# Patent

## Title
Recombinant expression of heterologous nucleic acids in protozoa

## Abstract

The ciliated protozoan Tetrahymena exemplifies a recombinant system for the expression of heterologous nucleic acids, preferably on the plasma membrane surface. Integration of a heterlogous nucleic acid into the β-tubulin gene, BTU1, of a paclitaxel-sensitive T. thermophila mutant that possesses btu1-IK350M β-tubulin allele allows screening for transformants using negative selection, as transformants have restored paclitaxel resistance. Transgenic ciliated protozoa of the invention can serve as live vaccines. For example, transgenic Tetrahymena expressing Ichthyophthirius multifiliis i-antigen protein on their surface are effective vehicles for vaccination of freshwater fish against infection by I. multifiliis.

## Background
This application is a continuation-in-part of application of patent application Ser. No. 09/498,612, filed on Feb. 4, 2000, entitled RECOMBINANT EXPRESSION OF HETEROLOGOUS NUCLEIC ACIDS IN PROTOZOA, now U.S. Pat. No. 6,846,481 which claims the benefit of U.S. Provisional Application Ser. No. 60/131,121, filed Apr. 27, 1999; U.S. Provisional Application No. 60/118,634, filed Feb. 4, 1999; U.S. Provisional Application No. 60/122,372, filed Mar. 2, 1999; and U.S. Provisional Application No. 60/124,905, filed Mar. 17, 1999, each of which is incorporated herein by reference in its entirety.


STATEMENT OF GOVERNMENT RIGHTS
This invention was made with government support under grants from the National Institutes of Health (GM-54017-03) and the United States Department of Agriculture National Research Initiative Competitive Grants Program (NRICGP) (95-37204-2139). The U.S. government has certain rights in this invention.


CROSS REFERENCE TO RELATED APPLICATION
This application incorporates the content of U.S. patent application Ser. No. 09/497,967, entitled “Diagnostic and Protective Antigen Gene Sequences of Ichthyophthirius,” filed Feb. 4, 2000.
FIELD OF THE INVENTION
The present invention relates to the field of recombinant protein production, particularly recombinant protein production in nonpathogenic protozoa, such as the ciliate Tetrahymena. 
BACKGROUND OF THE INVENTION
Efficient and high-level recombinant production of heterologous proteins is an important alternative to chemical synthesis and the isolation of proteins from native sources. Recombinant protein production is especially useful when the native protein is normally produced in limited amounts or by sources which are impossible, expensive and/or dangerous to obtain or propagate. Although a number of recombinant expression systems have proven useful for production of various heterologous proteins, none of these systems is universally applicable for the production of all proteins. For instance, E. coli appears to lack the ability to provide many post-translational modifications to heterologous proteins. Yeast can provide only some post-translational modifications (e.g., glycosylation patterns), and rapid degradation of heterologous proteins in yeast is common. Additionally, heterologous proteins secreted by yeast may contain long, untrimmed oligosaccharide chains, which sometimes results in biologically inactive or antigenically altered proteins. Moreover, a replacement of the natural mammalian signal peptide with a yeast signal peptide is almost always required for efficient secretion of mammalian proteins by yeast. Expression of heterologous eukaryotic proteins in insect or mammalian cells can be more reliable but both require expensive media for cell propagation. Moreover, cultured insect cells and mammalian cells have a relatively long doubling time compared to conventional bacterial systems such as E. coli and certain protozoa such as Tetrahymena. 
Protozoa represent an alternative for the recombinant production of heterologous proteins, however few protozoa have been characterized to the extent necessary for routine heterologous protein expression. Well-characterized pathogenic protozoa that have been genetically engineered to express heterologous proteins include Trypanosoma cruzi, Trypanosoma brucei, and Leishmania spp. A number of shuttle vectors designed for episomal replication and coding region expression in pathogenic protozoa have been developed. An inducible coding region expression system has been established for pathogenic T. brucei (Wirtz, E., et al., Science, 268, 1179-1183 (1995)). Vectors that allow efficient coding region expression in different hosts like E. coli and mammalian cells have also been developed (Al-Qahtani, A., et al., Nucleic Acids Res., 24, 1173-1174 (1996)).
Protozoa are characterized by a glycosylphosphatidylinositol (GPI) anchoring system that allows targeted surface expression, or “display,” of various endogenous proteins. Recent experiments in the kinetoplastid Trypanosoma cruzi demonstrated that mammalian and protozoan signal peptides function in T. cruzi to target a heterologous protein to different cellular compartments, and further showed both secretion and GPI-anchored surface expression in T. cruzi of a heterologous protein (Garg et al., J. Immunol., 158: 3293-3302 (1997)). Surface display in T. cruzi of chicken ovalbumin (OVA) was achieved using a construct comprising the signal sequence of T. cruzi glycoprotein, gp-72, that targets the protein to the endoplasmic reticulum, followed by a coding region for OVA, followed by 45 amino acids of amastigote surface protein I of T. cruzi which provided a C-terminal hydrophobic tail containing GPI anchor cleavage/attachment site. The protein thus anchored to the surface of the protozoan via a GPI structure was found to be readily presented in association with class I MHC by parasite-infected host cells.
Heterologous proteins have also been expressed in the slime mold Dictyostelium discoideum. A number of proteins have been expressed in this system including surface expression of the malaria circumsporozoite antigen (CSP) (Reymond et al., J. Biol. Chem. 1995, 270: 12941-12947); see Williams et al., Current Opin. Biotechnol., 1995, 6:538-542, for a review).
Bioactive cytokines (IL-2 and IFN-γ) have also been produced in both T. cruzi and Leishmania (La Flamme et al., Mol. Biochem. Parasitol., 75:25-31 (1995), and Tobin et al., J. Immunol., 150:5059-5069 (1993)) in experiments that suggest that mammalian signal peptides are recognized and processed by these protozoa. However, pathogenic protozoa have not been exploited as a general purpose protein expression system, presumably because they are difficult or expensive to grow in large numbers and/or are infectious to human beings.
The nonpathogenic ciliate protozoan Tetrahymena has also been explored as a vehicle for expression of heterologous genes, but with limited success to date. T. thermophila has been successfully transformed using self-replicating palindromic ribosomal DNA (rDNA) purified from macronuclei (Tondravi et al., Proc. Natl. Acad. Sci. USA 83:4369-4373 (1986)). Selection of transformants relied on a dominant paromomycin-resistance mutation in the 17S rRNA. rDNA-based shuttle vectors capable of autonomously replicating in Tetrahymena as well as in E. coli have also been developed; these plasmids contained a replication origin (ori) from the T. thermophila rDNA minichromosome (Yu et al., Proc. Natl. Acad. Sci. USA 86:8487-8491 (1989)).
rDNA vectors are usually circular vectors containing both regulatory regions and “coding” regions for Tetrahymena rRNA. A typical somatic rDNA vector contains a 5′ nontranscribed sequence (5′-NTS), followed by a “coding” region for rRNA, followed by a 3′ nontranscribed sequence (3′-NTS). A transgene is inserted into the 3′ NTS. Somatic rDNA vectors contain the macronuclear version of rDNA and transform either by replacement of the macronuclear rDNA gene via homologous recombination or by autonomous replication as an extrachromosomal element. Processing rDNA vectors, on the other hand, contain additional processing signals upstream and downstream from the 5′-NTS and the 3′-NTS, respectively, obtained from the micronuclear version of rDNA. Processing rDNA vectors mimic what happens to the micronucleus rDNA in the newly developing macronucleus. After introduction of the vector into the developing new macronucleus during the sexual process of ciliates known as conjugation, the vector-borne micronuclear rDNA undergoes excision and is maintained as an rDNA minichromosome (Yao et al., Mol. Cell. Biol. 9:1092-1099 (1989)).
Both somatic and processing rDNA vectors have been used to insert a heterologous nucleic acid into a 3′ nontranscribed spacer region of rDNA. For example, M.-C. Yao et al. (Proc. Nat'l. Acad. Sci. USA 88:9493-9497 (1991)) expressed cycloheximide resistance in Tetrahymena using an rDNA vector having the rp129 cycloheximide resistant gene from T. thermophila inserted into the 3′ nontranscribed spacer region (NTS) of the rDNA sequence. Similarly, P. Blomberg et al. expressed neomycin resistance in T. thermophila using an rDNA vector having the neo gene inserted into the 3′ NTS, under control of rp129 flanking sequences (Mol. Cell. Biol., 17:7237-7247 (1997)).
Gaertig et al. described an rDNA-based shuttle vector, E. coli vector pH4T2, that contains two replication origin (ori) fragments, followed by a 300 base pair 5′ untranslated region obtained from the HHF1 gene of Tetrahymena, followed by the prokaryotic gene for neomycin resistance, neo, followed by a 3′ untranslated region from BTU2 from Tetrahymena (J. Gaertig et al., Nucleic Acids Res. 22:5391-5398 (1994)). Haddad et al. reported a small circular rDNA-based vector containing a repeat of the replication origin of rDNA (i.e., a 5′ NTS), a neo2 gene cassette (consisting of the neo gene under the control of histone HHF1 promoter and the BTU2 transcription terminator) as a selectable marker, and a green fluorescent protein (GFP) cassette (also under control of HHF1 promoter and BTU2 terminator) (A. Haddad et al., Proc. Nat'l. Acad. Sci. USA 94:10675-10680 (1997)). Rusconi et al. reported a circular vector containing the rDNA replication origin, neo2 cassette, and a tRNA gene (Genes Dev. 10:2870-2880, 1996)).
A typical rDNA-based vector is a circular bacterial vector that contains a 5′NTS comprising two or more of ori sequences from Tetrahymena rDNA, followed by a selectable cassette marker such as the neo 2 cassette (Gaertig et al., Nucleic. Acids Res. 22:5391-5398 (1994). A nucleic acid fragment containing a heterologous coding region such as a transgene, flanked by a 5′ untranslated region of a Tetrahymena gene (most often the  ̃30 bp 5′ untranslated region of the HHF1 gene of Tetrahymena) and a 3′ untranslated region of a Tetrahymena gene (most often  ̃300 bp of the 3′ untranslated region of the Tetrahymena gene BTU2), is typically inserted downstream of the selectable marker.
An rDNA construct that contains relatively short 5′ and 3′ untranslated sequences from two different protein coding genes of Tetrahymena, such as HHF1 and BTU2, is unlikely to integrate into the Tetrahymena genome via homologous recombination at the corresponding protein-coding loci. It is more likely to insert into Tetrahymena rDNA as a result of a single crossover event which involves the replication origin fragment. In addition, an rDNA-based vector can be maintained as an extrachromosomal element; the ori from Tetrahymena rDNA is known to support extrachromosomal replication. The marker gene (e.g., neo), and the transgene, if present, are therefore most likely expressed from the transforming rDNA-based plasmid and/or as a result of insertion into genomic rDNA, and not by recombination with endogenous genes other than rDNA.
Due to frequent and unpredictable integration of sequences from rDNA vector and rDNA-based vectors into the native rDNA, however, levels of expression of recombinant gene products are presumed to be highly variable. See J. Gaertig et al., Nucleic Acids Res. 22:5391-5398 (1994); R. W. Kahn et al., Proc. Natl. Acad. Sci. USA 90:9295-9299 (1993); W. J. Pan et al., Nucleic Acids Res. 23:1561-1569 (1995); and W. J. Pan et al., Mol. Cell Biol., 15:3372-3381 (1995). When relying on rDNA vectors for transformation, there is no way to control the level of integration into the host chromosome, hence no way to control copy number and, as a result, the expression level of a heterologous protein. Tetrahymena contain about 45 copies of each protein coding gene in the macronucleus, and each copy contains about 10,000 pallindromic copies per macronucleus. Thus, using either of these types of vectors, it is possible for a transgene to integrate at a similar copy number (10,000+). Overexpression of a transgene can be toxic to the protozoan host cell. Moreover, the loss of transgenes using these vectors cannot be prevented since this recombinant method generally lacks a reliable and sustainable means for selection. For example, a vector can contain both a transgene and a selectable marker, and both may initially integrate into the protozoan host genome. However, subsequent cross-over events can eliminate the transgene while leaving the marker gene in the host genome, resulting in selection of cells that do not necessarily contain the transgene.
A protein expression system that provides for the efficient expression and isolation of both prokaryotic and eukaryotic heterologous proteins in a nonpathogenic protozoan host is needed. In particular, a protein expression system that could provide surface expression of a heterologous prokaryotic or eukaryotic protein would constitute a much desired advance in the art.
SUMMARY OF THE INVENTION
The invention provides a protein expression system that utilizes a protozoan for the production of eukaryotic and prokaryotic polypeptides, including proteins. In one aspect, the recombinant protein expression system of the invention includes a transgenic protozoan host cell that is resistant to paclitaxel, wherein the host cell comprises a heterologous nucleic acid encoding a polypeptide. The recombinant protozoan host cell of this aspect of the invention is selectable by negative selection using paclitaxel. The protozoan host cell that is transformed with the heterologous nucleic acid is preferably a Tetrahymena host cell containing a btu1-1K350M β-tubulin allele. In another aspect, the recombinant protein expression system of the invention includes a transgenic ciliated protozoan host cell that contains a heterologous protein displayed on the plasma membrane surface of the host cell. Preferably, the surface-displayed heterologous protein is attached to the plasma membrane by a GPI anchor derived from an Ichthyophthirius multifiliis i-antigen.
Also provided by the invention is a novel protein expression vector. The vector contains a 5′ flanking region followed by a heterologous nucleic acid encoding a polypeptide comprising at least one targeting amino acid sequence encoded by a portion of an i-antigen-encoding nucleotide sequence from I. multifiliis, followed by a 3′ flanking region. At least a portion of each of the 5′ flanking region and the 3′ flanking region is complementary to an endogenous gene of an intended host, so as to allow for integration into endogenous gene by way of homologous recombination. In a preferred embodiment, the 5′ flanking region and the 3′ flanking region each contain a nucleic acid sequence selected from at least a portion of the Tetrahymena genes HHF1, rp129, BTU1, BTU2, SerH3 and the gene encoding actin.
Also provided by the invention is a Tetrahymena strain having a germline micronuclear genotype homozygous for btu1-1K350M/btu1-1K350M, and a somatic macronuclear phenotype exhibiting resistance to oryzalin (or-r); sensitivity to paclitaxel (tx-s); and, optionally, resistance or sensitivity to one or more marker drugs selected from the group consisting of cycloheximide (cy-r), 6-methylpurine (mp-r) and paromomycin (pm-r). Preferred embodiments of the Tetrahymena strain include a strain having a genetic makeup represented by btu1-1K350M/btu1-1K350M, mpr1-1/mpr1-1 (btu1-1K350M; mpr1-1; or-r, tx-s, mp-r), a strain having a genetic makeup represented by btu1-1K350M/btu1-1K350M, chx1-1/chx1-1 (btu1-1K350M; chx1-1; or-r, tx-s, cy-r); and a strain having a genetic makeup represented by btu1-1K350M/btu1-1K350M (btu1-1K350M; or-r, tx-s). Examples of the three preferred strains include T. thermophila CU522 (mating type IV), T. thermophila CU725 (mating type VII), and T. thermophila CU727 (mating type V), respectively.
The invention further provides a transgenic Tetrahymena that contains at least a portion of an I. multifiliis i-antigen protein, preferably a portion of an I. multifiliis i-antigen protein that includes a targeting amino acid sequence.
Further, the invention provides a transgenic cell containing a heterologous protein that includes at least one targeting amino acid sequence encoded by an i-antigen-encoding nucleotide sequence from I. multifliis. The transgenic cell is not limited and can be a bacterial cell, a fungus cell, a protozoan cell, or an animal cell, for example. The targeting amino acid sequence is an N-terminal targeting sequence, a GPI cleavage/attachment sequence, or both. Preferably, the the heterologous protein is displayed on the surface of the plasma membrane of the transgenic cell.
The invention also provides a method for making a polyclonal antibody. An antigenic polypeptide is expressed on the surface of the plasma membrane of a transgenic protozoan host cell, then the transgenic protozoan host cell is administered to an animal to generate an antibody response to the antigenic polypeptide. In another aspect of this embodiment of the invention, the antigenic polypeptide is cleaved from the surface of the host cell, isolated, then administered to an animal to generate an antibody response to the antigenic polypeptide. Optionally, the antibody is isolated from the animal.
The invention further provides a method for detecting antibodies to an antigenic polypeptide that involves expressing the antigenic polypeptide on the surface of a transgenic protozoan host cell; exposing the protozoan host cell to an antibody; and determining whether the protozoan host cell is immobilized. Immobilization of the protozoan host cell is indicative of the presence of antibodies to the antigenic polypeptide. This method can be used to detect antibodies to a pathogenic parasite in the bodily fluid of a patient suspected of being infected with the parasite.
Also provided by the invention is a method for screening drugs for the ability to bind a polypeptide. Preferably, the drug to be screened is one that has cross-linking capability, but the drug screening method of the invention is not limited to just those drugs. The polypeptide is expressed on the surface of a transgenic protozoan host cell and the host cell is exposed to the drug. Binding of the drug is evidenced by an observable change in the swimming pattern of the host cell which may, but need not, included complete immobilization of the host cell. In the case of a drug having cross-linking capability, the drug is caused to cross-link. Cross-linking of the drug will generally immobilize the host cell, indicating that the drug has bound to the polypeptide.
The invention further provides a vaccine containing a transgenic nonpathogenic immunogenic protozoan which exhibits a surface-displayed antigenic polypeptide. The vaccine can be a live vaccine or a killed vaccine. In a preferred embodiment, the nonpathogenic immunogenic protozoan is Tetrahymena and the antigenic polypeptide includes at least an antigenic portion of an I. multifiliis i-antigen protein.
Also provided by the invention is a method for stimulating an immune response in a vertebrate that includes delivering to the vertebrate a transgenic nonpathogenic immunogenic protozoan comprising a surface-displayed antigenic polypeptide.
The invention further includes a novel recombinant method for producing a polypeptide. A heterologous nucleic acid encoding the polypeptide is introduced into a protozoan host cell, preferably a protozoan host cell that is sensitive to paclitaxel, to yield a transgenic protozoan host cell selectable by negative selection using paclitaxel. The polypeptide is then expressed in the transgenic protozoan host cell. Optionally, the polypeptide is displayed on the plasma membrane of the transgenic protozoan host cell and cleaved to release the polypeptide. Also optionally, the polypeptide is isolated from the transgenic protozoan host cell. In another aspect, the recombinant method for producing a polypeptide includes introducing a heterologous nucleic acid encoding the polypeptide into a host cell to yield a transgenic host cell, wherein the polypeptide comprises at least one targeting amino acid sequence encoded by an i-antigen-encoding nucleotide sequence from I. multifiliis, then expressing the polypeptide in the transgenic host cell.
DEFINITIONS 
An “expression vector” is a nucleic acid molecule containing a nucleotide sequence encoding a polypeptide that is capable of being expressed in a host cell. Generally, when the term “vector” or “vector construct” is used herein, an expression vector is intended. Typically, an expression vector is a DNA molecule that contains a gene, and expression of the gene is under the control of regulatory elements that can, but need not, include one or more constitutive or inducible promoters, tissue-specific regulatory elements, and enhancers. Such a gene or other nucleic acid fragment is said to be “operably linked” to the regulatory elements.
A “cloning vector” is a nucleic acid molecule, typically a DNA molecule, that contains one or more restriction endonuclease recognition sites at which foreign nucleic acid fragments can be inserted in a determinable fashion without loss of an essential biological function of the vector, and often contain a nucleotide sequence encoding a detectable and/or a selectable marker (i.e., “marker genes”) that can be used to identify and/or select cells transformed with the cloning vector. Marker genes typically include nucleic acid fragments that encode polypeptides which can confer a phenotypic characteristic to the transformed cell, such as antibiotic resistance, test compound metabolism, and the like.
Cloning and expression vectors can include naturally occurring or modified DNA or RNA, and can take the form of a plasmid, cosmid, or bacteriophage. Vectors can be linear or circular.
The terms “exogenous” or “heterologous,” which are used interchangeably herein, denote some item, typically a nucleic acid fragment or a protein, that is foreign to its surroundings. In particular, the terms apply to nucleic acid fragments that have been inserted into a host organism, but are not found in the normal genetic complement (i.e., genome) of the host organism. A nucleic acid fragment that is heterologous with respect to an organism into which it has been inserted or transferred is sometimes referred to herein as a “transgene.” A “transgenic” organism (whether microorganism or an animal) is a host organism that has been genetically engineered to contain exogenous (heterologous) nucleic acid fragments, including vectors. Introduction of the heterologous nucleic acids into a host cell to create a transgenic cell is not limited to any particular mode of delivery, but includes, for example, microinjection, adsorption, electroporation, particle gun bombardment, liposome-mediated delivery and the use of viral and retroviral vectors.
Preferably, the heterologous nucleic acid fragments are stably integrated into the host genome, but they may, alternatively, be maintained extrachromosomally. The heterologous nucleic acid fragments may but need not be inheritable.
A nucleic acid fragment is “excised” from genomic DNA by isolating genomic DNA from the host, as by cutting the nucleic acid fragment at one or more predetermined sites, for example at a restriction enzyme recognition site.
An excised nucleic acid fragment can be ligated into a vector and assayed for recombination. Successful recombination can be detected, either directly or indirectly, as by using a laboratory assay or other detection procedure. Preferably, the presence or absence of a recombinant nucleic acid fragment is detectable by way of a chemical or biological assay. Detection can be mediated through the use of “reporter” nucleic acid fragments typically contained in the vector, such as a particular nucleic acid fragment that can confer metabolic pathways for particular nutrient utilization or antibiotic resistance. For example, in a lac operon-based mutation detection system commonly used in E. coli, a mutation in a lacI mutation target gene affects the expression of the lacZ reporter gene, and expression of the reporter gene is detectable in an E. coli host by assaying the ability of the host to produce the lacZ gene product (β-galactosidase) and thus metabolize a chromogenic substrate.
An “immunogenic” or “immune system stimulating” polypeptide, also referred to as a polypeptide antigen or an antigenic polypeptide, is one that activates at least one cell type of the immune system of an animal, including phagocytic cells such as macrophages, as well as T cells and B cells. An example of an immune-stimulating ciliated protozoan is one that displays a polypeptide antigen on its cell surface such that an immune response to the antigen is elicited in an animal exposed to the immune-stimulating protozoan. Likewise, an immunogenic composition comprises an immunogenic polypeptide and optionally contains a pharmaceutically acceptable buffer, such as phosphate buffered saline (PBS) or another buffer, recognized in the art as suitable and safe for introduction of proteins into a host to stimulate the immune system.
As used herein, the term “effective amount” refers to an amount of a substance that is effective to produce a desired result. For instance, an effective amount of an immune-stimulating composition is one that is effective to activate cells of the immune system, including phagocytic cells such as macrophages, as well as T cells and B cells. The actual amount varies depending upon the health and physical condition of a subject's immune system, i.e., to synthesize antibodies, the degree of protection desired, the formulation prepared and other relevant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials.
As used herein, the term “polypeptide” refers to a chain of amino acids linked through peptide bonds between an α-carboxyl carbon of one amino acid residue and the α-nitrogen of the next amino acid. The term polypeptide is used herein as a general term that includes polypeptides of any length, including what are commonly referred to in the art as peptides, oligopeptides, and proteins. A “protein” contains one or more polypeptide chains that fold to adopt a particular conformation that has some type of biological activity or function. The properties and function of any particular protein are generally determined by the physical and chemical properties of the molecule. The order of the nucleotides in a nucleic acid fragment determines the order of amino acid residues in a polypeptide and protein, i.e., the nucleic acid fragment “encodes” the polypeptide (protein).



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a schematic of the vector pBICH3.
FIG. 2 shows full restriction maps of (a) BTU1::neo1 construct (SEQ ID NO:1 and its complement, SEQ ID NO:2) and (b) pBICH3 vector construct (SEQ ID NO:3), as shown in as shown in FIG. 1 (and its complement, SEQ ID NO:4); positions of restriction endonucleases sites are shown, with unique sites underlined; translation start and stop sites are boxed.
FIG. 3 shows (a) an alignment of the deduced amino acid sequences of 48 kD (SEQ ID NO:5, upper line) and 55 kD (SEQ ID NO:6, lower line) i-antigens of I. multifiliis, where asterisks indicate identities between the two deduced protein sequences, double dots indicate highly homologous amino acids, and single dots indicate moderately homologous amino acids; boxes indicate conserved regions; (b) an alignment of the nucleotide sequences of the coding regions of the IAG48 [G1] gene (SEQ ID NO:7, upper line) and the IAG55 [G5] gene (SEQ ID NO: 8, lower line) of I. multifiliis, where asterisks indicate identities between the two nucleotide sequences.
FIG. 4 is a schematic showing the experimental design used to introduce the Ichthyophthirius i-antigen into the BTU1 locus of T. thermophila. A hybrid gene composed of the I. multifiliis i-antigen coding sequence inserted between regulatory sequences of BTU1 is integrated into the endogenous paclitaxel-sensitive BTU1 locus by homologous recombination.
FIG. 5 is a Western blot analysis identifying a putative 48 kD I. multifiliis i-antigen expressed by transgenic T. thermophila. 
FIG. 6A-6D are photomicrographs using immunofluorescence for detection of surface expression of a putative 48 kD I. multifiliis i-antigen in transgenic T. thermophila. 
FIG. 7 shows Western blots of (a) total protein extracts of transformant cells; and (b) total culture medium from which transformed cells were removed, probed using anti-I. multifiliis i-antigen antibodies; the load of the medium shown in (b) is about 1/30th of the load of the cells shown in (a).
FIG. 8 shows a Western blot of a total protein extract from Tetrahymena transformed with chicken ovalbumin, probed with anti-chicken ovalbumin antibodies.
FIG. 9 is Western blot showing expression and secretion from a transformed Tetrahymena of a G1 i-antigen with C-terminal truncation.
FIG. 10 shows ELISA results for fish vaccinated with Tetrahymena expressing (a) membrane associated G1 i-antigen and (b) secretary form of G1 i-antigen.
FIG. 11 is a 10× magnification of serotype A I. multifiliis an immobilization test conducted using sera (1:20 dilution) from (a) fish vaccinated with live Tetrahymena expressing neo (“anti-live Tneo,” the negative control) and (b) fish vaccinated with live Tetrahymena expressing the full-length 48 kD i-antigen protein from a G1 I. multifiliis isolate (“anti-live TG1”).



DETAILED DESCRIPTION
The invention provides a protein expression system that utilizes a protozoan, preferably a nonpathogenic ciliate, more preferably Tetrahymena, for the production of eukaryotic and prokaryotic polypeptides, including proteins. The protein expression system of the invention is useful to produce virtually any polypeptide for any purpose. It is suited to both large scale and analytical scale production of recombinant polypeptides, and is particularly useful for expression of polypeptides that are difficult to produce in conventional recombinant protein expression systems.
Ciliated Protozoa
Protozoa, particularly nonpathogenic protozoa, are well-suited for use as recombinant protein expression systems. Not only are many protozoa capable of secreting proteins, but they often contain an anchoring system (known as a GPI anchor) that allows surface expression, or “display,” of various endogenous proteins without secretion. Some protozoa, like Tetrahymena, have major membrane proteins that are GPI-anchored; they in essence contain a GPI-anchored coat of surface-displayed proteins on the plasma membrane. These displayed proteins can often be cleaved from the cell surface of a protozoan by phospholipase C (typically isolated from B. thuringiensis). Many nonpathogenic protozoa are fast-growing and inexpensive to culture. Nonpathogenic ciliated protozoa can be environmentally friendly if the desired genetic modifications are performed within their somatic genomes localized to the macronucleous; heterologous nucleic acids that have integrated into the macronucleus, such as those that disrupt the BTU1 gene in Tetrahymena, are lost when the protozoan undergoes the sexual process of conjugation. The old macronucleus disintegrates, and the new macronucleus is formed as a result of differentiation of the zygotic micronucleus. As a result, a nucleic acid that had integrated into the macronucleus is not inherited or otherwise perpetuated, a feature which enhances environmental safety by preventing heterologous nucleic acids from entering the gene pool.
Protozoa are also more effective than yeast in providing post-translational modifications to certain eukaryotic proteins. For example, yeast apparently lacks a number of post-translational modifications typically found on tubulins, such as acetylation of Lys40 in α-tubulin, polyglutamylation and polyglycylation of α- and β-tubulin (T. MacRae et al., Eur. J. Biochem. 244:265-278 (1997)). On the other hand, these tubulin modifications were found in Tetrahymena and other ciliates like Paramecium (J. Gaertig et al., J. Cell Biol. 129:1301-1310 (1995)); V. Redeker et al., Science 266:1688-1691 (1994)). Ciliates, in particular, are excellent candidates for heterologous polypeptide expression; the presence of cilia vastly increases cell surface area, providing more opportunity for expression of GPI-anchored polypeptides.
A transgenic nonpathogenic ciliated protozoan of the invention is preferably a free-living ciliate; that is, it can propagate without a host. Examples of nonpathogenic free-living ciliates include Tetrahymena, Paramecium, Blepharisma, Colpidium, Euplotes, Stylonichia and Oxytricha. More preferably, the free-living transgenic nonpathogenic ciliate is Tetrahymena. Tetrahymena can be grown in large volume cultures using a variety of inexpensive media including skimmed milk powder. Generation time is short (1.5-3 hr) and cells attain remarkably high density given their size ( ̃50 μm in length). Indeed, it has been reported that fermentation in perfused bioreactors has permitted growth to concentrations as high as 2.2×107 cells/ml, equivalent to a dry weight of 48 g/l. See, e.g., T. Kiy et al., Appl. Microbiol. & Biotech., 38:141-146 (1992). Further, Tetrahymena has the ability to secrete proteins into the growth medium, and mutant strains defective in the release of hydrolytic enzymes have been isolated (P. Hunseler et al., Dev. Genet. 13:167-173 (1992). Mutant strains lacking or exhibiting reduced levels of secreted hydrolytic proteases are preferred for surface expression or secretion of a heterologous polypeptide that is sensitive to proteolysis by hydrolytic enzymes. Finally, a large part of the cell metabolism is devoted to the production of abundant surface membrane proteins known as immobilization antigens (i-antigens), whose expression is tightly regulated by environmental conditions. This feature makes Tetrahymena a preferred host because expression of a heterologous protein containing an endogenous GPI anchor can potentially be controlled by changes in temperature. J. R. Preer, The Molecular Biology of Ciliated Protozoa, pp. 301-339 (ed. J. G. Gall), Academic Press, New York (1986).
Tetrahymena, which has genomic DNA generally on the order of 75% A-T, offers additional advantages as a host system for the cloning and expression of genes from other organisms with AT-rich genomes. For example, a number of human pathogens (for example, malarial plasmodia, mycoplasmas, etc.) have extremely AT-rich genomes. Genomic DNA contains four bases (A, T, C, G), and DNA duplexes typically hybridize by means of A-T and G-C base pairing. In the genomes of many organisms, the amounts of A, T, C, and G are relatively equal, thus their genomic DNA contains roughly the same number of A-T and G-C base pairs. “AT-rich” genomes or nucleic acids are genomes or nucleic acids that have an AT content of more than about 50% of the total bases in the fragment, preferably about 65% or more, and more preferably about 70% or more. Notably, AT-rich fragments are inherently unstable in conventional systems such as E. coli, making cloning genes from AT-rich organisms into conventional systems difficult. As an AT-rich host, however, T. thermophila is expected to stably maintain heterologous nucleic acid fragments having “AT rich” sequences.
Tetrahymena, like other ciliates, utilizes UAA and UAG as codons for the amino acid glutamine, while most other organisms recognize those as termination codons. Thus, Tetrahymena is particularly useful to express heterologous genes that are derived from other ciliates. Expression of ciliate genes in conventional (eukaryotic and prokaryotic) protein expression systems often requires that the ciliate gene be mutated so as to utilize the conventional nucleic acid code in order to produce a full-length protein.
Furthermore, immobilization of Tetrahymena in culture with specific antibodies offers a potential bioassay for detection of specific antibodies in biological samples that would shorten the time and lower the cost for screening, and would obviate the need for chemical detection substrates used in more standard diagnostic tests.
Transformation of the Protozoan Host with a Heterologous Nucleic Acid
The protozoan host is transformed with a heterologous nucleic acid, which can be either integrated into the host's genome or maintained extrachromosomally on an autonomous plasmid or other construct. The heterologous nucleic acid encodes a polypeptide that is expressed by the resulting transgenic host. There is no limitation on the type of heterologous polypeptide that can be expressed in the protozoan host. The polypeptide coding region of the vector construct can, for example, be a coding region derived from a pathogenic protozoan, or from another eukaryotic or prokaryotic organism. As already noted, a protozoan host such as Tetrahymena is especially useful as a vehicle for creating an expression library for organisms with AT-rich genomes, particularly pathogenic organisms, such as Plasmodium (the protozoan agent of malaria). Genomic fragments from these organisms are difficult to clone and stably maintain in E. coli. Another example of a preferred heterologous nucleic acid sequence is one that encodes at least a portion of an antigenic polypeptide in that is capable of stimulating an immune response in an animal upon exposure to the polypeptide. In a particularly preferred embodiment of the invention, a transgenic ciliated protozoan displays an antigenic polypeptide on its cell surface.
The location of the expressed polypeptide is determined by the protein targeting sequences, if any, encoded by the heterologous nucleic acid and thereby incorporated into the resulting polypeptide. The heterologous polypeptide can accumulate in the cytosol, can be secreted from the host cell, or can be embedded in or anchored to the host cell plasma membrane, as is further described below.
Preferably, the heterologous nucleic acid is introduced into the ciliate host on an expression vector that is capable of integrating into the host's genome. In a particularly preferred embodiment of the invention, expression vectors operate by way of homologous recombination with a highly expressed gene that is endogenous to the protozoan host, such as a β-tubulin gene as described below. On the other hand, an expression vector that does not rely on the regulatory sequences of an endogenous gene for expression can, optionally, be maintained extrachromosomally in the ciliated protozoan host cell. An expression vector maintained as an extrachromosomal element is preferably an rDNA-based vector containing ori from Tetrahymena rDNA, which is known to support extrachromosomal replication. Such a vector further includes a 5′ regulatory region from an endogenous Tetrahymena gene containing a promoter region operably linked to the heterologous coding region and, optionally, a 3′ regulatory region from the same or, preferably, a different Tetrahymena gene. For example, expression vectors can contain regulatory regions from ciliate genes such as HHF1, rp129, BTU1, BTU2, SerH3, and those encoding actin.
Expression Vectors
Expression vectors useful for transforming protozoa in accordance with the invention can be generally classified into three types: replacement vectors, rDNA vectors, and rDNA-based vectors. Replacement vectors accomplish DNA-mediated transformation by replacing or altering endogenous genes using homologous recombination. Integration of the heterologous nucleic acid into the host's genome at the targeted site is accomplished via homologous recombination involving a double crossover event with the vector containing the heterologous nucleic acid. An example of an expression vector useful for genomic incorporation of a heterologous nucleic acid by replacement is one that includes a heterologous coding sequence flanked by portions of the endogenous BTU1 gene of Tetrahymena. 
A replacement vector thus preferably includes a 5′ region, followed by a heterologous coding region, followed by a 3′ region, wherein at least a portion of each of the 5′ and 3′ regions is complementary to 5′ and 3′ regions on an endogenous gene of the host, to allow for genomic integration of the heterologous coding region via homologous recombination. The 5′ and 3′ regions of the vector optionally contain regulatory elements, such as a promoter and a terminator; alternatively, the necessary regulatory elements are supplied by the endogenous gene into which the heterologous coding region integrates. Preferably, the 5′ and 3′ regions of an expression vector useful in Tetrahymena include sequences complementary to the BTU1, BTU2, SerH3 or HHF1 genes of Tetrahymena. Optionally, a replacement vector further includes a nucleotide sequence encoding a selectable marker, such as neo. Preferably the marker sequence is under the control of its own promoter, thus another regulatory region is included 5′ to the sequence encoding the selectable marker; and example is the neo2 cassette.
β-Tubulin is a cytosolic protein in Tetrahymena that is a monomeric constituent of cytoskeletal elements known as microtubules. An α/β tubulin dimer is the building block of microtubules, and both α-tubulin and βtubulin are essential proteins. T. thermophila expresses two major β-tubulin genes, BTU1 and BTU2, which encode identical β-tubulin proteins (J. Gaertig et al., Cell Mot. Cytoskel., 25:245-253 (1993)). It was determined that either of these two genes (but not both at once) can be disrupted without a detectable change in the cell phenotype.
Substitution of lysine (K) 350 by methionine (M) in the BTU1 gene to yield the Btu1-1K350M allele confers increased resistance to several microtubule-depolymerizing drugs (oryzalin, colchicine, vinblastin), and increased sensitivity to a microtubule-stabilizing agent, paclitaxel (J. Gaertig et al., Proc. Nat'l. Acad. Sci. USA 91:4549-4553 (1994)). The phenotype of the Btu1-1K350M allele is expressed even in the presence of wild-type copies of the second β-tubulin gene, BTU2. Cells carrying the btu1-1K350M allele can be transformed to paclitaxel resistance by gene replacement of btu1-1K350M with a wild-type BTU1 gene fragment, thus eliminating the need to incorporate a means for positive selection. Because the BTU1 gene is not essential for survival, any loss-of-function mutation of btu1-1K350M in the presence of wild-type BTU2 gene confers paclitaxel resistance.
It has been discovered as part of this invention that heterologous nucleic acids can be inserted into a β-tubulin gene of T. thermophila for successful cell-surface expression that is advantageously maintained by way of negative selection. Expression of a heterologous protein in T. thermophila is preferably accomplished using a transgenic T. thermophila that contains the negatively selectable Btu1-1K350M allele of the β-tubulin gene (BTU1) to direct heterologous nucleic acid fragments to this highly expressed locus by homologous recombination. A transformed cell line can thus be readily identified by paclitaxel selection, in that successful transformation restores paclitaxel resistence.
Accordingly, a preferred expression vector in accordance with the present invention preferably includes a nucleic acid fragment capable of integration into either the BTU1 or BTU2 gene of T. thermophila, preferably the BTU1 gene, more preferably the Btu1-1K350M allele of the BTU1 gene. The BTU1 gene contains 5′ and 3′ regulatory regions that flank the coding region; hence the preferred expression vector contains at least a portion of each of these regulatory regions, which portions are sufficient to allow for homologous recombination with the endogenous gene. The flanking sequences of BTU1 that are included in the vector (e.g., FIGS. 1 and 2) allow for targeting of the heterologous coding region into the endogenous BTU1 gene via homologous recombination with the endogenous gene.
The protozoan host to be transformed with the vector is preferably T. thermophila which contains a β-tubulin gene (BTU1) wherein lysine 350 is substituted by methionine (btu1-1K350M). The expression vector disrupts the btu1-1K350M gene by homologous recombination-mediated insertion of a heterologous nucleic acid, thereby restoring resistence to paclitaxel in the resulting transgenic host. Homologous recombination can take place at sites within the coding region of the highly expressed target gene or at sites that flank the gene target, which include but are not limited to flanking regulatory regions; all that is required is that the expression of the target gene be disrupted. When BTU1 is the target gene, a second β-tubulin gene (BTU2) remains available to provide the essential function of β-tubulin in vivo, such that BTU1 can be fully replaced with btu1-1K350M (or heterologous nucleic acid sequence) without adverse effects to the organism. When T. thermophila having the btu1-1K350M allele of the BTU1 gene is used as the host, transformants can be maintained by negative selection, since transformed mutants are not sensitive to paclitaxel while nontransformed mutants are. Transformants are this readily identified by negative selection by growth on in media containing paclitaxel; there is no need to engineer drug-resistance or other means of selection into the genome of the transgenic host. Additionally, there is no limitation on the nature of the heterologous nucleic acid sequence that can be targeted to the BTU1 locus of T. thermophila. 
The heterologous nucleic acid sequence that is incorporated into the host genome in accordance with the present invention optionally encodes a selectable marker. For example, an expression vector can include a BTU1 derivative, BTU1-2::neo1 (see FIG. 2) which substitutes the coding region of a prokaryotic gene, neo1, for that of BTU1, to provide a means for positive selection of transformants. The neo1 gene confers resistance to paromomycin in T. thermophila, and a BTU1-2::neo1 fragment can then be used to generate BTU1 gene knockouts by homologous recombination and positive selection with paromomycin. Of course, when the host organism is a T. thermophila mutant containing the btu1-1K350M allele of BTU1, transformants are identified with negative selection and a positive selection is not necessary.
Optionally, a replacement vector for use in Tetrahymena includes a temperature-regulatable promoter region to facilitate controlled expression of the heterologous coding region. The temperature-regulatable promoter can be supplied instead of or in addition to another promoter, such as the promoter region of the endogenous BTU1 gene. The temperature-regulatable promoter is preferably positioned within the 5′ untranslated region of the vector, more preferably between a 5′ BTU region and the heterologous coding region. Because Tetrahymena SerH3 encodes an i-antigen whose expression is temperature dependent, the 5′ regulatory region of the SerH3 gene of Tetrahymena may include a temperature-regulatable promoter that is useful in the invention.
Also optionally, the replacement vector contains a second promoter region, in addition to the promoter region supplied by the endogenous target gene, for enhanced expression of the heterologous protein.
In a representative example of the invention, the expression vector (pBICH3, FIG. 1) includes the entire coding sequence of the i-antigen gene inserted in a correct translational frame between the regulatory sequences of the BTU1 gene. This vector contains a complete plasmid sequence commercially available under the trade designation PBLUESCRJPT SK (+), from Stratagene, La Jolla, Calif., and is generally useful for integration of any heterologous coding region into the β-tubulin gene of T. thermophilis. One skilled in the art will recognize that other plasmids may be equally suitable, such as those commercially available under the trade designation pCRScript, from Stratagene, La Jolla, Calif.; pGEM from Promega, Madison, Wis.; and pCRII, from Invitrogen, Carlsbad, Calif.
FIG. 2(b) shows the full restriction map of pBICH3, represented by SEQ ID NOs:3 and 4. The complete nucleic acid sequence (SEQ ID NO:7) and deduced amino acid sequence (SEQ ID NO:5) of the DNA encoding the 48 kD Ich i-antigen is presented in FIG. 3. Nucleic acid sequence SEQ ID NO:7 of FIG. 3(b) is included in pBICH3 at base pair 1000 to base pair 2325 as shown in FIG. 2(b). The fragment GCAAGCTTG at base pair 991 to 999, which follows the start codon ATG and immediately precedes the i-antigen coding sequence, is a cloning residual from the parent construct, HHF1::neo (R. Kahn et al., Proc. Nat'l. Acad. Sci. USA 90:9295-9299 (1993)). The resulting vector construct can be propagated in E. coli as a shuttle vector as well.
Gene regulatory elements useful in such transformation systems include both upstream (5′) and downstream (3′) regulatory elements. For example, in prokaryotic and eukaryotic genes, the upstream region contain promoter elements that specify correct initiation of mRNA synthesis. Although classical promoters have not yet been identified in ciliates, examination of the upstream regions of various ciliate genes shows the presence of sequence elements that are highly conserved, and which are known to be required for gene expression in a wide variety of other eucaryotic systems. For example, TATA sequences that play a critical role in transcription initiation in most eukaryotes, are present in the 5′ flanking regions of a number of ciliate genes (for example, Cupples et al. (1986) Proc. Natl. Acad. Sci. USA 83:5160-5164; Brunk et al. (1990) Nucl. Acids Res. 18:323-329; Tondravi et al. (1990) Mol. Cell. Biol. 10:6091-6096; Prat et al. (1986) J. Mol. Biol. 189:47-60). Less common eucaryotic promoter elements (consisting of CCAAT sequences) are also present. The upstream regions of ciliate genes contain information that is both necessary and sufficient for promoter function.
Because promoter elements are subject to differential regulation and have profound effects on RNA transcription levels in vivo, different promoters can be used for the expression of the heterologous nucleic acid. These include the promoters from the actin, histone H4 and SerH3 i-antigen genes from Tetrahymena thermophila (Cupples et al. (1986) Proc. Natl. Acad. Sci. USA 83:5160-5164; Brunk et al. (1990) Nucl. Acids Res. 18:323-326; and Tondravi et al. (1990) Mol. Cell. Biol. 10:6091-6096). Expression from the actin promoter is typically constitutive, while expression from the histone and SerH3 promoters are cell-cycle and temperature-dependent, respectively. Expression vectors capable of autonomous replication must include a promoter element; however, when the heterologous nucleic acid is genomically integrated, inclusion of a heterologous promoter element in the construct is optional, as the 5′ regulatory region of the endogenous gene can be utilized instead.
The sequences required for correct 3′ processing of mRNA transcripts in ciliates (that is, transcription termination and polyadenylation) lie in close proximity to (and approximately 100 bp on either side of) the 3′ terminus of most ciliate RNA transcripts. For example, an additional region from the 3′ end of the SerH3 i-antigen gene from T. thermophila can be added to the heterologous nucleic acid prior to cloning and expression.
rDNA vectors and rDNA-based vectors, including the typical components of each, were discussed in detail in the background. Although not preferred embodiments of the invention, these vectors can nevertheless be effectively used to express heterologous proteins in Tetrahymena. Depending upon the vector design, rDNA vectors and rDNA-based vectors can integrate into the host genome, for example via homologous recombination or a single cross-over event, or they can be maintained extrachromosomally. Either type of vector can be constructed to include a heterologous protein containing an N-terminal targeting sequence, a C-terminal targeting sequence (i.e., a GPI anchor) or both, for targeted expression of a heterologous protein in Tetrahymena and other ciliates. Preferably, the N-terminal targeting sequence and/or the C-terminal targeting sequence is derived from an i-antigen of I. multifiliis. 
Targeted Protein Production
Advantageously, the invention allows the recombinant production of a heterologous polypeptide to be targeted within or outside of a cell. The targeting mechanism is not limited to protozoan hosts but can be used in any type of cell, for example a mammalian cell, a yeast cell, a protozoan cell, or a bacterial cell. Preferably, however, the cell is a cell of a ciliated protozoan. Optionally, therefore, a recombinant genetic construct of the invention (i.e., expression vector or transgenic organism) contains a heterologous nucleic acid that encodes a protein comprising an N-terminal protein targeting sequence or a C-terminal protein targeting sequence, or both. An N-terminal targeting sequence directs a protein to the endoplasmic recticulum (ER), and as a result can cause the protein to embed in the plasma membrane or to be secreted out of the cell. A C-terminal targeting sequence, specifically a GPI anchor, can cause the protein to be displayed on the membrane surface of the host cell. These targeting sequences can be either endogenous to the host cell, as where the heterologous nucleic acid is introduced into the host's genome by way of homologous recombination with a native coding sequence, or heterologous to the host cell.
Thus, to direct a heterologous polypeptide to the plasma membrane surface (“surface display”), the vector construct preferably encodes a heterologous polypeptide comprising (I) an amino terminal signal peptide and (2) a GPI cleavage/attachment sequence (i.e., a “GPI anchor”). The expression system of the invention is thus uniquely suited for expression of membrane proteins such as receptor proteins or proteins that utilize a GPI anchor. In other applications in which secretion of a heterologous polypeptide is intended, the vector construct preferably encodes a heterologous polypeptide comprising an amino terminal signal peptide but not a GPI cleavage/attachment sequence. Finally, for intracellular production of the heterologous polypeptide, the heterologous polypeptide encoded by the vector construct preferably includes neither an amino terminal signal peptide nor a GPI cleavage/attachment sequence.
Surprisingly, surface display of heterologous proteins in Tetrahymena is not limited to the use of a GPI anchor modification domain that is native to Tetrahymena. It has been discovered, for example, that proteins that contain a GPI anchor derived from an immobilization antigen (“i-antigen”) of Ichthyophthirius multifliis are displayed on the membrane surface of Tetrahymena (Example II). Likewise, it is not necessary to use N-terminal signal peptides derived from Tetrahymena; it is shown in Example VI that the N-terminal signal peptides of both I. multifiliis i-antigen and T. cruzi gp-72 protein work well in Tetrahymena. 
Thus, protein targeting sequences can be derived, for example, from I. multifiliis, T. cruzi, Paramecium, Dictyostelium, Leishmania, Toxoplasma, Crithidia, Plasmodium and Chlamydomonas. An example of an N-terminal protein targeting sequence from T. cruzi is the N-terminal signal peptide of the gp-72 surface protein. Heterologous protein targeting sequence obtained from I. multifiliis are described in T. Clark et al., Proc. Nat. Acad. Sci. USA, 89:6363-6367 (1992) and T. Clark et al., Gene 229:91-100 (1999); additional exemplary N-terminal and C-terminal targeting sequences, derived from the 48 kD and 55 kD I. multifiliis i-antigens (SEQ ID NOs:5 and 6, FIG. 3(a)), are described in provisional U.S. patent application Ser. No. 60/124,905, filed Mar. 17, 1999. The coding sequence of an I. multifiliis i-antigen includes two putative signal elements. For example, the N-terminal portions (i.e., about the first 20 amino acids) of the 48 kD i-antigen (SEQ ID NO:5, FIG. 3(a)) and the 55 kD i-antigen (SEQ ID NO:6, FIG. 3(a)) form highly hydrophobic domains which are similar to the signal peptides required in other organisms for translocation of newly translated polypeptides into the endoplasmic reticulum (ER). The C-terminal portions (i.e., about the last 20 to 23 amino acids) of the 48 kD i-antigen (SEQ ID NO:5, FIG. 3(a)) and the 55 kD i-antigen (SEQ ID NO:6, FIG. 3(a)) contain sequences that are homologous to the signals required for addition of a glycosylphosphatidylinositol (GPI) anchor and membrane anchoring of surface-displayed polypeptides. Surprisingly, the targeting signals of the I. multifiliis 48 kD i-antigen have been discovered according to the invention to be fully functional in Tetrahymena, causing surface display on the Tetrahymena plasma membrane of the i-antigen of I. multifiliis. Heterologous fusion proteins comprising one or both of these I. multifiliis signal sequences are therefore fully expected to be targeted correctly in Tetrahymena. For example, the targeting sequences of the I. multifiliis i-antigen can be used for surface display in Tetrahymena of heterologous surface membrane proteins such as surface antigens or receptors. Moreover, these targeting sequences are also expected to allow surface display or secretion of a polypeptide that is not normally expressed on a cell surface. For example, the protein expression system of the invention can be used for surface display of proteins that may be toxic to the cell when expressed intracellularly, such as proteases that can degrade Tetrahymena's own essential cytosolic proteins.
It should be understood that this aspect of the invention involving protein targeting using, for example, N-terminal and C-terminal targeting sequences from I. multifiliis and other protozoa applies not just to protein targeting in protozoa but in other cells such as bacterial cells, fungus cells and animal cells including vertebrate cells such as mammalian cells.
Further, other types of targeting sequences are well-known and can be used in the practice of the invention. For example, targeting to the surface of a ciliate can also be achieved if the protein includes a known transmembrane domain, such as the C-terminal 80 amino acids of human membrane cofactor, in place of a GPI anchor (see e.g., J. Seeber et al., J. Cell Sci., 111:23-29 (1998)). In this embodiment, the protein can be partially embedded in the membrane and partially exposed on the outside of the cell.
It should also be understood that recombinant genetic constructs of the invention encode proteins that preferably do, but need not, contain N-terminal and/or C-terminal targeting sequences; a protein without such signaling sequences will simply remain in the cytosol of the host cell.
Cell Surface Expression of Antigens
The ability to express polypeptides on a protein surface, in particular, gives this system advantages over others known in the art for many purposes. For example, antigens, including haptens, can be expressed on the cell surface as fusion proteins, cleaved, isolated, and injected into laboratory animals to generate antibodies for further use. Alternatively, antigens expressed on the surface of a host cell can be used to identify antibodies directly using a in vitro immobilization reaction or chemokinesis of swimming cells. Antisera directed against the i-antigens of hymenostomatid ciliates (including Paramecium, Tetrahymena and Ichthyophthirius spp.) cross-link cilia and cause rapid immobilization of corresponding cell types in culture (J. Preer, “Surface Antigens of Paramecium” in J. Gall, ed., Molecular Biology of Ciliated Protozoa, Academic Press, London, 301-339 (1986); F. Caron et al., Ann. Rev. Microbiol. 43:23-42 (1989); Clark et al., Ann. Rev. Fish Dis. 5:113-131 (1995)). For example, an immobilization assay can be conducted on the transgenic cells to detect antibody in serum samples of a parasite-infected patient. A positive reaction is detected by immobilization of the live transgenic protozoan cells, due to cross-linking of antibodies bound to surface-displayed parasitic proteins. This method can be extended to detect serum antibodies to other bacterial, parasitic, or fungal infections or diseases, using a live transgenic protozoan genetically engineered in accordance with the invention to display the appropriate antigen on its surface. Likewise transgenic cells of the invention that display antigens on their surface can be used to isolate and purify antibodies. Screening of chemical agents (drugs) for the ability to bind to polypeptides, and purification of drugs thus identified, can also be readily accomplished using the invention, as long as the candidate drugs possess cross-linking capability. Cross-linking capabilities include the provision of multiple potential binding sites on the candidate drugs, or the addition of chemical or radiation-dependent cross-linking sites on the candidate drugs. In the latter case, cross-linking is initiated after binding of the drug to the live ciliate, and the mechanism for cross-linking must be selected such that it does not itself cause immobilization of the transgenic ciliate. For example, the protein expression system could be used for screening multivalent ligands that bind to human neurotransmitter receptors expressed on the surface of transgenic Tetrahymena according to the invention.
Preparative Protein Production
The invention includes a method for producing a polypeptide that involves introducing into a ciliated protozoan host an expression vector containing a heterologous nucleotide sequence encoding a polypeptide, then expressing the polypeptide. After the vector is introduced into the ciliate host, the host is cultured under conditions that allow expression of the coding region such that the polypeptide encoded by the coding region is produced. The polypeptide can be present within the host cell, secreted from the host cell or is anchored to the surface of the host cell. Optionally, the method further includes isolating the polypeptide. The amino acid sequence of the heterologous polypeptide encoded by the coding region of the vector used to transform the ciliate host optionally includes protein targeting sequences. The polypeptide produced by the transformed host preferably includes either an amino terminal signal peptide or a GPI cleavage/attachment site or both. More preferably, the polypeptide includes both an amino terminal signal peptide and a GPI cleavage/attachment site.
Transgenic Ciliate
The present invention also provides a ciliated protozoan, preferably a nonpathogenic ciliated protozoan, more preferably Tetrahymena, that has been genetically engineered to express a heterologous polypeptide, preferably on its cell surface. A surface-expressed heterologous protein is attached by way of a “GPI anchor” that is encoded by a GPI cleavage/attachment sequence. Preferably, the ciliate contains a vector containing a coding region that encodes the heterologous protein, wherein the coding region is integrated into the BTU1 gene of T. thermophila. 
Live and Killed Vaccines
Success in expressing polypeptides on the surface of a ciliated protozoan has immediate implications for vaccine development. Surface antigens are important targets of the humoral immune response against a wide range of microbial pathogens. Accordingly, the present invention provides a system for vaccination that makes use of surface expression of heterologous antigenic polypeptides encoded by heterologous nucleic acid fragments in a ciliated protozoan.
A vaccine effective for the prevention of infection in an organism is one that elicits the production of a protective immune response in an organism exposed to the vaccine. The immune response can be a cellular response and/or involve the production of antibodies. The goal of vaccination is to elicit a population of lymphocytes, which upon subsequent exposure to the disease causing agent, such as a parasite, proliferate and produce antibodies and/or effector cells specific to the parasite, resulting in protection against lethal infections.
The vaccine of the invention can be either a live vaccine or a killed vaccine. It is useful to prevent disease in vertebrates, including humans, dogs, cats, reptiles, poultry, cattle, swine and fish. Preferably, the vaccine of the invention is effective to prevent disease in fish, more preferably it is effective to prevent parasitic infection in fish. The vaccine preferably comprises a live or killed host ciliated protozoan having, attached to its plasma membrane and displayed on it surface, a heterologous antigenic polypeptide. The heterologous protein is preferably GPI-anchored to the plasma membrane. In a particularly preferred embodiment of the vaccine, the heterologous antigenic polypeptide that is surface expressed comprises all or an immunogenic portion of an immobilization antigen (“i-antigen”) of a pathogenic ciliated protozoan. I-antigens are surface protein that are generally abundant on the surface of a ciliate; an antibody that is specific for an i-antigen causes a loss of protozoan motility, and can cause agglutination of the cilia. Use of a whole cell vaccine, whether live or killed, has the additional advantage of potentially serving as an adjuvant, thus further stimulating the immune system of the recipient.
White spot disease, also called “Ich,” is a disease caused by the parasite I. multifiliis, a holotrichous ciliated protozoan which is an obligate parasite of freshwater fish. Under conditions of intensive aquaculture, Ich frequently has a high morbidity and mortality, resulting in significant financial losses to fish producers. Attempts to control or prevent I. multifiliis infections have met with only limited success. Killed I. multifiliis cells and I. multifiliis cilia alone do not elicit protective immunity. Nor has vaccination of fish with the cells or cilia of other ciliates, such as T. thermophila cells or cilia, generated protective immunity against Ich infection (Gratzek et al., U.S. Pat. No. 4,309,416). Chemical treatments are likewise unsatisfactory because carcinogenicity and/or toxicity are typically associated with these therapeutic agents. See Burkart et al., J. Fish Dis., 13:401-410 (1990), for a summary. Moreover, I. multifiliis can only be grown in association with its host, and efforts to produce i-antigens in conventional protein expression systems are inconvenient at best.
Significantly, Tetrahymena is nonpathogenic and is normally present in freshwater ecosystems. It thus represents an ideal vehicle for vaccination against I. multifiliis infection and other fish diseases. The use of T. thermophila for the expression and delivery of the antigens will make possible large-scale, cost-effective fish vaccination programs.
A vaccine against I. multifiliis infection preferably comprises live or killed T. thermophila that have been engineered according to the invention to express all or an immunogenic portion of an i-antigen from I. multifiliis on its surface. Preferably, the i-antigen used in the live or killed T. thermophila vaccine of the invention is encoded by i-antigen encoding sequences of either IAG48[G1] or IAG55[G5] (FIG. 3(b)). In a particularly preferred embodiment, the vaccine comprises transgenic T. thermophila wherein expression of the I. multifiliis i-antigen is achieved by insertion of the i-antigen into the endogenous btu1-1K350M locus. Because this transformant can be maintained by negative selection, a selectable drug-resistance gene does not need to be introduced into the transgenic host, eliminating the possible introduction of antimicrobial resistance genes into the environment upon release of transgenic Tetrahymena. 
In the ciliated protozoan genetic code, TAA and TAG encode glutamine, whereas they serve as stop codons in the “universal” genetic code. The presence of glutamine-encoding TAA and TAG codons in the native coding sequence of the i-antigen creates barriers to expression of this sequence in conventional bacterial gene expression systems. Advantageously, T. thermophila recognizes UAA and UAG codons as glutamine codons as does I. multifiliis. In addition, post-translational modifications, particularly glycosylation, are expected to occur more normally in organisms related to Ichthyophthirius (for example, Tetrahymena) than in prokaryotes such as E. coli, or more distantly related eukaryotes. Because such modifications can play a critical role in immune recognition, Tetrahymena is particularly advantageous in accordance with the present invention.
As shown in the following Examples describing the surface localization of Ichthyophthirius proteins in Tetrahymena IAG48[G1] transformants, the N-terminal and C-terminal protein targeting peptides associated with I. multifiliis i-antigen function appropriately in Tetrahymena, i.e., the antigenic protein is expressed on the surface of transgenic Tetrahymena. Moreover, the overall distribution of I. multifiliis antigens in transformed Tetrahymena cells bear a striking resemblance to the pattern seen in the parasite itself where they are found in ciliary and plasma membrane, and in the cell cortex in association with secretory mucocysts.
The invention further includes a method for vaccinating an animal that includes contacting the animal with a genetically engineered nonpathogenic ciliated protozoan, preferably Tetrahymena, so as to elicit a protective immune response in the animal to the heterologous antigen displayed on the surface of the protozoan host. For example, an animal can be exposed to an ingestable composition, such as food, water, or both, that contains an immunogenic genetically engineered nonpathogenic ciliate of the invention. Alternatively, an animal can be immersed in or sprayed with an aqueous solution that includes the immunogenic ciliate. For example, fish can be vaccinated in accordance with the invention by exposing the fish to a composition including transgenic T. thermophila expressing an antigenic polypeptide (e.g., the I. multifiliis i-antigen to vaccinate against white spot disease). The fish can be immersed in an aqueous solution comprising transgenic T. thermophila expressing the I. multifiliis i-antigen. Because the antigenic proteins are presented to the immune system, probably through the lateral line and gills, the fish can begin to produce protective antibodies to at least a portion of the I. multifiliis i-antigen.
The vaccine can also be administered by injecting the animal with live or killed genetically engineered nonpathogenic immunogenic ciliated protozoa, by injecting the animal with a purified or partially purified membrane fraction of cells of the genetically engineered nonpathogenic immunogenic ciliated protozoa, or by injecting the animal with cilia from cells of the genetically engineered nonpathogenic immunogenic ciliated protozoa. Additionally, genetically engineered protozoa that display an antigen on the surface according to the present invention can also be used to generate monoclonal antibodies directed to the surface-expressed polypeptide.
EXAMPLES
The following examples are provided for illustrative purposes only and are not intended to limit the scope of the invention.
The examples utilize many techniques well-known and accessible to those skilled in the arts of molecular biology, and in the transformation of Tetrahymena. Enzymes are obtained from commercial sources and are used according to the vendors' recommendations or other variations known in the art. Reagents, buffers and culture conditions are also known to the art. References containing standard molecular biological procedures include Sambrook et al. (1989) Molecular Cloning, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Wu (ed.) (1979) Methods Enzymol. 68; Wu et al. (eds.) (1983) Methods Enzymol. 100 and 101; Grossman and Moldave (eds.) (1980) Methods Enzymol. 65; Miller (ed.) (1972) Experiments in Molecular Genetics, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.; Old and Primrose (1981); Principles of Gene Manipulation, University of California Press, Berkeley, Calif.; Schlief and Wensink (1981) Practical Methods in Molecular Biology; Glover (ed.) (1985) “DNA Cloning”, Vols. I and II, IRL Press, Oxford, UK; Hames and Higgins (eds.) (1985) Nucleic Acid Hybridization, IRL Press, Oxford, UK; Setlow and Hollaender (1979) Genetic Engineering: Principles and Methods, Vols. 1-4, Plenum Press, New York, which are expressly incorporated by reference herein.
References containing molecular biological techniques, procedures and protocols that are particularly useful in ciliated protozoa include J. Boothroyd et al. (eds.) Molecular Approaches to Parasitology, John Wiley & Sons, New York and J. Gall (ed.) (1986) The Molecular Biology of Ciliated Protozoa, Academic Press, Inc., Orlando, Fla., both of which are also expressly incorporated by reference herein.
Abbreviations and nomenclature, where employed, are deemed standard in the field and commonly used in professional journals such as those cited herein.
Example I 
Plasmid Construction: pBAB1 and pICH3
The pBTU1 plasmid containing a 3.7 kb Bgl II/Hind III fragment of the Tetrahymena thermophila β-tubulin gene, BTU1, was used to construct a derivative, pBAB1, in which the entire coding sequence was replaced with the coding sequence of the neomycin resistance gene, neo1 (R. Kahn et al., Proc. Nat'l. Acad. Sci. USA 90:9295-9299 (1993)). Thus, the expression of neo1 gene on pBAB1 is driven by the flanking sequences of the BTU1 gene. The plasmid pBAB1 was used to construct another derivative in which the neo coding region was replaced with the entire coding sequence of the Ichthyophthirius i-antigen (isolate G1) pre-protein. T. G. Clark et al., Proc. Natl. Acad. Sci. USA, 89: 6363-6367 (1992). To this end, the pBAB1 plasmid was amplified with the NEO257 primer (5′-AGCCAGTCCCTTCCCGCTTCAGTGACAA-3′ (SEQ ID NO:9) (provided by J. Bowen and M. Gorovsky, University of Rochester, N.Y.) whose sequence encodes the antisense strand of the neo1 gene, and primer BTN3 (5′-CGGGATCCAGCGAACTGAATCGGTCAGCT-3′) (SEQ ID NO: 10), corresponding to the 3′ noncoding region of BTU1 located immediately downstream from the stop codon, TGA, and running in the same direction as the sense coding strand. The BTN3 primer contains a BamH I restriction site sequence at its 5′ end, positioned immediately downstream from the stop codon, TGA. The product of PCR amplification of pBAB1 using NEO257 and BTN3 primers contained the noncoding sequences of BTU1, an N-terminal half of the neo1 gene coding region and the vector sequence. A single Hind III site is located almost immediately downstream from the translation initiation codon, ATG, of the neo1 gene. The amplified product was digested with BamH I and Hind III to obtain a smaller fragment containing the entire flanking sequences of BTU1 and the plasmid vector. A plasmid carrying a 2 kb EcoR I genomic fragment of the Ichthyophthirius i-antigen gene was amplified with primers IC5 (5′-ACCCAGCTTGAAATATAATATTTTATTAATTTTAATT-3′) (SEQ ID NO:11) and IC3 (5′-AGGGATCCTCACAATAAATAGAAAGAAATAA3′) (SEQ ID NO:12). These primers amplified the entire coding sequence of the Ich i-antigen gene and introduced Hind III, and BamH I restriction sites at positions encoding the N-terminal and C-terminal end of the protein respectively and corresponding to the positions of the same restriction sites present on the amplified fragment of pBAB1. This PCR product was digested with Hind III and BamH I, and ligated to the BamH I-Hind III digest of amplified pBAB1 to give pBICH3 plasmid, which contains the entire coding sequence of the i-antigen gene inserted in a correct translational frame between the regulatory sequences of the BTU1 gene (see FIG. 1). This new hybrid gene was designated BTU1-4::MAG48[G1].
Example II
DNA-Mediated Transformation of T. thermophila 
Transformation
A Tetrahymena thermophila strain, CU522 (provided by Dr. Peter Bruns, Cornell University, Ithaca N.Y.) was used as a transformation host. This strain carries a single substitution (K350M) in the β-tubulin, BTU1 gene. This mutation was originally described for Chlamydomonas reinhardtii (Bolduc et al., Proc. Nat'l. Acad. Sci. USA 85:131-135 (1988)), and was later found to confer a similar phenotype in T. thermophila, namely, increased resistance to several microtubule depolymerizing drugs, such as oryzalin and colchicine, and increased sensitivity to a microtubule stabilizing agent, paclitaxel (J. Gaertig et al., Proc. Nat'l. Acad. Sci. USA 91:4549-4553 (1994)).
Cells were grown in 50 ml of SPP medium (J. Gaertig, Proc. Nat'l. Acad. Sci. USA 91:4549-4553 (1994)), supplemented with 100 U/ml penicillin, 100 μg/ml streptomycin and 0.25 μg/ml amphotericin B (SPPA medium), in 250 ml Erlenmayer flasks with shaking at 150 rpm at 30° C. Prior to transformation, the CU522 cells were grown to a density of about 6×105 cells/ml in SPPA with shaking at 30° C. Twenty-four hrs before transformation, 50 ml of growing cells were washed and suspended in 10 mM Tris-HCl (pH 7.5) buffer in the original volume. After 4-5 hrs starving cells were counted again, cell concentration adjusted to 3×105 cells/ml and cells left at 30° C. without shaking for another 18-20 hrs.
To target the BTU1 gene derivatives to the endogenous BTU1 locus of T. thermophila, either pBAB1 or pBICH3 plasmids were digested with Sac I and Sal I restriction endonucleases to separate the insert (either BTU1-2::neo1 or BTU1-4::IAG48[G1]) from the plasmid. Fifty micrograms of digested DNA was purified by a single phenol/chloroform/isoamyl alcohol (25:24:1) extraction followed by chloroform/isoamyl alcohol (24:1) extraction, precipitated with an equal volume of isopropyl alcohol in the presence of 0.15 M sodium acetate, dried and resuspended at 1 mg/ml.
The transformation method used in this study targets genes into the somatic macronucleus of vegetative cells using biolistic bombardment (D. Cassidy-Hanley et al., Genetics 146:135-147 (1997)). Ten micrograms of linearized plasmid DNA was used to coat 60 mg of 0.6 μm gold particles (Bio-Rad) using the Sanford Large Batch DNA Coating Method, as described by J. C. Sanford et al., Technique, 3:3-16 (1991). An aliquot of 2.4×107 of starved cells was spun down at 600×g for 3 min, washed with 45 ml of 10 mM Tris (pH 7.5) and resuspended in 3 ml of Tris buffer. One ml of cells was bombarded using 10 μg of DNA-coated gold particles at 900 psi using DuPont Biolistic PDS-1000/He particle delivery system (Biorad). Bombarded cells were resuspended in 50 ml of SPPA, left for 2-3 hours at 30° C. Paclitaxel was added to the final concentration of 20 μM and cells were plated on microtiter plates using 100 μl cells per well and plates were incubated in moist boxes at 30° C. (in darkness, to prevent photobreakdown of paclitaxel). Wells containing paclitaxel-resistant transformants were apparent after 2-3 days of selection.
To identify sequences integrated into the BTU1 locus of T. thermophila, total genomic DNA was isolated from transformants using the fast urea method as described by J. Gaertig (Proc. Nat'l. Acad. Sci. USA 91:4549-4553 (1994)) and used as a template for PCR with primers: BTU1-75 (5′-AAAAAATAAAAGTTTGAAAAAAA-3′) (SEQ ID NO:13), sequence located 53-75 bp upstream to the ATG translation initiation codon in the BTU1 5′ flanking region, and primer BTU1-3, (5′-GTTTAGCTGACCGATTCAGTTCG-3′) (SEQ ID NO:14), located close to the TGA stop codon in the 3′ flanking region of BTU1. The resulting amplified products were digested with Nsi I restriction endonuclease and run on a TAE-agarose 0.7% gel.
Immunocytochemistry
For immunofluorescent detection of the I. multifiliis i-antigen in transgenic Tetrahymena cells, 10 mls of exponentially growing cultures (2'105 cells/ml) were harvested, washed with 10 mls of 10 mM Tris (pH 7.5) and resuspended in 0.5 ml. Cells were fixed with 3.5 mls of 2% paraformaldehyde in PHEM buffer (60 mM Pipes, 25 mM HEPES, 10 mM EGTA, 2 mM MgCl2, pH. 6.9) for 30 minutes at room temperature. Fixed cells were washed once with 3 mls of PHEM buffer and 2 times with 3 mls of modified phosphate buffered saline, PBS (130 mM NaCl, 2 mM KCl, 8 mM Na2HPO4, 2 mM KH2PO4, 10 mM EGTA, 2 mM MgCl2, pH. 7.2) and resuspended in 0.5 ml. For antibody labeling, 100 μl of fixed cells were washed 3 times for 10 minutes with 3 mls of PBS-BT, (3% bovine serum albumin, 0.1% Tween 20 in PBS), and concentrated in 100 μl. One μl of affinity-purified rabbit antiserum directed against Ichthyophihirius G1 i-antigen (T. L. Lin et al., J. Protozool., 39:457-463 (1992)), was added, followed by incubation overnight at 4° C., three washes in PBS-BT and incubation with the detection antibodies (at 1:100 dilution) for 45 minutes at room temperature.
Secondary antibodies were goat anti-rabbit IgG coupled to FITC (Zymed). Labeled cells were washed 3 times with PBS, concentrated in 0.1 ml of PBS plus 10 μl of DABCO mounting medium (100 mg/ml 1,4-diazobicyclo-[2,2,2]-octane, Sigma Chemical Co., dissolved in 90% glycerol in PBS). To mount, 5 μl of cells were combined with 5 μl of DABCO medium, covered with a cover-slip and sealed with nail polish. Slides were examined with a Bio-Rad MRC 600 Laser Scanning Confocal Microscope at the UGA Center for Advanced Ultrastructural Research. Sets of optical sections of individual cells were processed to obtain complete 3-D reconstructions.
Immunoblotting
Protein extracts were prepared from 1-2×106 cells taken from exponentially growing cultures. Cells were spun down at 2000 rpm for 5 minutes, washed with 10 mls of ice-cold 10 mM Tris, pH 7.5, and resuspended in 125 μl of ice-cold Tris buffer supplemented with a mixture of protease inhibitors which included 0.5 μg/ml leupeptin, 10 μg/ml E-64, 10 μg/ml chymostatin and 12.5 μg/ml antipain (A. Turkewitz, personal communication, all inhibitors from Sigma), combined with 125 μl of boiling 2×SDS-PAGE sample buffer and boiled for 5-10 min. Ten μl of extracts were loaded on a 10% SDS-PAGE minigel and proteins transferred on nitrocellulose using semi-dry transfer system (Biorad). The filter was blocked for 2 hr in PBS-T buffer containing 5% dried milk, followed by incubation with the anti-I. multifiliis i-antigen antibodies (1:10000) overnight at 4° C. The filter was washed extensively with PBS with 0.1% Tween-20 (PBST) and incubated in the same buffer containing the goat-anti-rabbit IgG antibodies conjugated to alkaline phosphatase (Bio-Rad) for 1 hr at room temperature. The membrane was washed in PBST and developed using NBT/BCIP (Bio-Rad) as described by M. Gorovsky, J. Protozool., 20:19-25 (1973).
Immobilization Assay
Growing Tetrahymena cells were washed with 10 mM Tris, pH 7.5 and resuspended at 2000 cells/ml. Cells were incubated with a series of dilutions of monospecific rabbit polyclonal antiserum against the parasite i-antigen 48 kD protein on microtiter plates at 1000 cells/ml in 100 microliter/well aliquots. After 15-60 minutes wells were scored under a dissecting scope. The behaviors of both BTU1-4::IAG48[G1] transformants and controls (neo1 transformants) were examined, and the percentage of immobilized cells was estimated.
Results
Cells were selected for resistance to either paclitaxel (30 μM) or paromomycin (120 μg/ml). As shown in Table 1, transformants were readily obtained following selection with either drug, but were not detected in a mock transformation experiment. Furthermore, random clones that had been selected for growth in paclitaxel were all found to be cross-resistant to paromomycin (n=40), and nearly all transformants originally selected with paromomycin, produced clones resistant to 30 μM paclitaxel (89%, n=71). Thus, acquisition of the transformed phenotype (in most, if not all cases) resulted from disruption of the host btu1-1K350M gene, and negative paclitaxel selection based on BTU1 gene loss-of-function was nearly as effective as a positive selection based on paromomycin resistance conferred by the transgene.







TABLE I







Transformation of T. thermophila using biolistic bombardment











Targeting
Selection
Frequency



Fragment
method
(transf./μg DNA)















BTU1-2::neo1
tx*
115



BTU1-2::neo1
pm¶
204



No DNA
tx
0



No DNA
pm
0



BTU1-2::neo1
tx
37



BTU1-4::IAG[G1]
tx
31



No DNA
tx
0







*30 μM paclitaxel.



¶120 μg/ml paromomycin.






Unlike the bacterial neo gene, the product of the i-antigen gene of I. multifiliis is not inherently selectable. Nonetheless, as shown in Table I, paclitaxel-resistant transformants were obtained with a frequency comparable to that seen with the control BTU1-2::neo1 gene construct. Western blotting studies (FIG. 5) using polyclonal antiserum against affinity purified i-antigens of Ichthyophihirius showed that a protein of apparent MW of 50 kDa was detected in all transformants carrying the IAG48[G1] gene (lanes 1-5), but not in a control cell line transformed with neo1 (lane 6). The size of the detected protein was in close agreement with the MW of the corresponding surface antigen of Ichthyophihirius. An additional band of about 100 kDa seen in both BTU1-4::IAG48[G1] and control extracts, most likely represents an endogenous Tetrahymena protein that shares immunological determinants with the parasite antigen.
It should be noted that because the macronucleus of T. thermophila is polyploid and contains about 45 copies of each chromosome, only partial replacement of endogenous genes occurs following initial transformation. Nevertheless, chromosomes are distributed to daughter nuclei through an imprecise form of allelic segregation known as amitosis, and complete replacement of endogenous genes by transgenic copies can be achieved by continuous growth in selective media. In this case, PCR analysis revealed that about one half of endogenous copies of the BTU1 gene were replaced by the IAG48[G1] transgene during early stages of selection. Following growth in the presence of increasing concentrations of paclitaxel, however, endogenous copies of the BTU1 gene could no longer be detected, and a corresponding increase in the copy number of IAG48[G1] was seen, indicating that they had lost all copies of the endogenous BTU1 allele.
In Ichthyophthirius, the 48-kDa protein is a major component of the cell surface and is bound to ciliary and plasma membranes through a glycosylphosphatidylinositol (GPI) anchor. Nevertheless, the sequence elements responsible for membrane targeting in ciliates are not well-understood, and while Ichthyophthirius and Tetrahymena are taxonomically related, it was not know whether signal peptides from such widely diverged species could function interchangeably.
Transformed cell lines were therefore fixed (without permeabilization), reacted with antibodies against the 48-kDa antigen and analyzed for the presence of the I. multifiliis protein on their surface by indirect immunofluorescence using confocal microscopy. Strong labeling of oral and somatic cilia was observed (FIG. 6A, 6B and 6C), wherein somatic cilia are shown in FIG. 6A and oral cilia are shown in FIG. 6C. Surface cortical fluorescence was seen in the form of longitudinal rows (shown in FIG. 6B). Dividing cells showed labeling in both the preexisting and newly formed oral apparatus, indicating that as the new structure is formed, parasite antigens are rapidly inserted into the cell membrane (FIG. 6C). Control cells (transformed with neo1) showed no obvious labeling (FIG. 6D). Fluorescence was only seen in controls when cells were permeabilized with methanol prior to fixation with paraformaldehyde. This appeared as a generalized background staining, and was not surprising given the presence of a cross-reacting (100 kDa) band in Western blots of control cell extracts.
A further demonstration of the presence of I. multifiliis proteins on the surface of Tetrahymena came from immobilization assays with living cells. In the immobilization assay, at antisera dilutions of 1:100 or less, rabbit antisera against the 48-kDa protein caused an immediate reduction in swimming velocity of the BTU1-4::IAG48[G1] transformants, followed by a complete loss of motility within 50 minutes. In contrast, neo1 transformants showed no immediate effect, but eventually became immobilized after 90 minutes. The difference in the response of BTU1-4::IAG48[G1] versus neo1 transformants indicates that I. multifiliis antigens are accessible to antibodies at the surface of live cells. Furthermore, because immobilizing antibodies recognize 3-dimensional epitopes on the 48 kDa protein, the antigen itself is likely to assume a native conformation in Tetrahymena. 
Example III
Expression of Green Fluorescent Protein in Tetrahymena 
Using the Tetrahymena BTU1 targeting system (Examples I and II), a modified version of the G1 i-antigen was constructed in which the green fluorescent protein (GFP) tag coding sequence was inserted in a correct frame into the G1 i-antigen of I. multifiliis, about 10 amino acids downstream from the site of cleavage of the N-terminal signal peptide. The G1-GFP construct was thereby targeted to the BTU1 locus, and transformants were selected with paclitaxel. The fusion protein was detected inside transformed cells using Western blotting and anti-gfp antibodies. A fraction of the fusion protein was found to be associated with the Triton X-114 extractable membranes of transformant cells, although no fusion protein was found on the cell surface.
Example IV
Expression of Malaria Surface Protein in Tetrahymena 
Malaria is caused by parasitic protozoa of the genus Plasmodium, and is responsible for 2 million deaths a year worldwide. Current control efforts are focused on the mosquito vector, and treatment of the disease with anti-malarial drugs. No vaccine is yet available. Over the past four decades the parasite has become resistant to many anti-malarial drugs, and an effective vaccine is seen as best hope for controlling morbidity and mortality caused by this pathogen.
Most of the candidate molecules from Plasmodium suggested for inclusion in a vaccine are proteins that bind to receptors on host target cells. Necessary for vaccine development is the identification and characterization of the role played by these proteins. Unfortunately, this effort has been hampered by difficulties in procuring enough parasite protein to allow thorough study. Several heterologous expression systems have been utilized, but none has proven to be ideal, especially for the production of functional protein.
In this preliminary study, the Tetrahymena BTU1 targeting system (Examples I and II) was evaluated for use in expression of the Plasmodium falciparum surface proteins implicated in interactions with the host cells. A 1,900 bp region of a putative P. falciparum erythrocyte binding protein, EBL-1, was directly inserted in frame, at a NsiI restriction site, into the coding sequence of the G1 i-antigen of I. multifiliis flanked by the BTU1 targeting sequences. The resulting construct had a coding region encoding a chimeric fusion protein having the N-terminal portion of the i-antigen (representing about 2⁄3 of the i-antigen protein), followed by the EBL-1 domain encoded by the 1,900 bp region, followed by the C-terminal portion of the i-antigen (representing about 1⁄3 of the i-antigen protein), under control of the Tetrahymena BTU1 promoter.
This construct was expressed in Tetrahymena, demonstrating that the presence within the P. falciparum coding sequence of codons that are very rare in Tetrahymena did not abrogate expression. However, this EBL1::G1 fusion protein was expressed in Tetrahymena as a cytosolic protein, and no association with the cell membrane or the cell surface was observed despite the fact that the N-terminal and C-terminal targeting sequences of G1 i-antigen were present in the fusion protein. This result could be explained by improper folding of the multi-domain chimeric fusion protein; insertion of the EBL-1 coding sequence into the middle of the G1 i-antigen coding sequence arbitrarily divided the i-antigen sequence into two portions, possibly disrupting folding of the protein or otherwise interfering with the production of a protein that was competent to translocate into or across a membrane. A second experiment replacing the i-antigen coding sequence (between the two targeting sequences) with the EBL-1 domain instead of simply inserting it within the i-antigen coding sequence will provide more insight into targeted expression of EBL-1 in Tetrahymena. 
Example V
Deletion of GPI Anchor Modification Domain
A truncated version of the G1 i-antigen gene from I. multifiliis was prepared in which the C-terminal domain implicated in the GPI anchor addition was deleted. The truncated gene was expressed in Tetrahymena as in Example II. FIG. 7 shows Western blots of total protein extracts of transformant cells (FIG. 7(a)) and total culture medium from which transformant cells were removed (FIG. 7(b)). The first four lanes from the left contained either cells (FIG. 7(a)) or culture medium (FIG. 7(b)) of four independent transformants of T. thermophila in which a truncated version of the G1 antigen lacking the GPI-anchoring C-terminal domain was incorporated into the BTU1 locus. Controls contained either the neo gene or a full-length G1 i-antigen of I. multifiliis expressed in the BTU1 locus. The amount of culture medium loaded (FIG. 7(b)) corresponds to about 1/30 of the amount of cells loaded (FIG. 7(a)). The truncated protein was expressed at essentially the same level observed for surface-targeted expression of the gene (Example II) (FIG. 7, top). However, about 1⁄2 of total expressed truncated G1 i-antigen protein was found in the culture medium, in contrast to the full length G1 i-antigen protein which was not detected in the culture medium. Thus, the elimination of the GPI anchor domain caused the i-antigen to be secreted out of the cell, as expected.
Example VI
Expression of Chicken Ovalbumin in Tetrahymena 
To test the feasibility of Tetrahymena thermophila for expression of vertebrate proteins, we prepared two constructs in which the region of the coding sequence of chicken ovalbumin protein (amino acids 139-385; GenBank Acc. Numbers M34346 and M25173; J. Catterall et al., Nature 275:510-513 (1978)) was fused to an N-terminal signal peptide of either the gp-72 surface protein of T. cruzi (Tryp./OVA) or of the G1 antigen of I. multifiliis (Ich/OVA) subcloned between the flanking sequences of the BTU1 gene of T. thermophila. These constructs were integrated into the BTU1 locus using biolistic transformation of the paclitaxel-sensitive host cells, and protein extracts of several paclitaxel-resistant transformants were analyzed by a Western blot using anti-chicken ovalbumin antibodies (Sigma Chemical Co.). Two protein bands close to the expected molecular weight of about 30 kD were detected in transformants but not in the negative control cells in which the BTU1 locus was transformed using the bacterial neomycin resistance gene (neo) (FIG. 8). The presence of two bands may be the result of posttranslational modifications or proteolysis in Tetrahymena. Interestingly, the fusion protein containing the signal peptide of T. cruzi gp72 protein was expressed at several fold higher level compared to the fusion protein with the I. multifiliis signal peptide. Also, it is striking that the levels of expression are extremely reproducible among individual transformants.
Example VII
Immune Response of Channel Catfish to Live Vaccine: Transformed Tetrahymena Expressing Full-length or Truncated I. multifiliis (Serotype A) 48 kD I-antigen Protein and Heterologous Challenge with I. multifiliis (Serotype D)
The IAG48[G1] gene of Ichthyophthirius multifiliis G1 encodes the GPI anchored 48-kDa i-antigen. The extreme 3′ region of the gene encodes a stretch of 14 mostly hydrophobic amino acids separated by a short spacer from three small amino acids (CAS). This sequence encodes the protein's GPI anchor addition site. Tetrahymena thermophila cells transformed with the entire IAG48[G1] gene produce an intact i-antigen anchored to the cells' surface. Tetrahymena cells transformed with a modified IAG48[G1] gene construct lacking the 3′ sequence which includes the GPI addition site would be expected to produce a truncated protein lacking the GPI anchor.
Tetrahymena cells were transformed with either the entire Ichthyophthirius G1 48-kDa i-antigen protein, or a truncated gene sequence which encodes the i-antigen protein lacking 19 amino acids at the carboxy terminus. Transformants encoding the intact or C-terminal truncated i-antigen were grown in standard Tetrahymena growth medium. Cell pellets and supernatant fluids were collected at the time points indicated. I-antigen was detected in cell cytosol, cell membrane or cell culture supernatants by Western blots using rabbit antisera against affinity purified Ichthyophthirius G5 i-antigen (see FIG. 9). It is clearly seen that the truncated protein is secreted into the culture medium.
Groups of channel catfish (6 fish per group) were immunized by bath exposure (106 or 105 cells/fish) or intraperitoneal injection with T. thermophila transformants (106, 105, or 104 cells/fish) producing intact or truncated i-antigen. A third group of fish was immunized with membrane protein extracts (1 mg or 0.1 mg/fish) from T. thermophila producing the full length protein.
Immunization by bath exposure to Tetrahymena transformants. Two groups of fish (6 fish in each group) were immunized by bath exposure. The fish were exposed to either 106 or 105 cells /fish for a period of 24 hours. Two immunogens were used: 1) transformed Tetrahymena cells expressing the entire Ichthyophthirius G1 48-kDa protein, and 2) transformed cells secreting a truncated form of the i-antigen lacking the GPI anchor. Fish in the control group were exposed to Tetrahymena transformants expressing the neo1 gene product. Fish were exposed twice at a 30 day interval and challenged 30-60 days after the last immunization with the G5 Ichthyophthirius isolate. There were no significant differences (z test) between test and control groups (see Table 1). Immunized fish were challenged with a heterologous strain of Ichthyophthirius expressing a different i-antigen (serotype D; Gs isolate) than that produced by the recombinant Tetrahymena used for vaccination. It is expected that challenge with a strain of Ichthyophthirius producing an i-antigen homologous to the G1 48 i-antigen would show increased levels of protection.







TABLE 1







Vaccination by bath exposure














Dose
Number
Number





Immu-
(cells/
of fish
of fish
%

MDD4 ±


nogen
fish)
challenged
surviving
survival
RSP3
SD5
















Neo
106
5
2
40
N.A.
17.0 ± 1.0


control


TG11
105
5
3
60
33.3
18.5 ± 2.1


TG1
106
6
3
50
25.0
13.3 ± 4.9


sTG12
105
6
3
50
25.0
21.0 ± 4.6


sTG1
106
6
4
66.7
40.0
17.0 ± 1.4





1Tetrahymena expressing intact membrane form of Ichthyophthirius G1 i-antigen.


2Tetrahymena secreting truncated form of G1 i-antigen.


3Relative Survival Percent = 1 − (number of dead fish in test group/number of dead fish in control group) × 100%


4Mean days to death


5Standard deviation






Immunization by injection of Tetrahymena transformants. Fish in each group were injected intraperitoneally with 106, 105, or 104 live transformed Tetrahymena cells/fish. The same immunogens and controls were tested as in the immersion vaccinations. Fish were injected two times at a 30 day interval, and challenged 21 days after the last immunization with G5 Ichthyophthirius. A greater degree of protection was elicited in immunized fish compared to controls (Table 2).







TABLE 2







Vaccination by injection














Dose
Number
Number





Immu-
(cells/
of fish
of fish
%

MDD4 ±


nogen
fish)
challenged
surviving
survival
RSP3
SD5
















Neo
105
6
2
33.3
N.A.
15.3 ± 3.6


control


TG11
106
5
3
60
44.5
19.0 ± 2.8


TG1
105
5
4
80
58.4
15.0 ± 0.0


TG1
104
6
2
33.3
0
14.0 ± 1.4


sTG12
106
6
5
83.3
50.0
21.0 ± 4.6


sTG1
105
6
3
50.0
25.0
20.0 ± 5.7





1Tetrahymena expressing intact membrane form of Ichthyophthirius G1 i-antigen.


2Tetrahymena secreting truncated form of G1 i-antigen.


3Relative Survival Percent = 1 − (number of dead fish in test group/number of dead fish in control group) × 100%


4Mean days to death


5Standard deviation






Serum antibody production. Fish serum antibody responses against recombinant G1 Ichthyophthirius i-antigen were determined by ELISA at 2, 4, and 6 weeks after immunization. Serum antibodies from immunized fish were detected with a sandwich ELISA technique that used wells coated with a cross-reactive rabbit antibody against Ichthyophthirius G5 i-antigen to capture recombinant G1 i-antigen produced in transformed Tetrahymena. Sera from test and control fish were added to wells and antibodies that bound to the captured i-antigen were detected using an alkaline phosphatase labeled mouse mAb against the immunoglobulin heavy chain of channel catfish. ELISA controls consisted of antibody-coated wells reacted with membrane protein from Tetrahymena cells transformed with the neo1 gene.
Fish injected with Tetrahymena membrane protein produced high levels of serum antibody against the recombinant i-antigen. The antibody response elicited by fish immunized with live cells was almost an order of magnitude lower. The antibody response of fish immunized by bath or i.p. injection with live cells secreting recombinant i-antigen was approximately two-fold greater than the antibody response of fish immunized with Tetrahymena producing the membrane-bound, intact i-antigen. In FIG. 10, the differences in antibody production between fish immunized with the (a) membrane associated or (b) secreted form of the i-antigen are shown. These results suggest that live cells secreting antigen are more efficacious in eliciting the production of serum antibodies. The mucosal antibody response was not determined in these experiments.
Example VIII
Immune Response of Channel Catfish to Live Vaccine: Transformed Tetrahymena Expressing Full-length or Truncated I. multifiliis (Serotype A) 48 kD I-antigen Protein and Homologous Challenge with I. multifiliis (Serotype A)
Tetrahymena cells were transformed with either the entire Ichthyophthirius G1 48-kDa i-antigen protein, or a truncated gene sequence which encodes the i-antigen protein lacking 19 amino acids at the carboxy terminus as in Example VII.
Groups of channel catfish (70 fish per group) were vaccinated by intraperitoneal injection with 106 T. thermophila transformants producing intact or truncated i-antigen. A third group of fish (control group) was vaccinated with T. thermophila transformants expressing neo. No adjuvant was used in any of the vaccinations. The fish were boosted 2 weeks following the initial injection and bled at 3 weeks following the initial injection. Sera from 3 fish per group were pooled.
A 96 well ELISA plate was seeded with a homologous strain (i.e., serotype A) of I. multifiliis (strain NY1, a G1 isolate), 200 cells per well. Fish sera were serially diluted and added to the wells, and the effect on the motility of I. multifiliis was observed. Immobilization of I. multifiliis was immediately evident at serum dilutions of 1:20, and at higher concentrations the organisms exhibited clumping (see FIG. 1). Sera from the control group did not cause any detectable change in motility of I. multifiliis. 
As another control, additional wells were seeded with a heterologous strain of I. multifiliis (a G5 isolate). The motility of these organisms was not affected by sera from any of the groups of vaccinated fish, confirming that the immobilization epitopes on I. multifiliis i-antigens are highly specific.
For comparison, two other groups of fish were vaccinated with purified subunit proteins produced from recombinant Tetrahymena (either the full-length 48 kD i-antigen protein or the C-terminal truncated version). The subunit proteins were adjuvanted with Freund's Complete Adjuvant. In a plate assay similar to the one described above using the homologous strain of I. multifiliis, some immobilization was observed but not to the degree caused by the “live vaccine.” This observation lends support to the expectation that the “live vaccine” will prove to be more efficacious than the analogous protein subunit vaccine.
Example IX
Construction of CU522, CU725 and CU727
T. thermophila strains CU522, CU725 and CU727 were produced by micronuclear transformation of a mating between T. thermophila strains CU427 [chx1-1/chx1-1 (CHX1; cy-r, V1)] and CU428 [mpr1-1/mpr1-1 (MPR1; mp-r, VII)]. CU427 is a functional heterokaryon, homozygous in the germinal micronucleus for the dominant cycloheximide resistance gene chx1-1, expressing the wild type allele CHX1 in the somatic macronucleus and therefore resistant to cycloheximide (cy-r), and mating type VI. CU428 is also a functional heterokaryon, homozygous in the germinal micronucleus for the dominant 6-methylpurine resistance gene mpr1-1, expressing the wild type allele MPR1 in the somatic macronucleus and therefore resistant to to 6-methylpurine (mp-r), and mating type VII. Genetic nomenclature rules for T. thermophila are listed in “The Seventh International Meeting on Ciliate Molecular Biology Genetics Nomenclature.” S. Allen et al., Genetics 1998 May:149(1):459-462.
Mating pairs were biolistically co-transformed using the following plasmids: pH41A, which carries the HHF1A::neo construct (bacterial neomycin resistance gene, which confers resistance to paromomycin in Tetrahymena, inserted within the flanking regions of the histone 4 gene); and pBTU1M350, which carries a modified β-tubulin 1 gene (btu1-1K350M) with a single base mutation which confers oryzalin resistance (or-r), and taxol (also known as paclitaxel) sensitivity (tx-s), plus the β-tubulin 1 gene 5′ and 3′ flanking sequences. Potential transformants were initially selected on the basis of paromomycin resistance (pm-r). To differentiate germline and somatic transformants, the pm-r clones were tested for true progeny formation by replication into cycloheximide and 6-methylpurine and selected for double resistance (cycloheximide resistance, cy-r, and 6-methylpurine resistance, mp-r). Somatic transformants arising from non-mating cells retain the parental phenotype and are therefore sensitive to both drugs. Pm-r clones were also tested for resistance to oryzalin (or-r) to identify clones successfully co-transformed with the pBTU1M350.
Using this procedure, one clone (A10) was identified which was a successful co-transformant with the following genetic makeup: heterozygous for all relevant markers in the germinal micronucleus [CHX1/chx1-1; MPR1/mpr1-1; btu1-1K350M/BTU1; HHF1/HHF1A::neo], and heterozygous for all relevant alleles in the somatic macronucleus and therefore expressing resistance to all marker drugs (CHX1/chx1-1; MPR1/mpr1-1; btu1-1K350M/BTU1; HHF1/HHF1A::neo; cy-r, mp-r, pm-r, or-r, tx-r).
A star mating (a mating to a line with a defective germinal micronucleus which results in incomplete conjugation) was used to homozygose the entire micronuclear genome without affecting the phenotypically expressed somatic macronucleus. In this process, two rounds of mating were used. In the first round of mating (Round I mating), individual mating pairs were isolated into hanging drops, grown, and replicated into individual microtiter plate arrays for further analysis. From individual Round I clones, exconjugants were induced to undergo a second round of mating (Round II mating). Individual Round II pairs were isolated from each parental Round I clone, grown, and tested for immaturity, cycloheximide, 6-methylpurine, oryzalin and paclitaxel resistance to determine the genotype of the homozygous parental Round I clones and the isolated Round II progeny clones (genotypes of both the Round I parent and the Round II progeny are directly reflected in the phenotype of the Round II isolated progeny). Single cell exconjugants from various Round I clones expressing different combinations of drug resistance markers were isolated by hand, and the non-star partner identified by outcrosses to each parental line. These Round I clones were frozen in liquid nitrogen to prevent cell senescence and loss of the genotype. Individual Round II progeny cells, derived from each of the unique Round I genotypes, were isolated and grown, and the mating type of each clone was determined. Round II clones derived from each of the unique Round I genotypes were frozen to prevent senesence.
CU522, CU725 and CU727 are Round II subclones obtained using this process. They have the following genetic makeup (micronuclear genotype is shown first, macronuclear genotype and phenotype are shown in parentheses). Only the resistance phenotypes are listed. Relevant genes not indicated are the wild type allele and result in the wild type drug sensitive phenotypes.
CU 522
btu1-1K350M/btu1-1K350M: mpr1-1/mpr1-1 (btu1-1K350M; mpr1-1; or-r, tx-s, mp-r, IV)
This strain is phenotypically paclitaxel sensitive, oryzalin resistant, 6-methylpurine resistant, mating type IV.
CU725
btu1-1K350M/btu1-1K350M, chx1-1/chx1-1 (btu1-1K350M; chx1-1; or-r, tx-s, cy-r, VII)
This strain is phenotypically paclitaxel sensitive, oryzalin resistant, cycloheximide resistant, and mating type VII.
CU727
btu1-1K350A/btu1-1K350M (btu1-1K350M; or-r, tx-s, V)
This strain is phenotypically paclitaxel sensitive, oryzalin resistant, and mating type V.
It should be noted that mating type is a developmental function, but is important in future genetic uses of the strains. Tetrahymena of the same mating type cannot mate and therefore at least two different mating types are required for subsequent genetic work. The combination of different markers and different mating types allows for subsequent genetic crosses and direct selection of appropriate progeny.
The complete disclosures of all patents, patent applications including provisional patent applications, and publications, and electronically available material (e.g., GenBank amino acid and nucleotide sequence submissions) cited herein are incorporated by reference. The foregoing detailed description and examples have been provided for clarity of understanding only. No unnecessary limitations are to be understood therefrom. The invention is not limited to the exact details shown and described; many variations will be apparent to one skilled in the art and are intended to be included within the invention defined by the claims.

## Claims

1. A Tetrahymena strain comprising a germline micronuclear genotype homozygous for btu1-1K350M/btu1-1K350M and a somatic macronuclear phenotype exhibiting resistance to oryzalin (or-r); sensitivity to paclitaxel (tx-s); and resistance or sensitivity to one or more marker drugs selected from the group consisting of cycloheximide (cy-r), 6-methylpurine (mp-r) and paromomycin (pm-r).

2. The Tetrahymena strain of claim 1 comprising a genetic makeup represented by btu1-1K350M/btu1-1K350M, mpr1-1/mpr1-1 (btu1-1K350M; mpr1-1; or-r, tx-s, mp-r).

3. The Tetrahymena strain of claim 2 which is a mating type IV.

4. T. thermophila strain CU522.

5. The Tetrahymena strain of claim 1 comprising a genetic makeup represented by btu1-1K350M/btu1-1K350M; chx1-1/chx1-1 (btu1-1K350M; chx1-1; or-r, tx-s, cy-r).

6. The Tetrahymena strain of claim 5 which is a mating type VII.

7. T. thermophila strain CU725.

8. The Tetrahymena strain of claim 1 comprising a genetic makeup represented by btu1-1K350M/btu1-1K350M (btu1-1K350M; or-r, tx-s).

9. The Tetrahymena strain of claim 8 which is a mating type V.

10. T. thermophila strain CU727.