YYFRVTCKEE KVLRNNKNFS
 540


 


TVDIQKNGVK FTNSKLTSLN EEYTKNKTEY EEAQDAIVKE IVNISSGYVE PMQTLNDVLA
 600


 


QLDAVVSFAH VSNGAPVPYV RPAILEKGQG RIILKASRHA CVEVQDEIAF IPNDVYFEKD
 660


 


KQMFHIITGP NMGGKSTYIR QTGVIVLMAQ IGCFVPCESA EVSIVDCILA RVGAGDSQLK
 720


 


GVSTFMAEML ETASILRSAT KDSLIIIDEL GRGTSTYDGF GLAWAISEYI ATKIGAFCMF
 780


 


ATHFHELTAL ANQIPTVNNL HVTALTTEET LTMLYQVKKG VCDQSFGIHV AELANFPKHV
 840


 


IECAKQKALE LEEFQYIGES QGYDIMEPAA KKCYLEREQG EKIIQEFLSK VKQMPFTEMS
 900


 


EENITIKLKQ LKAEVIAKNN SFVNEIISRI KVTT
 934


 


MSH2 (human cDNA)
(SEQ ID NO:14)


ggcgggaaac agcttagtgg gtgtggggtc gcgcattttc ttcaaccagg aggtgaggag
 60


 


gtttcgacat ggcggtgcag ccgaaggaga cgctgcagtt ggagagcgcg gccgaggtcg
 120


 


gcttcgtgcg cttctttcag ggcatgccgg agaagccgac caccacagtg cgcctcttcg
 180


 


accggggcga cttctatacg gcgcacggcg aggacgcgct gctggccgcc cgggaggtgt
 240


 


tcaagaccca gggggtgatc aagtacatgg ggccggcagg agcaaagaat ctgcagagtg
 300


 


ttgtgcttag taaaatgaat tttgaatctt ttgtaaaaga tcttcttctg gttcgccagt
 360


 


atagagttga agtttataag aatagagctg gaaataaggc atccaaggag aatgattggt
 420


 


atttggcata taaggcttct cctggcaatc tctctcagtt tgaagacatt ctctttggta
 480


 


acaatgatat gtcagcttcc attggtgttg tgggtgttaa aatgtccgca gttgatggcc
 540


 


agagacaggt tggagttggg tatgtggatt ccatacagag gaaactagga ctgtgtgaat
 600


 


tccctgataa tgatcagttc tccaatcttg aggctctcct catccagatt ggaccaaagg
 660


 


aatgtgtttt acccggagga gagactgctg gagacatggg gaaactgaga cagataattc
 720


 


aaagaggagg aattctgatc acagaaagaa aaaaagctga cttttccaca aaagacattt
 780


 


atcaggacct caaccggttg ttgaaaggca aaaagggaga gcagatgaat agtgctgtat
 840


 


tgccagaaat ggagaatcag gttgcagttt catcactgtc tgcggtaatc aagtttttag
 900


 


aactcttatc agatgattcc aactttggac agtttgaact gactactttt gacttcagcc
 960


 


agtatatgaa attggatatt gcagcagtca gagcccttaa cctttttcag ggttctgttg
1020


 


aagataccac tggctctcag tctctggctg ccttgctgaa taagtgtaaa acccctcaag
1080


 


gacaaagact tgttaaccag tggattaagc agcctctcat ggataagaac agaatagagg
1140


 


agagattgaa tttagtggaa gcttttgtag aagatgcaga attgaggcag actttacaag
1200


 


aagatttact tcgtcgattc ccagatctta accgacttgc caagaagttt caaagacaag
1260


 


cagcaaactt acaagattgt taccgactct atcagggtat aaatcaacta cctaatgtta
1320


 


tacaggctct ggaaaaacat gaaggaaaac accagaaatt attgttggca gtttttgtga
1380


 


ctcctcttac tgatcttcgt tctgacttct ccaagtttca ggaaatgata gaaacaactt
1440


 


tagatatgga tcaggtggaa aaccatgaat tccttgtaaa accttcattt gatcctaatc
1500


 


tcagtgaatt aagagaaata atgaatgact tggaaaagaa gatgcagtca acattaataa
1560


 


gtgcagccag agatcttggc ttggaccctg gcaaacagat taaactggat tccagtgcac
1620


 


agtttggata ttactttcgt gtaacctgta aggaagaaaa agtccttcgt aacaataaaa
1680


 


actttagtac tgtagatatc cagaagaatg gtgttaaatt taccaacagc aaattgactt
1740


 


ctttaaatga agagtatacc aaaaataaaa cagaatatga agaagcccag gatgccattg
1800


 


ttaaagaaat tgtcaatatt tcttcaggct atgtagaacc aatgcagaca ctcaatgatg
1860


 


tgttagctca gctagatgct gttgtcagct ttgctcacgt gtcaaatgga gcacctgttc
1920


 


catatgtacg accagccatt ttggagaaag gacaaggaag aattatatta aaagcatcca
1980


 


ggcatgcttg tgttgaagtt caagatgaaa ttgcatttat tcctaatgac gtatactttg
2040


 


aaaaagataa acagatgttc cacatcatta ctggccccaa tatgggaggt aaatcaacat
2100


 


atattcgaca aactggggtg atagtactca tggcccaaat tgggtgtttt gtgccatgtg
2160


 


agtcagcaga agtgtccatt gtggactgca tcttagcccg agtaggggct ggtgacagtc
2220


 


aattgaaagg agtctccacg ttcatggctg aaatgttgga aactgcttct atcctcaggt
2280


 


ctgcaaccaa agattcatta ataatcatag atgaattggg aagaggaact tctacctacg
2340


 


atggatttgg gttagcatgg gctatatcag aatacattgc aacaaagatt ggtgcttttt
2400


 


gcatgtttgc aacccatttt catgaactta ctgccttggc caatcagata ccaactgtta
2460


 


ataatctaca tgtcacagca ctcaccactg aagagacctt aactatgctt tatcaggtga
2520


 


agaaaggtgt ctgtgatcaa agttttggga ttcatgttgc agagcttgct aatttcccta
2580


 


agcatgtaat agagtgtgct aaacagaaag ccctggaact tgaggagttt cagtatattg
2640


 


gagaatcgca aggatatgat atcatggaac cagcagcaaa gaagtgctat ctggaaagag
2700


 


agcaaggtga aaaaattatt caggagttcc tgtccaaggt gaaacaaatg ccctttactg
2760


 


aaatgtcaga agaaaacatc acaataaagt taaaacagct aaaagctgaa gtaatagcaa
2820


 


agaataatag ctttgtaaat gaaatcattt cacgaataaa agttactacg tgaaaaatcc
2880


 


cagtaatgga atgaaggtaa tattgataag ctattgtctg taatagtttt atattgtttt
2940


 


atattaaccc tttttccata gtgttaactg tcagtgccca tgggctatca acttaataag
3000


 


atatttagta atattttact ttgaggacat tttcaaagat ttttattttg aaaaatgaga
3060


 


gctgtaactg aggactgttt gcaattgaca taggcaataa taagtgatgt gctgaatttt
3120


 


ataaataaaa tcatgtagtt tgtgg
3145


 


MLH1 (human)
(SEQ ID NO:15)


MSFVAGVIRR LDETVVNRIA AGEVIQRPAN AIKEMIENCL DAKSTSIQVI VKEGGLKLIQ
 60


 


IQDNGTGIRK EDLDIVCERF TTSKLQSFED LASISTYGFR GEALASISHV AHVTITTKTA
 120


 


DGKCAYRASY SDGKLKAPPK PCAGNQGTQI TVEDLFYNIA TRRKALKNPS EEYGKILEVV
 180


 


GRYSVHNAGI SFSVKKQGET VADVRTLPNA STVDNIRSIF GNAVSRELIE IGCEDKTLAF
 240


 


KMNGYISNAN YSVKKCIFLL FINHRLVEST SLRKAIETVY AAYLPKNTHP FLYLSLEISP
 300


 


QNVDVNVHPT KHEVHFLHEE SILERVQQHI ESKLLGSNSS RMYFTQTLLP GLAGPSGEMV
 360


 


KSTTSLTSSS TSGSSDKVYA HQMVRTDSRE QKLDAFLQPL SKPLSSQPQA IVTEDKTDIS
 420


 


SGRARQQDEE MLELPAPAEV AAKNQSLEGD TTKGTSEMSE KRGPTSSNPR KRHREDSDVE
 480


 


MVEDDSRKEM TAACTPRRRI INLTSVLSLQ EEINEQGHEV LREMLHNHSF VGCVNPQWAL
 540


 


AQHQTKLYLL NTTKLSEELF YQILIYDFAN FGVLRLSEPA PLFDLAMLAL DSPESGWTEE
 600


 


DGPKEGLAEY IVEFLKKKAE MLADYFSLEI DEEGNLIGLP LLIDNYVPPL EGLPIFILRL
 660


 


ATEVNWDEEK ECFESLSKEC AMFYSIRKQY ISEESTLSGQ QSEVPGSIPN SWKWTVEHIV
 720


 


YKALRSHILP PKHFTEDGNI LQLANLPDLY KVFERC
 756


 


MLH1 (human)
(SEQ ID NO:16)


cttggctctt ctggcgccaa aatgtcgttc gtggcagggg ttattcggcg gctggacgag
 60


 


acagtggtga accgcatcgc ggcgggggaa gttatccagc ggccagctaa tgctatcaaa
 120


 


gagatgattg agaactgttt agatgcaaaa tccacaagta ttcaagtgat tgttaaagag
 180


 


ggaggcctga agttgattca gatccaagac aatggcaccg ggatcaggaa agaagatctg
 240


 


gatattgtat gtgaaaggtt cactactagt aaactgcagt cctttgagga tttagccagt
 300


 


atttctacct atggctttcg aggtgaggct ttggccagca taagccatgt ggctcatgtt
 360


 


actattacaa cgaaaacagc tgatggaaag tgtgcataca gagcaagtta ctcagatgga
 420


 


aaactgaaag cccctcctaa accatgtgct ggcaatcaag ggacccagat cacggtggag
 480


 


gacctttttt acaacatagc cacgaggaga aaagctttaa aaaatccaag tgaagaatat
 540


 


gggaaaattt tggaagttgt tggcaggtat tcagtacaca atgcaggcat tagtttctca
 600


 


gttaaaaaac aaggagagac agtagctgat gttaggacac tacccaatgc ctcaaccgtg
 660


 


gacaatattc gctccatctt tggaaatgct gttagtcgag aactgataga aattggatgt
 720


 


gaggataaaa ccctagcctt caaaatgaat ggttacatat ccaatgcaaa ctactcagtg
 780


 


aagaagtgca tcttcttact cttcatcaac catcgtctgg tagaatcaac ttccttgaga
 840


 


aaagccatag aaacagtgta tgcagcctat ttgcccaaaa acacacaccc attcctgtac
 900


 


ctcagtttag aaatcagtcc ccagaatgtg gatgttaatg tgcaccccac aaagcatgaa
 960


 


gttcacttcc tgcacgagga gagcatcctg gagcgggtgc agcagcacat cgagagcaag
1020


 


ctcctgggct ccaattcctc caggatgtac ttcacccaga ctttgctacc aggacttgct
1080


 


ggcccctctg gggagatggt taaatccaca acaagtctga cctcgtcttc tacttctgga
1140


 


agtagtgata aggtctatgc ccaccagatg gttcgtacag attcccggga acagaagctt
1200


 


gatgcatttc tgcagcctct gagcaaaccc ctgtccagtc agccccaggc cattgtcaca
1260


 


gaggataaga cagatatttc tagtggcagg gctaggcagc aagatgagga gatgcttgaa
1320


 


ctcccagccc ctgctgaagt ggctgccaaa aatcagagct tggaggggga tacaacaaag
1380


 


gggacttcag aaatgtcaga gaagagagga cctacttcca gcaaccccag aaagagacat
1440


 


cgggaagatt ctgatgtgga aatggtggaa gatgattccc gaaaggaaat gactgcagct
1500


 


tgtacccccc ggagaaggat cattaacctc actagtgttt tgagtctcca ggaagaaatt
1560


 


aatgagcagg gacatgaggt tctccgggag atgttgcata accactcctt cgtgggctgt
1620


 


gtgaatcctc agtgggcctt ggcacagcat caaaccaagt tataccttct caacaccacc
1680


 


aagcttagtg aagaactgtt ctaccagata ctcatttatg attttgccaa ttttggtgtt
1740


 


ctcaggttat cggagccagc accgctcttt gaccttgcca tgcttgcctt agatagtcca
1800


 


gagagtggct ggacagagga agatggtccc aaagaaggac ttgctgaata cattgttgag
1860


 


tttctgaaga agaaggctga gatgcttgca gactatttct ctttggaaat tgatgaggaa
1920


 


gggaacctga ttggattacc ccttctgatt gacaactatg tgcccccttt ggagggactg
1980


 


cctatcttca ttcttcgact agccactgag gtgaattggg acgaagaaaa ggaatgtttt
2040


 


gaaagcctca gtaaagaatg cgctatgttc tattccatcc ggaagcagta catatctgag
2100


 


gagtcgaccc tctcaggcca gcagagtgaa gtgcctggct ccattccaaa ctcctggaag
2160


 


tggactgtgg aacacattgt ctataaagcc ttgcgctcac acattctgcc tcctaaacat
2220


 


ttcacagaag atggaaatat cctgcagctt gctaacctgc ctgatctata caaagtcttt
2280


 


gagaggtgtt aaatatggtt atttatgcac tgtgggatgt gttcttcttt ctctgtattc
2340


 


cgatacaaag tgttgtatca aagtgtgata tacaaagtgt accaacataa gtgttggtag
2400


 


cacttaagac ttatacttgc cttctgatag tattccttta tacacagtgg attgattata
2460


 


aataaataga tgtgtcttaa cata
2484


 


hPMS2-134 (human)
(SEQ ID NO:17)


MERAESSSTE PAKAIKPIDR KSVHQICSGQ VVLSLSTAVK ELVENSLDAG ATNIDLKLKD
 60


 


YGVDLIEVSD NGCGVEEENF EGLTLKHHTS KIQEFADLTQ VETFGFRGEA LSSLCALSDV
 120


 


TISTCHASAK VGT
 133


 


hPMS2-134 (human cDNA)
(SEQ ID NO:18)


cgaggcggat cgggtgttgc atccatggag cgagctgaga gctcgagtac agaacctgct
 60


 


aaggccatca aacctattga tcggaagtca gtccatcaga tttgctctgg gcaggtggta
 120


 


ctgagtctaa gcactgcggt aaaggagtta gtagaaaaca gtctggatgc tggtgccact
 180


 


aatattgatc taaagcttaa ggactatgga gtggatctta ttgaagtttc agacaatgga
 240


 


tgtggggtag aagaagaaaa cttcgaaggc ttaactctga aacatcacac atctaagatt
 300


 


caagagtttg ccgacctaac tcaggttgaa acttttggct ttcgggggga agctctgagc
 360


 


tcactttgtg cactgagcga tgtcaccatt tctacctgcc acgcatcggc gaaggttgga
 420


 


acttga
 426






The above disclosure generally describes the present invention. A more complete understanding can be obtained by reference to the following specific examples, which are provided herein for purposes of illustration only, and are not intended to limit the scope of the invention.
EXAMPLES
Example 1
hPMS2-134 Encodes a Dominant Negative Mismatch Repair Protein
A profound defect in MMR was found in the normal cells of two HNPCC patients. That this defect was operative in vivo was demonstrated by the widespread presence of microsatellite instability in non neoplastic cells of such patients. One of the two patients had a germ line truncating mutation of the hPMS2 gene at codon 134 (the hPMS2 134 mutation), while the other patient had a small germ line deletion within the hMLH1 gene. Leach et al., Cell, 1993, 75, 1215 1225. These data contradicted the two hit model generally believed to explain the biochemical and biological features of HNPCC patients. The basis for this MMR deficiency in the normal cells of these patients was unclear, and several potential explanations were offered. For example, it was possible that the second allele of the relevant MMR gene was inactivated in the germ line of these patients through an undiscovered mechanism, or that unknown mutations of other genes involved in the MMR process were present that cooperated with the known germ line mutation. It is clear from knock out experiments in mice that MMR deficiency is compatible with normal growth and development, supporting these possibilities. Edelmann et al., Cell, 1996, 85, 1125 1134. Alternatively, it was possible that the mutant alleles exerted a dominant-negative effect, resulting in MMR deficiency even in the presence of the wild type allele of the corresponding MMR gene and all other genes involved in the MMR process. To distinguish between these possibilities, the truncated polypeptide encoded by the hPMS2 134 mutation was expressed in an MMR proficient cell line its affect on MMR activity was analyzed. The results showed that this mutant could indeed exert a dominant-negative effect, resulting in biochemical and genetic manifestations of MMR deficiency. One embodiment of the present invention is demonstrated in Table 1, where a Syrian hamster fibroblast cell line (TK) was transfected with an expression vector containing the hPMS2-134 (TK-PMS2-134) or the empty expression vector (TKvect), which also contains the NEO gene as a selectable marker. TK-PMS2-134 cells were determined to be stably expressing the gene via western blot analysis (data not shown). Nuclear lysates from hPMS2-134 and control cells were measured for the ability to correct mismatched DNA substrates. As shown in Table 1, TK-PMS2-134 cells had a dramatic decrease in repair activity while TKvect control cells were able to repair mismatched DNA duplexes at a rate of  ̃4.0 fmol/15 minutes (p<0.01).







TABLE 1







Relative endogenous MMR activity of MMR-proficient


cells expressing an ectopically expressed morphogene


or an empty expression vector











5′ DNA Repair activity of G/T mismatch



Cell Lines
(fmol/15 minutes)














TKvect




1
3.5



2
2.9



3
5.5



TK-PMS2-134



1
0



2
0



3
0.5










These data show that the expression of the TK-PMS2-134 results in suppressed MMR of a host organism and allows for an enhanced mutation rate of genetic loci with each mitosis.

Example 2
hPMS2-134 Can Alter Genes in vivo
An example of the ability to alter mismatch repair comes from experiments using manipulation of mismatch repair TK cells (described above) that expressed the TK-hPMS2-134 mutant were used by transfection of the mammalian expression construct containing a defective β-galactosidase gene (referred to as pCAR-OF) which was transfected into TK-hPMS2-134 or TKvect cells as described above. The pCAR OF vector consists of a β-galactosidase gene containing a 29-basepair poly-CA tract inserted at the 5′ end of its coding region, which causes the wild-type reading frame to shift out-of-frame. This chimeric gene is cloned into the pCEP4, which contains the constitutively active cytomegalovirus (CMV) promoter upstream of the cloning site and also contains the hygromycin-resistance gene that allows for selection of cells containing this vector. The pCAR-OF reporter cannot generate β-galactosidase activity unless a frame-restoring mutation (i.e., insertion or deletion) arises following transfection into a host. Another reporter vector called pCAR-IF contains a β-galactosidase in which a 27-bp poly-CA repeat was cloned into the same site as the pCAR-OF gene, but it is biologically active because the removal of a single repeat restores the open reading frame and produces a functional chimeric β-galactosidase polypeptide (not shown). In these experiments, TK-hPMS2-134 and TKvect cells were transfected with the pCAR-OF reporter vector and selected for 17 days in neomycin plus hygromycin selection medium. After the 17 days, resistant colonies were stained for β-galactosidase production to determine the number of clones containing a genetically altered β-galactosidase gene. All conditions produced a relatively equal number of neomycin/hygromycin resistant cells, however, only the cells expressing the TK-hPMS2-134 contained a subset of clones that were positive for β-galactosidase activity. Representative results are shown in Table 2, which shows the data from these experiments where cell colonies were stained in situ for β-galactosidase activity and scored for activity. Cells were scored positive if the colonies turned blue in the presence of X-gal substrate and scored negative if colonies remained white. Analysis of triplicate experiments showed that a significant increase in the number of functional β-galactosidase positive cells was found in the TK-hPMS2-134 cultures, while no β-galactosidase positive cells were seen in the control TKvect cells.







TABLE 2







Number of TKmorph and TKvect cells containing


functional β-galactosidase activity













% Clones with


Cells
White Colonies
Blue Colonies
altered B-gal





Tkvect
65 +/− 9 
0
 0/65 = 0%


TK-PMS2-134
40 +/− 12
28 +/− 4
28/68 = 41%









TK-PMS2-134/pCAR-OF clones that were pooled and expanded also showed a number of cells that contained a functional β-galactosidase gene. No β-galactosidase positive cells were observed in TKvect cells transfected with the pCAR-OF vector. These data are shown in FIG. 1 where the dark staining in panel B represent β-galactosidase positive cells present in the TK-PMS2-134/pCAR-OF cultures while none are found in the TKvect cells grown under similar conditions (panel A). These data demonstrate the ability of the mutant mismatch repair gene, hPMS2-134, to generate gene alterations in vivo, which allows for the rapid screening of clones with altered polypeptides exhibiting new biochemical features.

To confirm that alterations within the nucleotide sequences of the β-galactosidase gene was indeed responsible for the in vivo β-galactosidase activity present in TK-hPMS2-134 clones, RNA was isolated from TK-hPMS2-134/pCAR-OF and TKvect/pCAR-OF and the β-galactosidase mRNA primary structure was examined by reverse transcriptase polymerase chain reaction (RT-PCR) amplification and sequencing. Sequence analysis of β-galactosidase message from TKvect cells found no structural alterations in the input gene sequence. Analysis of the β-galactosidase message from TK-hPMS-134 cells found several changes within the coding sequences of the gene. These sequence alterations included insertion and deletions of the poly CA tract in the amino terminus as expected. Other alterations included insertions of sequences outside of the polyCA repeat as well as a series of single base alterations contained throughout the length of the gene.
A summary of the genetic alterations are given in FIG. 2 where a schematic representation of the β-galactosidase gene is shown with the regions and types of genetic alterations depicted below.
Plasmids. The full length wild type hPMS2 cDNA was obtained from a human Hela cDNA library as described in Strand et al., Nature, 1993, 365, 274 276, which is incorporated herein by reference in its entirety. An hPMS2 cDNA containing a termination codon at amino acid 134 was obtained via RT PCR from the patient in which the mutation was discovered. Nicolaides et al., Mol. Cell. Biol., 1998, 18, 1635–1641, which is incorporated herein by reference in its entirety. The cDNA fragments were cloned into the BamHI site into the pSG5 vector, which contains an SV40 promoter followed by an SV40 polyadenylation signal. Nicolaides et al., Genomics, 1995, 29, 329 334, which is incorporated herein by reference in its entirety. The pCAR reporter vectors described in FIG. 1 were constructed as described in Palombo et al., Nature, 1994, 36, 417, which is incorporated herein by reference in its entirety.
β-galactosidase assay. Seventeen days following transfection with pCAR, β-galactosidase assays were performed using 20 μg of protein in 45 mM 2 mercaptoethanol, 1 mM MgCl2, 0.1 M NaPO4 and 0.6 mg/ml Chlorophenol red β-D galatopyranoside (CPRG, Boehringer Mannheim). Reactions were incubated for 1 hour, terminated by the addition of 0.5 M Na2CO3, and analyzed by spectrophotometry at 576 nm. Nicolaides et al., Mol. Cell. Biol., 1998, 18, 1635–1641. For in situ β-galactosidase staining, cells were fixed in 1% glutaraldehyde in PBS and incubated in 0.15 M NaCl, 1 mM MgCl2, 3.3 mM K4Fe(CN)6, 3.3 mM K3Fe(CN)6, 0.2% X Gal for 2 hours at 37° C.
Example 3
hPMS2-134 Causes a Defect in MMR Activity
The differences in β-galactosidase activity between PMS2 WT and PMS2 134 transfected cells can be due to the PMS2 134 protein disturbing MMR activity resulting in a higher frequency of mutation within the pCAR OF reporter and re establishing the ORF. To directly test whether MMR was altered, a biochemical assay for MMR with the individual clones described in Example 1 was employed. Nuclear extracts were prepared from the clones and incubated with heteroduplex substrates containing either a /CA\ insertion deletion or a G/T mismatch under conditions described previously. The /CA\ and G/T heteroduplexes were used to test repair from the 3′ and 5′ directions, respectively. There was a dramatic difference between the PMS2-134 expressing clones and the other clones in these assays (Table 3).







TABLE 3





MMR activity of nuclear extracts from


SH clones or pooled culturesa


















Amt of repaired substrate (fmol/15 min)












Cell line
3′/CA\3′G/T 5′ G/T 3′/CTG\
5′/CTG\







SH clonesb



PMS2-NOT



Clone A
10.2
3.5



Clone B
12.7
2.9



Clone C
13.5
5.5



PMS2-WT



Clone A
2.8
2.2



Clone B
5.7
4.8



Clone c
4.7
2.9



PMS2-134



Clone A
2.5
0.0



Clone B
2.4
0.0



Clone C
5.0
0.5











Pooled cultures














PMS2-NOT
2.07 ± 0.09
2.37 ± 0.37
3.45 ± 1.35
2.77 ± 1.37


PMS2-WT
1.65 ± 0.94
1.86 ± 0.57
1.13 ± 0.23
1.23 ± 0.65


PMS2-134
0.14 ± 0.2
 0.0 ± 0.0
1.31 ± 0.66
 0.0 ± 0.0





aThe extracts were tested for MMR activity with 24 fmol of heteroduplex.


bThese data represent similar results derived from more than five independent experiments.






While all clones repaired substrates from the 3′ direction (/CA\ heteroduplex), cells expressing the PMS2 134 polypeptide had very little 5′ repair activity. A similar directional defect in mismatch repair was evident with pooled clones resulting from PMS2 134 transfection, or when the heteroduplex contained a 2 4 base pair loop, examples of which are shown in Table 3. A small decrease in MMR activity was observed in the 3′ /CA\ PMS2-WT repair assays, perhaps a result of interference in the biochemical assays by over-expression of the PMS2 protein. No significant activity was caused by PMS2-WT in the in situ β-galactosidase assays, a result more likely to reflect the in vivo condition.

Biochemical assays for mismatch repair. MMR activity in nuclear extracts was performed as described, using 24 fmol of substrate, in Bronner et al., Nature, 1994, 368, 258 261 and Nicolaides et al., Mol. Cell. Biol., 1998, 18, 1635–1641, each of which is incorporated herein by reference in its entirety. Complementation assays were done by adding  ̃100 ng of purified MutL′′ or MutS′′ components to 100 μg of nuclear extract, adjusting the final KCl concentration to 100 mM. Bevins, Ciba Found. Symp., 1994, 186, 250–69 and Alderson et al., Res. Microbiol., 1993, 144, 665–72. The substrates used in these experiments contain a strand break 181 nucleotides 5′ or 125 nucleotides 3′ to the mismatch. Values represent experiments performed at least in duplicate.
Example 4
C-Terminus of hPMS2 Mediates Interaction Between hPMS2 and hMLH1
To elucidate the mechanism by which hPMS2 134 affected MMR, the interaction between hPMS2 and hMLH1 was analyzed. Previous studies have shown that these two proteins dimerize to form a functionally active complex. Bronner et al., Nature, 1994, 368, 258 261. Proteins were synthesized in vitro using reticulocyte lysates, employing RNA generated from cloned templates. The full length hMLH1 and hPMS2 proteins bound to each other and were co precipitated with antibodies to either protein, as expected (data not shown). To determine the domain of hPMS2 that bound to hMLH1, the amino terminus (codons 1–134 ), containing the most highly conserved domain among mutL proteins (Su et al., J. Biol. Chem., 1988, 263, 6829 6835 and Edelmann et al., Cell, 1996, 85, 1125 1134 ), and the carboxyl terminus (codons 135–862) were separately cloned and proteins produced in vitro in coupled transcription translation reactions. FIGS. 3A, 3B, and 3C show a representative immunoprecipitation of in vitro-translated hPMS2 and hMLH1 proteins. FIG. 3A shows labeled (indicated by an asterisk) or unlabelled proteins incubated with an antibody to the C-terminus of hPMS2 in lanes 1 to 3 and to hMLH1 in lanes 4 to 6. Lane 7 contains a nonprogrammed reticulocyte lysate. PMS2-135 contains codons 135 to 862 of hPMS2. The major translation products of hPMS2 and hMLH1 are indicated. FIG. 3B shows labeled hPMS2-134 (containing codons 1–134 of hPMS2) incubated in the presence or absence of unlabelled hMLH1 plus an antibody to hMLH1 (lanes 1 and 2, respectively). Lane 3 contains lysate from a nonprogrammed reticulolysate. FIG. 3C shows labeled proteins incubated with an antibody to the N terminus of hPMS2. Lane 6 contains a nonprogrammed reticulocyte lysate. In both panels A and B, autoradiographs of immunoprecipitated products are shown. When a 35S labelled, full-length hMLH1 protein (FIG. 3A, lane 5) was mixed with the unlabelled carboxyl terminal hPMS2 polypeptide, a monoclonal antibody (mAb) to the carboxyl terminus of hPMS2 efficiently immunoprecipitated the labeled hMLH1 protein (lane 1). No hMLH1 protein was precipitated in the absence of hPMS2 (lane 2). Conversely, when the 35S labelled carboxyl terminus of hPMS2 (lane 3) was incubated with unlabelled, full length hMLH1 protein, an anti hMLH1 mAb precipitated the hPMS2 polypeptide (lane 4). In the absence of the unlabelled hMLH1 protein, no hPMS2 protein was precipitated by this mAb (lane 6). The same antibody failed to immunoprecipitate the amino terminus of hPMS2 (amino acids 1 134 ) when mixed with unlabelled MLH1 protein (FIG. 3B, lane 1). This finding was corroborated by the converse experiment in which radiolabelled hPMS2-134 (FIG. 3C, lane 1) was unable to coprecipitate radiolabelled MLH1 when precipitations were done using an N terminal hPMS2 antibody (FIG. 3C, lane 2) while this antibody was shown to be able to coprecipitate MLH1 when mixed with wild type hPMS2 (FIG. 3C, lane 4).
The initial steps of MMR are dependent on two protein complexes, called MutS′′ and MutL′′. Drummond et al., Science, 1995, 268, 1909 1912. As the amino terminus of hPMS2 did not mediate binding of hPMS2 to hMLH1, it was of interest to determine whether it might instead mediate the interaction between the MutL′′ complex (comprised of hMLH1 and hPMS2) and the MutS′′ complex (comprised of MSH2 and GTBP). Because previous studies have demonstrated that MSH2 and the MutL′′ components do not associate in solution, direct hPMS2-134:MutS′′ interaction was unable to be assayed. A different approach was used to address this issue, and attempted to complement nuclear extracts from the various SH cell lines with MutS′′ or MutL′′. If the truncated protein present in the PMS2-134 expressing SH cells was binding to MutS′′ and lowering its effective concentration in the extract, then adding intact MutS′′ should rescue the MMR defect in such extracts. FIG. 4 shows complementation of MMR activity in transduced SH cells. Lysates from pooled clones stably transduced with PMS2-NOT, PMS2-WT, or PMS2-134 were complemented with purified MutS′′ or MutL′′ MMR components by using the 5′ G/T heteroduplex substrate. The values are presented as the percentage of repair activity in each case compared to that in lysates complemented with both purified MutL′′ and MutS′′ components to normalize for repair efficiency in the different lysate backgrounds. The values shown represent the average of at least three different determinations. Purified MutS′′ added to such extracts had no effect (FIG. 4). In contrast, addition of intact MutL′′ to the extract completely restored directional repair to the extracts from PMS2-134 cells (FIG. 4).
The results described above lead to several conclusions. First, expression of the amino terminus of hPMS2 results in an increase in microsatellite instability, consistent with a replication error (RER) phenotype. That this elevated microsatellite instability is due to MMR deficiency was proven by evaluation of extracts from stably transduced cells. Interestingly, the expression of PMS2-134 resulted in a polar defect in MMR, which was only observed using heteroduplexes designed to test repair from the 5′ direction (no significant defect in repair from the 3′ direction was observed in the same extracts). Interestingly, cells deficient in hMLH1 also have a polar defect in MMR, but in this case preferentially affecting repair from the 3′ direction. Huttner et al., Pediatr. Res., 1999, 45, 785–94. It is known from previous studies in both prokaryotes and eukaryotes that the separate enzymatic components mediate repair from the two different directions. Our results indicate a model in which 5′ repair is primarily dependent on hPMS2 while 3′ repair is primarily dependent on hMLH1. It is easy to envision how the dimeric complex between PMS2 and MLH1 might set up this directionality. The combined results also demonstrate that a defect in directional MMR is sufficient to produce a RER+ phenotype.
The dominant-negative function of the PMS2-134 polypeptide can result from its binding to MLH1 and consequent inhibition of MutL′′ function. This is based in part on the fact that the most highly conserved domain of the PMS2 gene is located in its amino terminus, and the only known biochemical partner for PMS2 is MLH1. The binding studies revealed, however, that the carboxyl terminus of PMS2, rather than the highly conserved amino terminus, actually mediated binding to MLH1. This result is consistent with those recently obtained in S. cerevisciae, in which the MLH1 interacting domain of PMS1 (the yeast homolog of human PMS2) was localized to its carboxyl terminus. Leach et al., Cell, 1993, 75, 1215 1225. The add back experiments additionally showed that the hPMS2-134 mutant was not likely to mediate an interaction with the MutS′′ complex (FIG. 4). The hPMS2-134 polypeptide does not inhibit the initial steps in MMR, but rather interacts with and inhibits a downstream component of the pathway, perhaps a nuclease required for repair from the 5′ direction.
The demonstration that the hPMS2-134 mutation can confer a dominant-negative MMR defect to transfected cells helps to explain the phenotype of the kindred in which this mutant was discovered. Three individuals from this kindred were found to carry the mutation, a father and his two children. Both children exhibited microsatellite instability in their normal tissues and both developed tumors at an early age, while the father had no evidence of microsatellite instability in his normal cells and was completely healthy at age 35. The only difference known to us with respect to the MMR genes in this family is that the father's mutant allele was expressed at lower levels than the wild type allele as assessed by sequencing of RT PCR products of RNA from lymphocytes. The children expressed both alleles at approximately equal levels. The dominant negative attribute of the hPMS2-134 mutant may only be manifest when it is present at sufficient concentrations (at least equimolar) thus, explaining the absence of MMR deficiency in the father. The reason for the differential expression of the hPMS2-134 allele in this kindred is not clear, though imprinting is a possibility. Ascertainment of additional, larger kindreds with such mutations will facilitate the investigation of this issue.
Western blots. Equal number of cells were lysed directly in lysis buffer (60 mM Tris, pH 6.8, 2% SDS, 10% glycerol, 0.1 M 2 mercaptoethanol, 0.001% bromophenol blue) and boiled for 5 minutes. Lysate proteins were separated by electrophoresis on 4 12% Tris glycine gels (for analysis of full length hPMS2) or 4 20% Tris glycine gels (for analysis of hPMS2-134). Gels were electroblotted onto Immobilon P (Millipore) in 48 mM Tris base, 40 mM glycine, 0.0375% SDS, 20% methanol and blocked overnight at 4° C. in Tris buffered saline plus 0.05% Tween 20 and 5% condensed milk. Filters were probed with a polyclonal antibody generated against residues 2–20 of hPMS2 (Santa Cruz Biotechnology, Inc.) and a horseradish peroxidase conjugated goat anti rabbit secondary antibody, using chemiluminescence for detection (Pierce).
In vitro translation. Linear DNA fragments containing hPMS2 and hMLH1 cDNA sequences were prepared by PCR, incorporating sequences for in vitro transcription and translation in the sense primer. A full length hMLH1 fragment was prepared using the sense primer 5′ ggatcctaatacgactcactatagggagaccaccatgtcgttcgtggcaggg 3′ (SEQ ID NO:1) (codons 1–6) and the antisense primer 5′ taagtcttaagtgctaccaac 3′ (SEQ ID NO:2) (located in the 3′ untranslated region, nt 2411 2433), using a wild type hMLH1 cDNA clone as template. A full length hPMS2 fragment was prepared with the sense primer 5′ ggatcctaatacgactcactatagggagaccaccatggaacaattgcctgcgg 3′ (SEQ ID NO:3) (codons 1–6) and the antisense primer 5′ aggttagtgaagactctgtc 3′ (SEQ ID NO:4) (located in 3′ untranslated region, nt 2670 2690) using a cloned hPMS2 cDNA as template. A fragment encoding the amino terminal 134 amino acids of hPMS2 was prepared using the same sense primer and the antisense primer 5′ agtcgagttccaaccttcg 3′ (SEQ ID NO:5). A fragment containing codons 135–862 of hPMS135 was generated using the sense primer 5′ ggatcctaatacgactcactatagggagaccaccatgatgtttgatcacaatgg 3′ (SEQ ID NO:6) (codons 135–141) and the same antisense primer as that used for the full length hPMS2 protein. These fragments were used to produce proteins via the coupled transcription translation system (Promega). The reactions were supplemented with 35S labelled methionine or unlabelled methionine, as indicated in the text. The PMS135 and hMLH1 proteins could not be simultaneously radiolabelled and immunoprecipitated because of their similar molecular weights precluded resolution. Lower molecular weight bands are presumed to be degradation products and/or polypeptides translated from alternative internal methionines.
Immunoprecipitation. Immunoprecipitations were performed on in vitro translated proteins by mixing the translation reactions with 1 μg of the MLH1 specific monoclonal antibody (mAB) MLH14 (Oncogene Science, Inc.), a polyclonal antibody generated to codons 2–20 of hPMS2 described above, or a polyclonal antibody generated to codons 843–862 of hPMS2 (Santa Cruz Biotechnology, Inc.) in 400:1 of EBC buffer (50 mM Tris, pH 7.5, 0.1 M NaCl, 0.5% NP40). After incubation for 1 hour at 4° C., protein A sepharose (Sigma) was added to a final concentration of 10% and reactions were incubated at 4° C. for 1 hour. Proteins bound to protein A were washed five times in EBC and separated by electrophoresis on 4 20% Tris glycine gels, which were then dried and autoradiographed.
Example 5
Syrian Hamster Tk-ts-13 Cells Produce a Novel Anti-Microbial Polypeptide Can Suppress the Growth of Bacillus subtilis 
The feasibility of creating microbial-resistant mammalian cells is demonstrated as follows. Syrian Hamster TK fibroblasts were transfected with a mammalian expression vector containing a novel anti-microbial polypeptide called mlg1 or the empty expression vector called psg. When cells expressing the mlg polypeptide (referred to as TK-mlg1) were grown in the presence of Bacillus subtilis, these cells were able to suppress the growth of the microbes and allow the TK host to remain viable in contrast to TK cells transfected with the empty vector (TK=psg), which all died from the toxic effects that Bacillus subtilis has on mammalian cells. FIG. 5 shows a photograph of TK-mlg1 and TK=psg cultures grown in the presence of Bacillus for 4 days. Syrian hamster Tk-ts13 cells were transfected with a eukaryotic expression vector that produces a novel antimicrobial polypeptide referred to as mlg1 (Panel A) or the expression vector lacking an inserted cDNA for expression (TK=psg, Panel B). Cells were plated at a density of 5×105 cells/ml in a 10 cm falcon pyrogenic-free petri dish in growth medium for 24 hours and then inoculated with 10:1 of an exponentially growing culture of Bacillus subtilis. Cultures were then incubated for 4 days at which time Bacilli grow and begin to lyse the Tk-ts13 parental culture as shown in panel B (indicated by arrows), while cells expressing the anti-microbial mlg1polypeptide (Panel A) remain viable in the presence of Bacillus (small granular structures present in panels A and B). These data demonstrate the feasibility of cells to survive in the presence of Bacillus contamination when they produce an anti-microbial agent. These data show that antimicrobial producing mammalian cells are capable of growing and surviving in the presence of toxic microbes.
Cell lines and transfection. Syrian Hamster fibroblast Tk ts13 cells were obtained from ATCC and cultured as described. Modrich, Science, 1994, 266, 1959 1960. Stably transfected cell lines expressing hPMS2 were created by cotransfection of the PMS2 expression vectors and the pLHL4 plasmid encoding the hygromycin resistance gene at a ratio of 3:1 (pCAR:pLHL4) and selected with hygromycin. Stably transfected cell lines containing pCAR reporters were generated by co transfection of pCAR vectors together with either pNTK plasmid encoding the neomycin resistance plasmid or with pLHL4. All transfections were performed using calcium phosphate as previously described in Modrich, Science, 1994, 266, 1959 1960, which is incorporated herein by reference in its entirety.
Example 6
TK-hPMS2-134 Cells can Suppress the Growth of Escherichia coli in vitro
While TK-hPMS2-134 TK-ts13 cells have been previously shown to be capable of altering genes in vivo (refer to Table 2 and FIG. 1), the ability to generate “naturally microbial-resistant” clones has not been reported in the literature. To generate microbial-resistant TK cells, TK-ts13 cells constitutively expressing the a dominant-negative mismatch repair gene, TK-hPMS2-134 or the empty vector (TKvect) that have been in culture for >3 months ( ̃60 passages) were seeded at 5×105 cells/ml in Dulbeicco's Modified Eagles Medium (DMEM) plus 10% fetal bovine serum (FBS) and plated into 10 cm dishes (Falcon) in duplicate. These cells were grown overnight at 37° C. in 5% CO2 to allow cells to adhere to the plastic. The next day, TK cultures were inoculated with 10:1 of an exponentially growing culture of Escherichia coli. Cultures were then grown at 37° C. in 5% CO2 and observed on day 7 and 14 for microbial-resistant cell clones; these cells appear as clones of cells surrounded by “cleared” areas on the plate. At day 7, all cells in the control transfected TKvect culture were dead, while a subset of cells were viable in the TK-hPMS2-134 transfected cultures. At day 14, there were no clones in the control transfected TKvect cultures, while there were 34 and 40 Escherichia coli-resistant colonies formed in the TK-hPMS2-134 transfected cultures. Growing clones from each dish were then pooled as individual cultures and grown to confluence. These cultures were named TK-hPMS2-134 (R1) and TK-hPMS2-134 (R2). Cultures were cured of Escherichia coli by the addition of 1 mg/ml G418, in which the TK-hPMS2-134 cells are resistant due to expression of the neomycin-resistance gene contained on the mammalian expression vector used to generate the cells.
TKvect, TK-hPMS2-134 (1) and TK-hPMS2-134 (R2) cells were plated at 5×105 cell/ml in 10 mls and plated into 10 cm dishes in duplicate. The next day, 10:1 of a logarithmic stage Escherichia coli culture was added to each TK culture and cultures were grown for 48 hours at 37° C. in 5% CO2. An aliquot of supernatant from each culture was harvested immediately after inoculation to establish a baseline density of bacteria for each culture. After 48 hours, 2 ml of supernatant were harvested from each culture as well as from uninfected TK cultures. One ml of each supernatant was then analyzed by a spectrophotometer at an OD600 to measure for bacterial density. Supernatants from uninfected cultures were used as a blank to correct for background. As shown in FIG. 6, bacterial growth was significantly suppressed in TK-hPMS2-134 (R1) and TK-hPMS2-134 (R2) cultures in contrast to TKvect control cells. These data demonstrate the feasibility of using a dominant-negative mismatch repair mutant hPMS2-134 on mammalian cells to produce genetically altered clones capable of producing a molecule(s) that can suppress microbial growth.
As those skilled in the art will appreciate, numerous changes and modifications may be made to the preferred embodiments of the invention without departing from the spirit of the invention. It is intended that all such variations fall within the scope of the invention. In addition, the entire disclosure of each publication cited herein is hereby incorporated herein by reference.

## Claims

1. A method for obtaining a genetically stable mammalian cell that is resistant to a selected microbe comprising:
growing a culture of mammalian cells wherein said cells comprise a dominant-negative allele of a mismatch repair gene, wherein said mismatch repair gene encodes the first 133 amino acids of PMS2, and allowing mutations to occur;
exposing said cells to said selected microbe;
selecting said mammalian cell that is resistant to said selected microbe; and
suppressing expression of said dominant negative allele of said mismatch repair gene; thereby obtaining a genetically stable mammalian cell that is resistant to a selected microbe.

2. The method of claim 1 wherein said mammalian cell is selected for resistance to a bacterium.

3. The method of claim 1 wherein said mammalian cell is selected for resistance to a fungus.

4. The method of claim 1 wherein said dominant negative allele of said mismatch repair gene is operably linked to an inducible promoter.

5. The method of claim 4 wherein expression of said dominant negative allele is suppressed by withdrawing an inducer of said inducible promoter.

6. The method of claim 1 wherein expression of said dominant negative allele is suppressed by knocking out said dominant negative allele.

7. The method of claim 1 wherein said step of selecting for microbial resistance comprises isolating and testing culture medium from said hypermutable cell.