# Patent

## Title
Genetically altered ciliates and uses thereof

## Abstract

Ciliate organisms are provided that comprise reduced proteolytic processing in granules. For example, ciliates are provided that lack detectable expression of one or more sortilin (SOR) gene product. Methods for producing such genetically altered ciliates and methods for protein production in a these organisms are also provided.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims priority to U.S. Provisional Patent Application Ser. No. 61/601,921, filed on Feb. 22, 2012, which is hereby incorporated by reference in its entirety.


The invention was made with government support under Grant No. GM077607 awarded by the National Institutes of Health. The government has certain rights in the invention.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates generally to the field of genetics and molecular biology. More particularly, it concerns genetically altered ciliate organisms and the use of such organisms in recombinant protein production.
2. Description of Related Art
Recombinant proteins are useful for a wide range of applications including as industrial enzymes and as therapeutics. For example, production of genetically engineered vaccine antigens, therapeutics (including antibodies and antibody fragments), industrial enzymes, biopolymers, and bioremediation agents now constitute a multibillion dollar-per-year industry. There is also a large market for recombinant proteins in the basic research arena (Pavlou and Reichert (2004); Langer (2005)).
Currently available platforms for the production of recombinant proteins are limited to a relatively small number of cell-based systems that include bacteria, fungi, and insect and mammalian tissue culture cells. Although bacteria can offer high yield and low cost alternatives for production of mammalian proteins, cell culture systems based on higher organisms such as insect cells or mammalian cell systems generally provide proteins having greater fidelity to the natural proteins in terms of protein folding and/or post-translational processing (e.g., glycosylation). Whole transgenic plants and animals have also been harnessed for the production of recombinant proteins, but the long development time from gene to final product can be a major drawback with these multicellular organisms, as can their high cost, low yield and many inherent difficulties in purification.
There remains a need in the art for improved methods for rapid, high-fidelity and cost-effective production and purification of recombinant polypeptides.
SUMMARY OF THE INVENTION
In a first embodiment a genetically altered ciliate is provided wherein the ciliate lacks detectable expression (or has reduced expression) of one or more SOR gene product. For example, the SOR gene product may be a product corresponding to SOR1 (SEQ ID NO: 1, 2), SOR2 (SEQ ID NO: 3, 4), SOR3 (SEQ ID NO: 5, 6) and/or SOR4 (SEQ ID NO: 7, 8; indicating the protein and nucleic acid coding sequence respectively). In some aspects, the ciliate may lack detectable expression of a SOR polypeptide or a SOR RNA corresponding to SOR1, SOR2, SOR3 and/or SOR4. In a further aspect, the ciliate lacks detectable expression of 2, 3 or 4 of the SOR1, SOR2, SOR3, or SOR4 genes. For example, a ciliate of the embodiments may lack detectable expression (or have reduced expression) of SOR1 and SOR2; SOR1 and SOR3; SOR1 and SOR4; SOR2 and SOR3; SOR2 and SOR4; SOR3 and SOR4; SOR1, SOR2 and SOR3; SOR1, SOR2 and SOR4; SOR1, SOR3 and SOR4; SOR2, SOR3 and SOR4; or SOR1, SOR2 SOR3 and SOR4.
In certain aspects, a ciliate of the embodiments comprises a genomic alteration, such as an insertion or a deletion in both copies of the germline genome that disrupts expression of one or more SOR gene product. For instance, the ciliate can comprise an insertion or deletion located in the open reading frame of a gene corresponding to SOR1, SOR2, SOR3 and/or SOR4. In some aspects, a genomic insertion comprises a selectable marker, such a drug resistance marker (e.g., a gene for tetracycline or neomycin resistance). Accordingly, in some aspects, a ciliate of the embodiments comprises an insertion or a deletion in all macronuclear copies of a gene corresponding to SOR1, SOR2, SOR3 and/or SOR4.
In further aspects a ciliate of the embodiments expresses a polynucleotide complementary to all or part of an RNA gene product corresponding to SOR1, SOR2, SOR3 and/or SOR4. For example, the ciliate can express an antisense RNA or a double stranded RNA (dsRNA) molecule, such as a small interfering RNA (siRNA), short hairpin RNA (shRNA) or micro RNA (miRNA), complementary to all or part of an RNA gene product corresponding to SOR1, SOR2, SOR3 and/or SOR4.
In still further aspects, a ciliate of the embodiments comprises a transgenic expression cassette, such as an expression cassette encoding a polypeptide. For example, the polypeptide can be a polypeptide for recombinant production in the ciliate. Polypeptides for use in accordance with the embodiments include, but are not limited to, enzymes, immunoglobulin (e.g., immunoglobulin light chains, immunoglobulin heavy chains or single chain antibodies), cytokines, chemokines, and antigens (e.g., bacterial or viral antigens). In some aspects the polypeptide coding sequence can comprise a sequence for cellular trafficking, such as a mucocyst-targeting sequence. For example, the polypeptide can encode a mucocyst-targeting sequence derived from a Tetrahymena Grl protein, such as Grl1, Gr12, Gr13, Gr14, Gr15, Gr16, Gr17, Gr18, Gr19 or Grl 10. In still further aspects, the polypeptide encodes a cleavable linker (e.g., between the polypeptide for expression and a mucocyst-targeting sequence).
In some specific aspects, a ciliate of the embodiments is a Tetrahymena, such as a T. thermophila or T. pyriformis. 
In yet a further embodiment there is provided a recombinant Tetrahymena germline genome (e.g., a recombinant T. thermophila or T. pyriformis genome) comprising a genomic insertion or deletion in both copies of one or more SOR gene selected from the group consisting of SOR1, SOR2, SOR3, and SOR4. For example, the genomic insertion or deletion can be located in the open reading frame of the gene. In some aspects, a genomic insertion comprises the insertion of a selectable marker, such a drug resistance marker. In still further aspects, a Tetrahymena germline genome comprises a genomic insertion or deletion in both copies of 2, 3 or 4 SOR genes corresponding to SOR1, SOR2, SOR3 or SOR4. Thus, the genome can comprise an insertion of deletion in the genes for SOR1 and SOR2; SOR1 and SOR3; SOR1 and SOR4; SOR2 and SOR3; SOR2 and SOR4; SOR3 and SOR4; SOR1, SOR2 and SOR3; SOR1, SOR2 and SOR4; SOR1, SOR3 and SOR4; SOR2, SOR3 and SOR4; or SOR1, SOR2 SOR3 and SOR4.
In a further embodiment there is provided a recombinant Tetrahymena germline genome comprising, an expression cassette comprising a sequence encoding a polynucleotide molecule complementary to all or part of an RNA gene product corresponding to SOR1, SOR2, SOR3, or SOR4. For example, genome can comprise sequences encoding an antisense RNA or a dsRNA, such as a siRNA, shRNA or miRNA, complementary to all or part of an RNA gene product corresponding to SOR1, SOR2, SOR3 and/or SOR4.
In still a further aspect of the embodiments a recombinant Tetrahymena germline genome can comprise a transgenic expression cassette, such as a cassette encoding a polypeptide, optionally including a mucocyst-targeting sequence.
In still yet a further embodiment there is provided a method of producing a genetically altered ciliate comprising: (a) transforming a ciliate with a polynucleotide comprising a sequence complementary to a SOR gene corresponding to SOR1, SOR2, SOR3 and/or SOR4; and (b) isolating a genetically altered ciliate wherein the ciliate lacks detectable expression of the gene product of said SOR gene. For example, step (b) can comprise isolating a genetically altered ciliate comprising an insertion or deletion in a SOR gene or isolating a genetically altered ciliate expressing a polynucleotide molecule complementary to all or part of an RNA gene product of a SOR gene. In further aspects, step (a) comprises transforming the ciliate with a polynucleotide comprising a sequence complementary to a SOR gene and comprising a selectable marker (e.g., a drug resistance marker). Thus, in some aspects, a genetically altered ciliate is isolated based on expression of a selectable marker (such as by drug selection). Detailed methods for genetic alteration of ciliates are well known in the art and are detailed in PCT Patent Publn. No. WO2010108182, the entirety of which is incorporated herein by reference.
In a further embodiment there is provided a method of producing a genetically altered ciliate of the embodiments comprising obtaining the genetically altered ciliate and vegetatively propagating the ciliate. In further aspects, a genetically altered ciliate can be a produced by sexually propagating a genetically altered ciliate and isolating progeny that comprise the genetic alterations.
In still yet a further embodiment a method of producing a polypeptide is provided comprising: (a) expressing a polynucleotide encoding the polypeptide in a ciliate of the embodiments; and (b) incubating the ciliate in a media under conditions permissible for expression of the polypeptide. In some aspects, the majority (or at least a portion) of the polypeptide is secreted from the ciliate and the method can comprise (c) purifying the expressed polypeptide from the media. In certain aspects, the majority (or at least a portion) of the polypeptide is not secreted by the ciliate and the method can comprise (c) purifying the ciliate from the media and, optionally, (d) purifying the protein from the ciliate. In still further aspects, a method of the embodiments further comprises transforming a ciliate with a polynucleotide encoding a polypeptide. Further methods for polypeptide expression in ciliates are detailed in PCT Patent Publn. No. WO2010108182, the entirety of which is incorporated herein by reference.
In some aspects a expressing a polynucleotide for expression in a ciliate is further defined as an expression cassette encoding a polypeptide. For example, the polypeptide can be a polypeptide of mammalian origin, such as a human polypeptide. In some aspects, the polypeptide comprises sequence encoding an enzyme, an immunoglobulin, a cytokine, a chemokine, or an antigen.
As used herein the specification, “a” or “an” may mean one or more. As used herein in the claim(s), when used in conjunction with the word “comprising”, the words “a” or “an” may mean one or more than one.
The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.” As used herein “another” may mean at least a second or more.
Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.
Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.



BRIEF DESCRIPTION OF THE DRAWINGS
The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.
FIG. 1: Two sortilin genes in Tetrahymena are dramatically up-regulated during induced granule formation (regranulation) in Tetrahymena. First column show fold induction of the genes, significance values are shown in third column.
FIG. 2: Analysis of the Tetrahymena genome indicates that it codes four sortilin/Vps10 genes. Diagram shows the homology between the four sortilin genes (Tt SOR1-4) and structurally related genes.
FIG. 3: Tetrahymena RNA expression was examined in putative SOR knockout lines (SORT, SOR2 and SOR4). In each case wild type (WT) Tetrahymena exhibited SOR RNA expression, whereas no expression was observed in the knockout lines.
FIG. 4: Tetrahymena sortilin knockout lines secrete unprocessed precursors of the granule protein Grl1p. Immunoblot media samples show that in the case of each of the SOR knockout lines unprocessed (high molecular mass) Grl1p precursors are released into the media.
FIG. 5: The sortilin knockout lines each make aberrant secretory granules, which are visualized here by immunefluorescence. Granule-specific immunefluorescence results for the indicated knockout cells (or for wild type “wt”) are shown in tangential section (upper panels) or equatorial section (lower panels).



DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS
Recombinant protein production has become very important for a variety of applications. For example, many modern therapeutics, such as enzymes and monoclonal antibodies, are proteins that are produced recombinantly. However, adequate and cost-effective protein production systems are lacking Bacterial expression systems, while low cost, often result in proteins that do not incorporate crucial post-translation modifications or are improperly folded. On the other hand, mammalian cell expression systems are very expensive to maintain and produce notoriously low yields of protein products that must be extensively purified. Accordingly, ciliate-based protein production systems could provide an attractive alternative existing systems. However, there remains a need for a ciliate system adapted to provide high quality recombinant protein yield.
Studies detailed herein identify four ciliate gens from Tetrahymena that are important regulators of cell trafficking and secretion pathways. In particular, the SOR genes mediate transport of proteases to granules allowing for proteolytic processing of the granule contents. The studies here demonstrate that SOR gene expression can effectively knocked-out (see, FIG. 3), and that such knockout is not lethal to the organism. Indeed, knockout of SORT, SOR2 and SOR4 all resulted in decreased proteolytic processing of products located in granules (FIG. 4) and a change in granule structure indicative of reduced proteolytic processing (FIG. 5).
Accordingly, modified ciliate organisms, such as Tetrahymena, are provided that have reduced expression of one or more sortilin gene product. Importantly, these organism exhibit reduced proteolytic processing in granules and are thereby ideal for recombinant protein production. Such organisms can be used to produce a wide range of protein products without aberrant cleavage of the products during expression. Moreover, recombinant proteins can be easily and cost-effectively purified by either isolating the ciliate cells comprising large quantities of highly concentrated (and uncleaved) protein product or by targeting the proteins for secretion and isolating the product from cell media.
I. Ciliates for Use According to the Embodiments
The embodiments may be practiced with a variety of different ciliates which include secretory granules called mucocysts. Heterologous polypeptides can be targeted to these secretory granules by encoding fusion proteins of the desired heterologous polypeptide and an appropriate targeting sequence. After exposing the ciliate to a secretory stimulus that causes the mucocysts to discharge their contents to the extracellular environment, the heterologous polypeptide can be recovered from the resulting matrix and medium.
The free-living ciliate protists are a large and diverse phylum (Ciliata) whose members display a structural and functional complexity comparable to that of higher metazoa (Fankel (2000); Turkewitz et al. (2002)), and include over 7,000 species with 11 major subdivisions. Tetrahymenids and Paramecium belong to the Oligohymenophoreans. Ciliates that include mucocysts useful in the invention include Tetrahymena species such as Tetrahymena thermophila and Tetrahymena pyriformis. Paramecium has dense core granules but does not secrete a proteinaceous gel. Both Tetrahymena thermophila and Tetrahymena pyriformis produce mucocysts, and both secrete a proteinaceous gel.
Tetrahymena spp. are amenable to genetic manipulation, can be grown on a large scale and have a doubling time of 1.5-3 hrs. Unlike T. thermophila, which has an optimal growth temperature of 35° C., the optimal growth temperature for T. pyriformis is lower (maximal growth temperature of 34° C.). Cells reach high-density in a short time on a variety of inexpensive media and can be expanded for growth in bioreactors up to several thousand liters in size (Hellenbroich et al. (1999); de Coninck et al. (2000)). Methods for transformation, along with robust, inducible promoters for driving high-level gene expression have recently been described for this system (Bruns and Cassidy-Hanley (2000); Gaertig and Kapler (2000); Shang et al. (2002); Boldrin et al. (2006)).
Tetrahymena spp. devote a large part of their metabolism to membrane protein production due to the hundreds of cilia that extend from its surface (Williams et al. (1980)). Additionally, Tetrahymena spp. lack a cell wall and display high-mannose N-glycan protein modifications that lack branched, immunogenic structures (Taniguchi et al. (1985); Becker and Rusing (2003); Weide et al. (2006)). Glycosylation patterns of secreted proteins in Tetrahymena spp. are uniform and consist of high-mannose N-glycan structures comprising Man3GlycNac2 core N-glycans similar to those which are produced in the endoplasmic reticulum of mammalian cells.
This glycosylation pattern is unlike the glycosylation pattern produced in other microbial systems. For example, such glycosylation is non-existent in bacteria, and is highly branched and immunogenic in fungi.
II. Genetic Alteration of Ciliates
Methods for genetic alteration of ciliates are well known in the art and may be used in accordance with the instant embodiments. For example, ciliates can be transformed with vectors that express nucleic acid to disrupt expression of a SOR gene (such as siRNAs). In some aspects, the ciliates is transformed with a vector to disrupt an endogenous SOR gene (e.g., by generating an insertion of deletion in a genomic copy of the gene). In still further aspects, a ciliate can be transformed with a vector for the expression of heterologous polypeptides, such as peptides that will be harvested from the cells.
Certain aspects of the embodiments concern ciliates that lack detectable expression (or have reduced expression) of one or more SOR gene product corresponding to SOR1, SOR2, SOR3 or SOR4. In some aspects the SOR gene product is an RNA at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the nucleic acid sequence of SOR1 (SEQ ID NO: 2), SOR2 (SEQ ID NO: 4), SOR3 (SEQ ID NO: 6) or SOR4 (SEQ ID NO: 8). In a further aspect, the SOR gene product is an polypeptide at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the amino acid sequence of SOR1 (SEQ ID NO: 1), SOR2 (SEQ ID NO: 3), SOR3 (SEQ ID NO: 5) or SOR4 (SEQ ID NO: 7). In yet further aspects the SOR gene product is an polypeptide comprising at least 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 441, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890 or 900, contiguous amino acids identical to the amino acid sequence of SOR1 (SEQ ID NO: 1), SOR2 (SEQ ID NO: 3), SOR3 (SEQ ID NO: 5) or SOR4 (SEQ ID NO: 7). In some specific aspects, the gene product corresponding to SOR1, SOR2, SOR3 or SOR4 is one of the gene products listed in the NCBI accession numbers of FIG. 2, each of which is incorporated herein by reference. Thus, in some aspects, a ciliate of the embodiments comprises an insertion or a deletion in such a gene corresponding to Tetrahymena SOR1, SOR2, SOR3 and/or SOR4. In yet further aspects, a ciliate can comprise an expression cassette encoding a polynucleotide (e.g., a dsRNA, siRNA, shRNA or miRNA) complementary to all or part of an RNA corresponding to a Tetrahymena SORT, SOR2, SOR3 and/or SOR4 RNA.
Transformation
Genes can be introduced into ciliates using established protocols or any method known to one skilled in the art. Transformation of ciliates can be achieved by microinjection (Tondravi and Yao (1986)), electroporation (Gaertig and Gorovsky (1992)), or biolistically (Cassidy-Hanley et al. (1997)).
Thus, in some embodiments, ciliate cells can be transformed with a chimeric gene by particle bombardment (also known as biolistic transformation) (Cassidy-Hanley et al. (1997)). Particle bombardment transformation can be achieved by several ways. For example, inert or biologically active particles can be propelled at cells under conditions effective to penetrate the outer surface of the cell and to be incorporated within the interior thereof. When inert particles are utilized, the vector can be introduced into the cell by coating the particles with the vector containing the chimeric gene. Alternatively, the target cell can be surrounded by the vector so that the vector is carried into the cell by the wake of the particle. Other variations of particle bombardment, now known or hereafter developed, can also be used.
Microcarrier bombardment can also be used to transform ciliate cells by means of DNA-loaded gold particles (U.S. Pat. No. 6,087,124; European Pat. EP 847 444; WO 1998/001572). In this approach, microcarrier bombardment with DNA-coated gold is used as a means of introducing foreign genes into ciliates. In one embodiment, microcarrier bombardment can be used to transform ciliates and introduce genes into the (germline) micronucleus
Methods for selection of transformed cells harboring foreign genes are known in the art. For example, the vector can further comprise a selectable cassette marker to permit selection for transformed cells {e.g., a neo 2 cassette) (Gaertig et al. (1994)).
Selection of transformants can be achieved by growing the cultured ciliates in a medium which allows only the transformants to survive. Suitable selection agents include antibiotics which will kill most all non-transformants but allow transformants (which also possess an antibiotic resistance gene) to survive. A number of antibiotic-resistance markers are known in the art. Any known antibiotic-resistance marker can be used to transform and select transformed host cells in accordance with the present invention. For example, selection of the transformants can be performed by means of a resistance marker such as a point mutation in the 17s rDNA, which confers resistance to paromomycin, can allow for selection of rDNA transformants (Spangler and Blackburn (1985); Bruns et al. (1985)). Other methods include the use of a mutant cell line that allows targeting of genes to the beta tubulin-1 locus of T. thermophila by homologous recombination, and allows efficient selection of transformed cell lines by growth in the microtubule-stabilizing agent (taxol) (U.S. Pat. No. 6,846,481). Another method for selection of transformed cells harboring foreign genes is to insert full length coding regions into the pD5HA vector (Cowan et al. (2005)). In this method, transcription is driven by the inducible MTT1 promoter. Once cells have been transformed with the pD5HA vector selection of positive transformants is determined by paromomycin resistance (i.e., cell growth in media containing the drug). Presence of the transgene is then verified by PCR and then induced with cadmium chloride to over-express the recombinant gene product.
Many other selectable marker systems are known in the art. Selectable marker genes that confer resistance or tolerance to a normally toxic selection agent allow only successfully transfected cells to survive in the presence of the selection agent, and are referred to as positive selectable markers. Examples of positive selectable marker genes and their corresponding selection agents are: aminoglycoside phosphotransferase (APH) and G418; dihydro folate reductase (DHFR) and methotrexate (Mtx); hygromycin-B-phosphotransferase (HPH) and hygromycin-B; xanthine-guanine phosphoribosyltransferase (XGPRT) and mycophenolic acid; and adenosine deaminase (ADA) and 9-β-D-xylofuranosyl adenine (XyI-A). In another example of a positive selectable marker system, thymidine kinase (TK) and aminopterin (included, e.g., in hypoxanthine-aminopterin-thymidine (HAT) medium) can be used in cells that are initially thymidine kinase deficient (tk ̃). The aminopterin will normally kill tk ̃ cells and, therefore, only successful TK transfectants will survive. Selectable marker genes that confer sensitivity or susceptibility to a normally nontoxic selection agent cause only successfully transfected cells to die in the presence of the selection agent, and are referred to as negative selectable markers. An example of a negative selectable marker system is thymidine kinase (TK) and gancyclovir. Phenotypic selectable marker genes permit selection based upon morphological or biochemical traits rather than cell death or survival. In some cases, the phenotypic marker is detectable only in the presence of an additional selection agent. An example of a phenotypic selectable marker system is β-galactosidase (lacZ) and X-gal.
III. Vectors and Polypeptide Expression
Heterologous nucleic acids can be introduced into the ciliate host on an expression vector that is capable of integrating into the host's genome. For example, expression vectors capable of homologous recombination with a highly expressed gene that is endogenous to the protozoan host, such as a P-tubulin gene are known in the art. Alternatively, a heterologous nucleic acid transformed into a ciliate can be maintained extrachromosomally on an autonomous plasmid.
Expression vectors useful for transforming ciliates in accordance with the methods described herein include but are not limited to 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 thermophile. 
A replacement vector can include 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 can also comprise regulatory elements, such as a promoter and a terminator. The necessary regulatory elements can also be supplied by the endogenous gene into which the heterologous coding region integrates. Suitable regulatory regions include, but are not limited to promoters, termination sequences, signal peptides and proprotein domains involved in the expression and secretion of proteins. For example, such regulatory elements can provide efficient heterologous expression of proteins in Tetrahymena spp. under control of promoters and/or terminators which are derived from genes in Tetrahymena ssp. Such vectors can comprise naturally occurring promoters and/or terminators from proteins secreted at a high level in Tetrahymena ssp. The expression of recombinant polypeptides in Tetrahymena spp. can be driven by strong promoters, pre/pro sequences and terminators. In one embodiment, the promoters and/or terminators can be selected from proteins secreted at a high level independent of the cell-cycle in Tetrahymena spp. (US Patent Application 2006/0127973; WO2003/078566). Inducible promoters from Tetrahymena spp. genes have also been described that allow robust expression of foreign genes. For example, heat-inducible promoters of the heat shock protein family of the ciliate Tetrahymena spp. are also suitable for use with the methods described herein. Suitable heat shock promoters from Tetrahymena spp. are known in the art (see WO2007/006812).
Methods for creating mitotically stable Tetrahymena spp. transformants, for example, by integration of a heterologous gene by homologous DNA recombination, are known in the art. Methods for generating Tetrahymena spp. having targeted gene knockouts by homologous DNA recombination are also known in the art (Bruns and Cassidy-Hanley (2000); Hai et al. (2000); Gaertig et al. (1999); Cassidy-Hanley et al. (1997)). The somatic macronucleus or the generative micronucleus can be transformed in alternation. For example, sterile transformants, which may provide improved safety parameters, can be obtained with macronucleus transformation.
Expression vectors can also be maintained extrachromosomally in the ciliates. An expression vector maintained as an extrachromosomal element can be a rDNA-based vector containing an on from Tetrahymena spp. rDNA, which is known to support extrachromosomal replication. Such a vector can further comprise a 5′ regulatory region from an endogenous Tetrahymena spp. gene containing a promoter region operably linked to the heterologous coding region and, optionally, a 3′ regulatory region from the same or a different Tetrahymena spp. gene. For example, regulatory regions from ciliate genes in such vectors can include, but are not limited to, regulatory regions from genes such as HHFI, rp129, BTU1, BTU2, SerH3, and actin.
There are a number of suitable vectors suitable for transformation of ciliates known in the art. For example, Tetrahymena spp. can be transformed with an rDNA vector (Tondravi and Yao (1986); Yu and Blackburn (1989)). The shuttle vector pXS76 allows insertion of transgenes downstream of a cadmium-inducible promoter from the MTT1 metallothionein gene of T. thermophila via homologous recombination and selection in paromomycin. Alternatively, inserts can be introduced into high copy number ribosomal DNA vectors (such as pD5H8) under control of the cadmium-inducible MTT1 promoter. The pD5H8 vector takes advantage of a biological feature of Tetrahymena spp. in which the ribosomal cistrons become amplified to extraordinarily high copy numbers following conjugation. An rDNA-based vector can be a circular vector that contains a 5′ non-translated sequence comprising two or more on sequences from Tetrahymena spp. rDNA. A nucleic acid fragment containing a heterologous coding region, for example a selectable marker or transgene, can also be added to the vector. The vector can further comprise a 5′ untranslated region of a Tetrahymena spp. gene and a 3′ untranslated region of a Tetrahymena spp. gene, inserted upstream and downstream of the selectable marker and/or the transgene. Methods for transformation, along with robust, inducible promoters for driving high-level gene expression have recently been described for this system (Bruns and Cassidy-Hanley (2000); Gaertig and Kapler (2000); Shang et al. (2002); Boldrin et al. (2006)).
Sequence variations within the origins of replication of rDNA from wild-type B- and C3-strains of T. thermophila convey a replicative advantage to the C3-form in B/C3 heterozygotes. Although both B- and C3-forms of rDNA are initially present in the macronucleus in approximately equal amounts, within 30 fissions only the C3 variant remains (Pan et al. (1982); Orias et al. (1988)). pIC19-based shuttle vectors containing the C3 origin of replication have been used as high-copy number vectors for the delivery of foreign DNA to Tetrahymena spp. (Yu and Blackburn (1989)) (FIG. 5).
Although such vectors can become unstable and be lost within about 50 to about 80 generations, micronuclear versions of the C3 rDNA is accurately processed (to form a palindrome) following introduction into T. thermophila B cell lines. The micronuclear version is maintained as a stable linear chromosome over many generations (Bruns et al. (1985)). Functional transgenes can be inserted into the 3′-nontranscribed spacer (3′-NTS) of such vectors with no effect on rDNA processing. Within 6-10 generations, recombinant molecules can comprise 50-100% of the total rDNA complement, with as many as 18,000 copies of the transgene per cell (Blomberg et al. (1997)). The use of this approach enables an increase in the number of cloned genes in transformed cell lines by orders of magnitude and leads to increased expression at the protein level. For example, the use of rDNA-based vectors in combination with the MTT1 promoter can be used to drive expression of the endogenous granule lattice protein GrI Ip to approximately 20% of total cell protein (Lin et al. (2002)). Similarly, pD5H8 rDNA-based vectors (Blomberg et al. (1997)) can be used to boost expression of proteins by at least 3-10 fold compared with trans formants in which respective transgenes are integrated at somatic gene loci. Other vectors suitable for use with the methods described here include vectors comprising a ribosomal DNA sequence. Such vectors can replicate at high copy numbers and can be used to deliver a heterologous DNA sequence to Tetrahymena spp. for purposes of RNA expression.
Heterologous Polypeptides
Suitable heterologous polypeptides for use with these methods include, but are not limited to, antibodies, antibody fragments, cytokines, growth factors, protein kinases, proteases, protein hormones or any fragment thereof. Similarly, the methods described herein are suitable for the production of specialty proteins. The use of such specialty proteins can include, but is not limited to, prototype vaccines for animal model studies, structural studies, or as therapeutic proteins. For example, quantities of antigens can be produced according to the methods described herein.
Isolation of Desired Polypeptides from the Mucocyst Matrix
In one aspect, the invention provides methods for protein purification from the extracellular matrix formed by the discharge of mucocysts. Because heterologous polypeptides targeted to the mucocyst compartment will be associated within the matrix, the invention provides matrix-based purification strategies. Advantageously, the matrix can be used for rapid purification of recombinant polypeptides associated with it.
Proteins within the gel matrix can be separated from cellular constituents by low-speed centrifugation (See Turkewitz et al. (2000)). Any other method known in the art suitable for separating intact cells, from the discharged material, including, but not limited to filtration harvesting using an appropriately selected mesh, can also be used in conjunction with the methods described herein. After isolation of the matrix, the desired heterologous polypeptide can be liberated from the secreted matrix gel. Methods for liberation of the protein can include chemical methods {e.g., high salt concentrations) and/or enzymatic methods {e.g., site-specific proteases).
Proteins can also be isolated in intact secretory granules. For example, the use of an exocytosis-defective mutant, MN 173, of T. thermophile where granules accumulate in the cytoplasm has been described for such purposes (Melia et al. (1998)).
EXAMPLES
The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.
Example 1
Sortilin Gene Control Granule Trafficking of Proteases in Tetrahymena 
Initial studies were undertaken to identify genes that are up-regulated upon regranulation in Tetrahymena cells. Results shown in FIG. 1 demonstrate that two sortilin genes are among the genes that are dramatically up-regulated during this process. In view of these studies, the Tetrahymena genome was analyzed in comparison with genes from other organisms and four Tetrahymena sortilin genes were identified (FIG. 2). The identified genes were SOR1, SOR2, SOR3, and SOR4, corresponding to NCBI accession nos. XM—001033316.2, XM—001020814.3, XM—001025035.2 and XM—001033494.2, each incorporated herein by reference.
To further determine the function of the SOR genes vectors were constructed to knockout each of the genes Tetrahymena (by homologous recombination targeting to the SOR ORFs). The vectors used in the studies are provided as SEQ ID NOs: 9-12, for targeting SOR1, SOR2, SOR3 and SOR4 respectively. Following transformation, knockout cells were successfully isolated for SOR1, SOR2 and SOR4. Studies shown in FIG. 3 confirm that in each case the knockout lines lack detectable expression of the indicated sortilin RNA. Moreover, knockout of the sortilin genes hampered proteolytic processing in the knockout cells. As shown in FIG. 5, unprocessed forms of Grl1p (pro-Grl1p) were observed in the media of the knockout lines, but not in that of wild type cells or a knockout of the Rab32 gene. Thus the sortilin knockouts result in an inability to effect the normal proteolytic processing of granule proteins.
Immunefluorescence studies were also performed to visualize granules in knockout and wild type cells. Results, shown in FIG. 5, demonstrate that wild type granules are elongated, a shape that is generated by the proteolytic processing of the content proteins. The granules in the sortilin knockout lines are spherical, consistent with the failure to proteolytically process the contents.
* * *
All of the methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.
References
The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.

    U.S. Pat. No. 6,846,481
    U.S. Pat. No. 6,087,124
    U.S. Patent Appln. 2006/0127973
    Becker and Rusing, J. Eukaryot. Microbiol., 50:235-239, 2003.
    Blomberg et al., Mol. Cell. Biol., 12:7237-747, 1997.
    Boldrin et al., Eukaryot Cell, 2:422-425, 2006.
    Bruns and Cassidy-Hanley, Meth. Cell Biol., 62:501-512, 2000.
    Bruns et al., Proc. Natl. Acad. Sci. USA, 9:2844-286, 1985.
    Cassidy-Hanley et al. Genetics, 146:135-147, 1997.
    Cowan et al., Mol. Cell. Biol., 16:4046-4060, 2005.
    de Coninck et al., J. Industr. Microbiol. Biotechnol., 24:285, 2000.
    European Patent EP 847 444
    Fankel, Meth. Cell Biol., 62:27-125, 2000.
    Gaertig and Gorovsky Proc. Natl. Acad. Sci. USA, 89:9196-9200, 1992.
    Gaertig and Kapler, Meth. Cell Biol., 62:486-500, 2000.
    Gaertig et al. Nucleic Acids Res., 22:5391-5398, 1994.
    Gaertig et al., Nature Biotech., 17:462-465, 1999.
    Hai et al., Meth. Cell Biol., 62:513-531, 2000.
    Hellenbroich et al. Appl. Microbiol. Biotechnol., 51:447, 1999.
    Langer, 3rd Annual Rept and Surv. Biopharm. Manufact. Capacity and Prod., BioPlan Assoc., Inc. (2005
    Lin et al. Gene, 288(1-2):85-94, 2002.
    Melia et al., J. Cell Sd. H, 1(Pt 1):131-140, 1998.
    Orias et al., Gene, 2:295-301, 1988.
    Pan et al., Cell, 3:595-604, 1982.
    Pavlou and Reichert, Nat. Biotechnol., 22:1513-1519, 2004.
    PCT Publn. WO 1998/001572
    PCT Publn. WO 2003/078566
    PCT Publn. WO 2007/006812
    PCT Publn. WO 2010/108182
    Shang et al., Proc. Natl. Acad. Sci. USA, 6:3734-379, 2002.
    Spangler and Blackburn, J. Biol. Chem., 10:6334-6340, 1985.
    Taniguchi et al., J. Biol. Chem., 260:13941-13946, 1985.
    Tondravi and Yao, Proc. Natl. Acad. Sci. USA, 83:4369-4373, 1986.
    Turkewitz et al., Meth. Cell Biol., GI-MI-IGI, 2000.
    Weide et al., BMC Biotechnol., 6:19, 2006.
    Williams et al., J. Biol. Chem., 255:296-303, 1980.
    Yu and Blackburn, Proc. Natl. Acad. Sci. USA, 21:8487, 891, 1989.

## Claims

1. A genetically altered ciliate wherein the ciliate lacks detectable expression of one or more sortilin (SOR) gene products selected from the group consisting of SOR1, SOR2, SOR3, and SOR4.

2. The ciliate of claim 1, wherein the one or more sortilin (SOR) gene products has a sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, and SEQ ID NO: 7.

3. The ciliate of claim 1, wherein the ciliate comprises a genomic alteration of one or more of SOR1, SOR2, SOR3, or SOR4.

4. The ciliate of claim 3, wherein the ciliate comprises a deletion in both copies of the ciliate's germline genome that disrupts expression of a SOR gene product.

5. The ciliate of claim 3, wherein the ciliate comprises an insertion in both copies of ciliate's germline genome that disrupts expression of a SOR gene product.

6. The ciliate of claim 5, wherein the insertion is located in the open reading frame of one or more SOR genes selected from the group consisting of SOR1, SOR2, SOR3, and SOR4.

7. The ciliate of claim 1, wherein the ciliate lacks detectable expression of 2, 3, or 4 gene products selected from the group consisting of SOR1, SOR2, SOR3, and SOR4.

8. The ciliate of claim 1, wherein the ciliate expresses a polynucleotide complementary to all or part of an RNA gene product selected from the group consisting of SOR1, SOR2, SOR3, and SOR4.

9. The ciliate of claim 8, wherein the polynucleotide molecule complementary to all or part of an RNA gene product is an antisense RNA or a double stranded RNA (dsRNA).

10. The ciliate of claim 1, wherein the ciliate is Tetrahymena.

11. A recombinant Tetrahymena germline genome comprising a genomic insertion or deletion in both copies of one or more SOR genes selected from the group consisting of SOR1, SOR2, SOR3, and SOR4.

12. The recombinant genome of claim 11, wherein the genomic insertion or deletion is located in the open reading frame of the one or more SOR genes.

13. The recombinant genome of claim 11 comprising a genomic insertion or deletion in both copies of 2, 3, or 4 SOR genes selected from the group consisting of SOR1, SOR2, SOR3, and SOR4.

14. A method of producing a genetically altered ciliate comprising:
(a) transforming a ciliate with a polynucleotide comprising a sequence complementary to a SOR gene selected from the group consisting of SOR1, SOR2, SOR3, and SOR4; and
(b) isolating a genetically altered ciliate wherein the ciliate lacks detectable expression of the gene product of said SOR gene.

15. The method of claim 14, wherein step (b) comprises isolating a genetically altered ciliate comprising an insertion or deletion in a SOR gene.

16. A method of producing a polypeptide comprising: expressing a polynucleotide encoding a polypeptide in the ciliate of claim 1.

17. The method of claim 16, further comprising:
(c) purifying the expressed polypeptide from media.

18. The method of claim 16, wherein the polypeptide is not secreted by the ciliate.

19. The method of claim 18, further comprising:
(c) purifying the ciliate from media.

20. The method of claim 19, further comprising:
(d) purifying the polypeptide from the ciliate.