# Patent

## Title
Dre recombinase and recombinase systems employing Dre recombinase

## Abstract

The invention provides a Dre/rox recombinase system. In particular, the invention provides Dre polypeptides that can catalyze site-specific recombination at rox sites but not at lox sites. The Dre/rox system can be utilized in a number of genetic manipulations either alone or in combination with other recombinase systems.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application claims priority from Provisional Application Ser. No. 60/623,701 filed on Oct. 29, 2004, which is hereby incorporated by reference in its entirety.


FIELD OF THE INVENTION
The current invention generally relates to Dre recombinase and recombinase systems employing Dre recombinase. In particular, the present invention relates to a Dre recombinase that can catalyze site specific recombination at a rox site. The Dre/rox system can be utilized in a number of genetic manipulations either alone or in combination with other recombinase systems.
BACKGROUND OF THE INVENTION
The use of site-specific DNA recombinases has expanded the spectrum of genetic manipulations that can be carried out in both prokaryotic and eukaryotic organisms. While various site-specific DNA recombinases, such as the yeast-derived Flp/frt, are becoming increasingly popular, the Cre/loxP system is currently the most widely used system. Because of its simplicity and versatility, Cre has found widespread use in conditional mutagenesis and gene expression, gene replacement and deletion, and chromosomal engineering experiments.
Cre is a site-specific DNA recombinase derived from the P1 bacteriophage and is a member of the lambda integrase or tyrosine family of site-specific recombinases (1). Members of this family catalyze DNA recombination by a common catalytic mechanism and recognize target recombination sites with similar structural features. In the case of the Cre protein, it recognizes 34 base pair sequences known as loxP sites. The loxP sequence is composed of an asymmetric eight base pair spacer region flanked by 13 base pair inverted repeats. Cre recombines the 34 base pair loxP DNA sequence by binding to the 13 base pair inverted repeats and catalyzing strand cleavage and religation within the spacer region. The staggered DNA cuts made by Cre in the spacer region are separated by 6 base pairs to give an overlap region that acts as a homology sensor to ensure that only recombination sites having the same overlap region recombine.
The P1 genome, the sequencing of which has recently been completed in its entirety (12), is relatively large for a temperate DNA bacteriophage: 95 kb. P1 is unusual among temperate bacteriophages in that it maintains itself as an extrachromosomal unit copy plasmid in the lysogenic state. Cre is expressed in P1 lysogens and its site-specific DNA recombination activity contributes to the stable maintenance of the P1 prophage during lysogeny. Cre resolves P1 dimers that arise by homologous recombination after DNA replication, thus helping to ensure segregation of a P1 monomer to each daughter cell at cell division (13).
The P1 Cre gene and its 34 bp recombination target site loxP lie in a relatively short interval of P1 DNA that includes two other phage functions with unusual features. To the left of Cre is the immC immunity region of P1 that encodes the C1 repressor and several other immunity proteins that modify its action. ImmC, in turn, lies just to the right of the two genes for the P1 pacase or terminase and the pac site at which P1 DNA packaging begins. DNA packaging in P1 is unusual because protein recognition of the P1 DNA packaging site is regulated by DNA adenine methylation (dam). Although immunity in P1 is orchestrated in a complex manner and includes several different immunity regions (16), including antirepressor components, the C1 protein is unusual compared to other phage repressors because it recognizes an asymmetric DNA binding site (17). To the left of the P1 Cre gene is c8, another immunity gene, followed by ref, a gene involved in the homologous recombination of short DNA repeats (18,19).
Several P1-related phages also maintain themselves as an extrachromosomal plasmid in the lysogenic state, but comparable recombinase function in these P-1 related phages has yet to be elucidated. In particular, Cre homologues that perform site specific recombination at sites distinguishable from the lox site have not been previously characterized.
SUMMARY OF THE INVENTION
Among the several aspects of the invention, therefore, is the provision of a Dre recombinase that catalyzes site specific recombination at a rox site instead of at a lox site. Advantageously, because of this difference in substrate specificity, the Dre recombinase of the present invention provides an additional tool that may be utilized either alone or in combination with other Cre/lox systems for conditional mutagenesis and gene expression, gene replacement and deletion, and chromosome engineering.
One aspect of the invention encompasses a purified Dre polypeptide that can catalyze site specific recombination at a rox site. In one embodiment, the Dre polypeptide has an amino acid sequence comprising SEQ ID NO. 1. In still another alternative of this embodiment, the Dre polypeptide has an amino acid sequence such that it specifically binds to an antibody that binds specifically to a polypeptide having the amino acid sequence of SEQ ID NO. 1.
Yet another aspect of the invention provides isolated nucleotide sequences that encode Dre mutant polypeptides that can catalyze site specific recombination at a rox site. In one alternative of this embodiment, the isolated nucleotide sequence comprises a sequence that encodes a polypeptide having the amino acid sequence of SEQ ID NO. 1, or of a fragment SEQ ID NO. 1 that is at least 15 amino acid residues in length. In another alternative of this embodiment, the isolated nucleotide sequence comprises a sequence that hybridizes under stringent conditions to a hybridization probe the nucleotide sequence of which encodes a polypeptide having the amino acid sequence of SEQ ID NO. 1.
A further aspect of the invention provides purified antibodies that are specific for a Dre polypeptide of the invention. In one embodiment, the purified antibody binds specifically to a polypeptide having the amino acid sequence of SEQ ID NO. 1. The purified antibodies may be either monoclonal or polyclonal antibodies and may be used to purify Dre polypeptides of the present invention.
An additional aspect of the invention encompasses an isolated rox nucleotide sequence having the following structure:




Yet another aspect of the invention encompasses a Dre/rox system. The system typically comprises a purified Dre polypeptide that can catalyze site specific recombination at a rox site.
A further aspect of the invention provides a method for producing site-specific recombination of nucleotide sequence having a target DNA segment. The method involves introducing a first rox site and a second rox site into the nucleotide sequence such that the rox sites flank the target DNA segment. The rox sites are then contacted with a Dre polypeptide that can catalyze site specific recombination at a rox site. When the Dre polypeptide is contacted with the rox sites, site specific recombination of the nucleotide sequence occurs.
An additional aspect of the invention encompasses a kit for producing site-specific recombination of nucleotide sequence. Typically, the kit will comprise a purified Dre polypeptide that can catalyze site specific recombination at a rox site; an isolated rox nucleotide sequence; and instructions for producing site specific recombination.
A further aspect of the invention encompasses cells and nucleic acid sequences having the Dre polypeptides and rox sites of the invention.
Other objects and features of the invention will be in part apparent and in part pointed out hereinafter.



BRIEF DESCRIPTION OF THE FIGURES
The application contains at least one drawing executed in color. Copies of this patent and/or application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
FIG. 1 depicts a schematic comparing the pac-c1 regions of P1 and D6. Shown is a 7623 bp region of P1 that includes the region from lpa (gene 10) to ref. Also shown is the corresponding 7644 bp region from D6. The degree of similarity between individual genes of P1 and D6 is indicated according to the color scale shown. P1 genes in white have no D6 equivalent in this region, D6 genes in black have no P1 equivalent. Below and aligned with the D6 map is diagrammed the DNA insert of several PU (pickup) clones obtained by site-specific recombination.
FIG. 2 depicts a schematic comparing the P1 and D6 pacA genes. Dam methylation sites for both genes are shown as vertical lines above the gene. A blowup of the 162 bp P1 pac site that includes two clusters of dam sites is shown above the P1 pacA gene, with dam sites represented as black boxes, the IHF binding site as a white rectangle and the region of cleavage as a vertical arrow. An asterisk at nucleotide position 182 of D6 pacA marks the maximum of a curvature-propensity plot calculated with DNase I-based trinucleotide parameters (37).
FIG. 3 depicts a schematic of the D6 c1-dre integenic region. The 394 bp region from D6 between c1 and dre is diagrammed along with the single dam site of this region. The sequence shown is a 70 bp portion of this region suspected to include the D6 rox site because of the presence of inverted repeat elements. Repeat elements of a DNA sequence shown not to be the recombination site are indicated by dashed arrows, the repeat elements of the actual rox site are indicated by solid arrows. The two DraI sites are shown in upper case.
FIG. 4 depicts a schematic comparing P1 Cre and D6 Dre. Sequence identity is shown in yellow, conserved amino acid changes are shown in green. Below the sequences the known secondary structure (α-helices as dark blue cylinders, β-strands as orange arrows) of Cre is shown (50). Below the depiction of Cre secondary structure is a functional map of Cre based on pentapeptide insertion (9): blue bars represent points of insertion which have little or no effect on recombinase activity, red bars indicate points at which insertion abolishes recombinase activity.
FIG. 5 is a photographic image depicting western blot detection of Dre recombinase. Size markers in kDa are shown to the right.
FIG. 6 is a schematic illustrating recombinase-mediated excision. Reporter plasmids were constructed by placing the zeo gene (diagonal bars) between two identical directly repeated recombination sites (black triangles). Shown are the sequences of the 32 bp rox site and the 34 bp loxP site. Horizontal arrows indicate the inverted repeat elements; positions of nucleotide identity between rox and loxP are indicated by the black boxes; and vertical arrows show the sites of Cre cleavage that define the 6 bp overlap region of the lox site.
FIG. 7A depicts a schematic illustrating recombination activation of gene expression by Dre. Expression of the EGFP gene from the EF1α promoter in the reporter plasmid pBS1083 is blocked by the interposed zeo gene and polyadenylation site (An). Dre-mediated recombination at the flanking rox sites (black triangles) removes this “STOP” signal to allow EGFP expression. Horizontal arrows indicate the PCR primers used to produce the 389 bp fragment diagnostic of recombination.
FIG. 7B is a photographic image depicting activation of EGFP expression by Dre. Epifluorescence (panels i-iii) and differential interference contrast (panels iv-vi) images of CHO cells 36 h after DNA transfection. Panels i and iv show Dre expression plasmid pBS1081+the rox2 STOP EGFP plasmid pBS 1083; panels ii and v show Cre expression plasmid pBS513+pBS 1083; panels iii and vi show control lacZ plasmid p324+the EGFP plasmid pBS504.
FIG. 7C is a photographic image detailing PCR detection of recombination. DNA from the transfected CHO cells shown in panel B was amplified using the primers shown in panel A. The following materials were placed in the lanes; lane 1: CHO cells transfected with the Dre expression plasmid pBS1081+the rox2 STOP EGFP plasmid pBS 1083; lane 2: CHO cells transfected with the Cre expression plasmid pBS513+pBS1083; lane 3: CHO cells transfected with the control lacZ plasmid p324+the EGFP plasmid pBS504; lane 4: EGFP plasmid pBS504; lane 5: rox2 STOP EGFP plasmid pBS1083.
FIG. 8 is a schematic illustrating use of the Dre/rox system in transgenic mice. Mice with Dre protein expression in a specific cell type are bred to mice that contain a target gene surrounded by rox sites. When the mice are bred, the cells carrying Dre will those cells to lose the target gene.



DETAILED DESCRIPTION OF THE PREFFERED EMBODIMENTS
The present invention provides a Dre recombinase and several Cre homologues identified from P1-related phages that can be employed in novel recombinase systems. Dre recombinase recognizes a rox site instead of a lox site. Because of this difference in substrate specificity, advantageously, the Dre/rox recombinase system of the present invention provides an additional tool that may be utilized either alone or in combination with other Cre/lox systems for conditional mutagenesis and gene expression, gene replacement and deletion, and chromosome engineering.
Dre Recombinase
One aspect of the invention provides a Dre recombinase polypeptide having SEQ ID NO. 1. Dre catalyzes site specific recombination at a rox site, the nucleotide sequence of which is described below. In particular, Dre and wild-type Cre are heterospecific in that Cre does not catalyze site specific recombination at a rox site and Dre does not catalyze site specific recombination at a lox site. In one alternative of this embodiment, a polypeptide is provided that has an amino acid sequence such that it specifically binds to an antibody that binds specifically to the Dre polypeptide having SEQ ID NO. 1. Typically, suitable polypeptides in this embodiment will have an amino acid sequence that is at least 50% identical to SEQ ID NO.1, and more typically, the polypeptide will have an amino acid sequence that is at least 75% identical to SEQ ID NO.1. Exemplary polypeptides, however, will have an amino acid sequence that is at least 90%, more preferably 95%, and even more preferably, 99% identical to SEQ ID NO. 1. In a further alternative of this embodiment, the polypeptide will have an amino acid sequence that comprises SEQ. ID. NO.1 with 1 to 50 conservative amino acid substitutions. In an exemplary alternative of this embodiment, the polypeptide will have an amino acid sequence that comprises SEQ ID NO. 1 with 1 to 15, and more typically, from 1 to 10 conservative amino acid substitutions. In each of these embodiments, typically the polypeptide can catalyze site specific recombination or excision at a rox site, but not a lox site.
Cre Homologues
A further aspect of the present invention provides, as detailed in the examples, Cre homologue polypeptides identified from P1-related phages that can catalyze site specific recombination at a lox site. In a one embodiment, the Cre homologue is a polypeptide having SEQ ID NO. 2. In one alternative of this embodiment, a polypeptide is provided that has an amino acid sequence such that it specifically binds to an antibody that binds specifically to a polypeptide having SEQ ID NO. 2. Typically, a polypeptide in this embodiment will have an amino acid sequence that is at least 50% identical to SEQ ID NO. 2, and more typically, the polypeptide will have an amino acid sequence that is at least 75% identical to SEQ ID NO. 2. Exemplary polypeptides, however, will have an amino acid sequence that is at least 90%, more preferably 95%, and even more preferably, 99% identical to SEQ ID NO. 2. In a further alternative of this embodiment, the polypeptide will have an amino acid sequence that comprises SEQ. ID. NO. 2 with 1 to 50 conservative amino acid substitutions. In an exemplary alternative of this embodiment, the polypeptide will have an amino acid sequence that comprises SEQ ID NO. 2 with 1 to 15, and more typically, from 1 to 10 conservative amino acid substitutions. In each of these embodiments, typically the polypeptide can catalyze site specific recombination or excision at a lox site.
In still another alternative embodiment, the Cre homologue is a polypeptide having SEQ ID No. 3. In one alternative of this embodiment, the polypeptide has an amino acid sequence such that it specifically binds to an antibody that binds specifically to a polypeptide having SEQ ID NO. 3. Preferably, polypeptides in this embodiment will have an amino acid sequence that is at least 50% identical to SEQ ID NO. 3, and more typically, the polypeptide will have an amino acid sequence that is at least 75% identical to SEQ ID NO. 3. Exemplary polypeptides, however, will have an amino acid sequence that is at least 90%, more preferably 95%, and even more preferably, 99% identical to SEQ ID NO. 3. In a further alternative of this embodiment, the polypeptide will have an amino acid sequence that comprises SEQ. ID. NO. 3 with 1 to 50 conservative amino acid substitutions. In an exemplary alternative of this embodiment, the polypeptide will have an amino acid sequence that comprises SEQ ID NO. 3 with 1 to 15, and more typically, from 1 to 10 conservative amino acid substitutions. In each of these embodiments, typically the polypeptide can catalyze site specific recombination or excision at a lox site.
In yet a further alternative embodiment, the Cre homologue is a polypeptide having SEQ ID No. 4. In one aspect of the invention, the polypeptide has an amino acid sequence such that it specifically binds to an antibody that binds specifically to a polypeptide having SEQ ID NO. 4. Typically, polypeptides in this embodiment will have an amino acid sequence that is at least 50% identical to SEQ ID NO.4, and more typically, the polypeptide will have an amino acid sequence that is at least 75% identical to SEQ ID NO. 4. Exemplary polypeptides, however, will have an amino acid sequence that is at least 90%, more preferably 95%, and even more preferably, 99% identical to SEQ ID NO. 4. In a further alternative of this embodiment, the polypeptide will have an amino acid sequence that comprises SEQ. ID. NO. 4 with 1 to 50 conservative amino acid substitutions. In an exemplary alternative of this embodiment, the polypeptide will have an amino acid sequence that comprises SEQ ID NO. 4 with 1 to 15, and more typically, from 1 to 10 conservative amino acid substitutions. In each of these embodiments, typically the polypeptide can catalyze site specific recombination or excision at a lox.
Because of the somewhat ubiquitous nature of the Dre polypeptide or Cre homologues of the invention, it will be appreciated by those skilled in the art that additional suitable Dre polypeptides or Cre homologue polypeptides exist other than the ones specifically detailed herein. It will also be appreciated that additional polypeptides may be present in a species in addition to the polypeptides detailed herein. The invention contemplates the use of all suitable Dre polypeptides or Cre homologue polypeptides having the structure and function as described herein.
In certain aspects, accordingly, a polypeptide that is a homolog, ortholog, or degenerative variant of a Dre polypeptide or Cre homologue polypeptide is also suitable for use in the present invention. Typically, the subject polypeptides include fragments that share substantial sequence similarity, binding specificity and function with any of the polypeptides detailed above, including any of the polypeptides having SEQ ID Nos. 1, 2, 3, or 4.
A number of methods may be employed to determine whether a particular homolog or degenerative variant possesses substantially similar biological activity relative to a Dre polypeptide or Cre homologue of the invention. In particular, the subject polypeptide, if suitable for use in the invention, will be able to catalyze site specific recombination or excision at a lox site or a rox site, depending upon the particular embodiment. In order to determine whether a particular polypeptide can function in this manner, either the in vitro or in vivo recombination assays detailed in the examples may be followed.
In determining whether a polypeptide is substantially homologous or shares a certain percentage of sequence identity with a polypeptide of the invention, sequence similarity may be determined by conventional algorithms, which typically allow introduction of a small number of gaps in order to achieve the best fit. In particular, “percent homology” of two polypeptides or two nucleic acid sequences is determined using the algorithm of Karlin and Altschul (Proc. Natl. Acad. Sci. USA 87:2264-2268, 1993). Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al. (J. Mol. Biol. 215:403-410, 1990). BLAST nucleotide searches may be performed with the NBLAST program to obtain nucleotide sequences homologous to a nucleic acid molecule of the invention. Equally, BLAST protein searches may be performed with the XBLAST program to obtain amino acid sequences that are homologous to a polypeptide of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST is utilized as described in Altschul et al. (Nucleic Acids Res. 25:3389-3402, 1997). When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) are employed. See http://www.ncbi.nlm.nih.gov for more details.
Dre polypeptides or Cre homologue polypeptides suitable for use in the invention are typically isolated or pure. An “isolated” polypeptide is unaccompanied by at least some of the material with which it is associated in its natural state, preferably constituting at least about 0.5%, and more preferably, at least about 5% by weight of the total polypeptide in a given sample. A pure polypeptide constitutes at least about 90%, preferably, 95% and even more preferably, at least about 99% by weight of the total polypeptide in a given sample. In certain embodiments a pure polypeptide is preferred because all unwanted material, such as cellular debris, is removed. In other embodiments, polypeptides that are not pure may be utilized. A skilled artisan can readily select a polypeptide having the desired degree of purity for any particular application.
The polypeptides may be synthesized, produced by recombinant technology, or purified from cells. In one embodiment, the polypeptide of the present invention may be obtained by direct synthesis. In addition to direct synthesis, the subject polypeptides can also be expressed in cell and cell-free systems (e.g. Jermutus L, et al., Curr Opin Biotechnol. October 1998; 9(5):534-48) from encoding polynucleotides, such as described below or naturally-encoding polynucleotides isolated with degenerate oligonucleotide primers and probes generated from the subject polypeptide sequences (“GCG” software, Genetics Computer Group, Inc, Madison Wis.) or polynucleotides optimized for selected expression systems made by back-translating the subject polypeptides according to computer algorithms (e.g. Holler et al. (1993) Gene 136, 323-328; Martin et al. (1995) Gene 154, 150-166). In other embodiments, any of the molecular and biochemical methods known in the art are available for biochemical synthesis, molecular expression and purification of a Dre polypeptide or Cre homologue polypeptide, see e.g. Molecular Cloning, A Laboratory Manual (Sambrook, et al. Cold Spring Harbor Laboratory), Current Protocols in Molecular Biology (Eds. Ausubel, et al., Greene Publ. Assoc., Wiley-Interscience, New York).
Dre and Cre Homologue Nucleotide Sequences
The present invention also encompasses the use of isolated nucleotide sequences that encode suitable Dre polypeptides or Cre homologue polypeptides. For example, the subject nucleotide sequences may be utilized as a means to produce a polypeptide having the structure and biological activity as detailed above.
The nucleotide sequence may be any of a number of such nucleotide sequences that encode a suitable Dre polypeptide or Cre homologue polypeptide, having the structure and function as described herein. In one embodiment, the isolated nucleotide is a sequence that encodes a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO. 1, 2, 3, or 4 or of a fragment of any of SEQ ID NO. 1, 2, 3, or 4 that is at least 15 amino acid residues in length.
In still another embodiment, the isolated nucleotide sequence will encode a polypeptide that has an amino acid sequence that is at least 50% identical to the amino acid sequence of any of SEQ ID NO. 1, 2, 3, or 4. More typically, however, the isolated nucleotide sequence will encode a polypeptide that has an amino acid sequence that is at least 75% identical to the amino acid sequence of any of SEQ ID NO. 1, 2, 3, or 4 and even more typically, 90% identical to the amino acid sequence of any of SEQ ID NO. 1, 2, 3, or 4. In a particularly preferred embodiment, the nucleotide sequence will encode a polypeptide that has an amino acid sequence that is at least 95%, and even more preferably, 99% identical to the amino acid sequence of any of SEQ ID NO. 1, 2, 3, or 4. In each of these embodiments, the isolated nucleotide sequence will preferably encode a polypeptide that will be able to catalyze site specific recombination or excision at a lox or rox site, depending upon the embodiment.
The invention also encompasses the use of nucleotide sequences other than a sequence that encodes a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO. 1, 2, 3, or 4. Typically, these nucleotide sequences will hybridize under stringent hybridization conditions (as defined herein) to all or a portion of the nucleotide sequences described above or their complement. The hybridizing portion of the hybridizing nucleic acids is usually at least 15 (e.g., 20, 25, 30, or 50) nucleotides in length. The hybridizing portion of the hybridizing nucleic acid is at least 80%, preferably, at least 90%, and is more preferably, at least 95% identical to the sequence of a portion or all of a nucleic acid sequence encoding a polypeptide suitable for use in the present invention, or its complement.
Hybridization of the oligionucleotide probe to a nucleic acid sample is typically performed under stringent conditions. Nucleic acid duplex or hybrid stability is expressed as the melting temperature or Tm, which is the temperature at which a probe dissociates from a target DNA. This melting temperature is used to define the required stringency conditions. If sequences are to be identified that are related and substantially identical to the probe, rather than identical, then it is useful to first establish the lowest temperature at which only homologous hybridization occurs with a particular concentration of salt (e.g., SSC or SSPE). Then, assuming at 1% mismatching results in a 1° C. decrease in the Tm, the temperature of the final wash in the hybridization reaction is reduced accordingly. For example, if sequences have greater than 95% identity with the probe is sought, the final temperature is approximately decreased by 5° C. In practice, the change in Tm can be between 0.5 and 1.5° C. per 1% mismatch. Stringent conditions involve hybridizing at 68° C. in 5×SSC/5×Denhardt's solution/1.0% SDS, and washing in 0.2×SSC/0.1% SDS at room temperature. Moderately stringent conditions include washing in 3×SSC at 42° C. The parameters of salt concentration and temperature can be varied to achieve the optimal level of identity between the probe and the subject nucleotide sequence. Additional guidance regarding such conditions is readily available in the art, for example, by Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, N.Y.; and Ausubel et al., (eds.), 1995, Current Protocols in Molecular Biology, (John Wiley & Sons, N.Y.) at Unit 2.10.
The various nucleic acid sequences mentioned above can be obtained using a variety of different techniques known in the art. The nucleotide sequences, as well as homologous sequences encoding a suitable polypeptide, can be isolated using standard techniques, or can be purchased or obtained from a depository. Once the nucleotide sequence is obtained, it can be amplified for use in a variety of applications, as further described below.
The invention also encompasses production of nucleotide sequences that encode suitable polypeptide homologs, derivatives, or fragments thereof, that may be made by any method known in the art, including by synthetic chemistry. After production, the synthetic sequence may be inserted into any of the many available expression vectors and cell systems using reagents well known in the art. Moreover, synthetic chemistry may be used to introduce additional mutations into a nucleotide sequence encoding a suitable polypeptide.
The nucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter a subject polypeptides-encoding sequences for a variety of purposes including, but not limited to, modification of the cloning, processing, and/or expression of the gene product. DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences. For example, oligonucleotide-mediated site-directed mutagenesis may be used to introduce mutations that create new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, and so forth.
Vectors
In order to express a biologically active Dre polypeptide, the nucleotide sequences encoding such polypeptides may be inserted into an appropriate expression vector. Non limiting examples of suitable expression vector are described in the examples. An “appropriate vector” is typically a vector that contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host. These elements generally will include regulatory sequences, such as enhancers, constitutive and inducible promoters, and 5′ and 3′ untranslated regions in the vector and polynucleotide sequences encoding a Dre polypeptide of the invention. Such elements may vary in their strength and specificity. Specific initiation signals may also be used to achieve more efficient translation of nucleotide sequences encoding Dre polypeptides. These signals, for example, include the ATG initiation codon and adjacent sequences (e.g. the Kozak sequence). In cases where nucleotide sequences encoding the subject polypeptide and its initiation codon and upstream regulatory sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed. But in cases where only coding sequence, or a fragment thereof, is inserted, exogenous translational control signals including an in-frame ATG initiation codon should be provided by the vector. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers appropriate for the particular host cell system used (See, e.g., Scharf, D. et al. (1994) Results Probl. Cell Differ. 20:125-162).
Depending upon the embodiment, either eukaryotic or prokaryotic vectors may be used. Suitable eukaryotic vectors that may be used include MSCV, Harvey murine sarcoma virus, pFastBac, pFastBac HT, pFastBac DUAL, pSFV, pTet-Splice, pEUK-C1, pPUR, pMAM, pMAMneo, pBI101, pBI121, pDR2, pCMVEBNA, YACneo, pSVK3, pSVL, pMSG, pCH110, pKK232-8, p3'SS, pBlueBacIII, pCDM8, pcDNA1, pZeoSV, pcDNA3, pREP4, pCEP4, and pEBVHis vectors. The MSCV or Harvey murine sarcoma virus is preferred. Suitable prokaryotic vectors that can be used in the present invention include pET, pET28, pcDNA3.1/V5-His-TOPO, pCS2+, pcDNA II, pSL301, pSE280, pSE380, pSE420, pTrcHis, pRSET, pGEMEX-1, pGEMEX-2, pTrc99A, pKK223-3, pGEX, pEZZ18, pRIT2T, pMC1871, pKK233-2, pKK38801, and pProEx-HT vectors.
Methods that are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding the Dre polypeptide and appropriate transcriptional and translational control elements. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. (See, e.g., Sambrook, J. et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview N.Y., ch. 4, 8, and 16-17; Ausubel, F. M. et al. (1995) Current Protocols in Molecular Biology, John Wiley & Sons, New York N.Y., ch. 9, 13, and 16).
It is also contemplated that a variety of expression vector/host systems may be utilized to contain and express nucleotide sequences encoding polypeptides of the invention. By way of non limiting example, these include microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems transformed with viral expression vectors (e.g., cauliflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems. (See, e.g., Sambrook, supra; Ausubel, supra; Van Heeke, G. and S. M. Schuster (1989) J. Biol. Chem. 264:5503-5509; Engelhard, E. K. et al. (1994) Proc. Natl. Acad. Sci. USA 91:3224-3227; Sandig, V. et al. (1996) Hum. Gene Ther. 7:1937-1945; Takamatsu, N. (1987) EMBO J. 6:307-311; The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York N.Y., pp. 191-196; Logan, J. and T. Shenk (1984) Proc. Natl. Acad. Sci. USA 81:3655-3659; and Harrington, J. J. et al. (1997) Nat. Genet. 15:345-355). In additional embodiments, expression vectors derived from retroviruses, adenoviruses, or herpes or vaccinia viruses, or from various bacterial plasmids, may be used for delivery of nucleotide sequences to the targeted organ, tissue, or cell population. (See, e.g., Di Nicola, M. et al. (1998) Cancer Gen. Ther. 5(6):350-356; Yu, M. et al. (1993) Proc. Natl. Acad. Sci. USA 90(13):6340-6344; Buller, R. M. et al. (1985) Nature 317(6040):813-815; McGregor, D. P. et al. (1994) Mol. Immunol. 31(3):219-226; and Verma, L M. and N. Somia (1997) Nature 389:239-242).
In one aspect of the invention, accordingly, a bacterial expression system is employed. In bacterial systems, a number of cloning and expression vectors may be selected depending upon the use intended for nucleotide sequence. For example, routine cloning, subcloning, and propagation of nucleotide sequences can be achieved using a multifunctional E. coli vector such as PBLUESCRIPT (Stratagene, La Jolla Calif.) or PSPORT1 plasmid (Life Technologies). Ligation of nucleotide sequences encoding Dre polypeptides into the vector's multiple cloning sites disrupts the lacZ gene, advantageously allowing a calorimetric screening procedure for identification of transformed bacteria containing the subject recombinant molecule. When large quantities of polypeptide are needed, vectors that direct high level expression of Dre polypeptides may be used. For example, vectors containing the strong, inducible SP6 or T7 bacteriophage promoter may be used for this embodiment.
A further aspect of the invention encompasses the use of yeast expression systems. In this embodiment, a number of vectors containing constitutive or inducible promoters, such as alpha factor, alcohol oxidase, and PGH promoters, may be used in the yeast Saccharomyces cerevisiae or Pichia pastoris. In addition, such vectors advantageously direct either the secretion or intracellular retention of expressed proteins and enable integration of foreign sequences into the host genome for stable propagation. (See, e.g., Ausubel, 1995, supra; Bitter, G. A. et al. (1987) Methods Enzymol. 153:516-544; and Scorer, C. A. et al. (1994) Bio/Technology 12:181-184).
In a further aspect of the invention, a plant system may also be used for expression of Dre polypeptides. Transcription of nucleotide sequences encoding the subject polypeptide may be driven by viral promoters, e.g., the 35S and 19S promoters of CaMV used alone or in combination with the omega leader sequence from TMV (Takamatsu, N. (1987) EMBO J. 6:307-311). Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters may be used. (See, e.g., Coruzzi, G. et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; and Winter, J. et al. (1991) Results Probl. Cell Differ. 17:85-105). These constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection. (See, e.g., The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York N.Y., pp. 191-196).
An additional aspect of the invention contemplates the use of a mammalian system for expression of Dre polypeptides. In mammalian cells, a number of viral-based expression systems may be utilized. For example, in cases where an adenovirus is used as an expression vector, nucleotide sequences may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential E1 or E3 region of the viral genome may be used to obtain infective virus that will express the subject polypeptide in host cells. (See, e.g., Logan, J. and T. Shenk (1984) Proc. Natl. Acad. Sci. USA 81:3655-3659). In addition, transcription enhancers, such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells. SV40 or EBV-based vectors may also be used for high-level protein expression.
Alternatively, human artificial chromosomes (HACs) may also be employed to deliver larger fragments of nucleotide sequence than can be contained in and expressed from a plasmid. HACs of about 6 kb to 10 Mb are constructed and delivered via conventional delivery methods (liposomes, polycationic amino polymers, or vesicles) for therapeutic purposes. (See, e.g., Harrington, J. J. et al. (1997) Nat. Genet. 15:345-355).
For long term production of recombinant proteins in mammalian systems, stable expression of Dre polypeptides in cell lines is preferred. For example, nucleotide sequences encoding Dre polypeptides can be transformed into cell lines using expression vectors that may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for about 1 to 2 days in enriched media before being switched to selective media. The purpose of the selectable marker is to confer resistance to a selective agent, and its presence allows growth and recovery of cells that successfully express the introduced sequences. Resistant clones of stably transformed cells may be propagated using tissue culture techniques appropriate to the cell type.
Any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase and adenine phosphoribosyltransferase genes, for use in tk− and apr− cells, respectively. (See, e.g., Wigler, M. et al. (1977) Cell 11:223-232; Lowy, I. et al. (1980) Cell 22:817-823.) Also, antimetabolite, antibiotic, or herbicide resistance can be used as the basis for selection. For example, dhfr confers resistance to methotrexate; neo confers resistance to the aminoglycosides neomycin and G-418; and als and pat confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively. (See, e.g., Wigler, M. et al. (1980) Proc. Natl. Acad. Sci. USA 77:3567-3570; Colbere-Garapin, F. et al. (1981) J. Mol. Biol. 150:1-14). Additional selectable genes have been described, e.g., trpB and hisD, which alter cellular requirements for metabolites. (See, e.g., Hartman, S. C. and R. C. Mulligan (1988) Proc. Natl. Acad. Sci. USA 85:8047-8051). Visible markers, e.g., anthocyanins, green fluorescent proteins (GFP; Clontech), β-glucuronidase and its substrate β-glucuronide, or luciferase and its substrate luciferin may be used. These markers can be used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system. (See, e.g., Rhodes, C. A. (1995) Methods Mol. Biol. 55:121-131).
Although the presence/absence of marker gene expression suggests that the nucleotide sequence of interest is also present, the presence and expression of the gene may need to be confirmed. For example, if the sequence encoding a Dre polypeptide is inserted within a marker gene sequence, transformed cells containing the subject polypeptide can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed in tandem with a sequence encoding a subject polypeptide under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.
Generally speaking, host cells that contain the nucleotide sequence encoding Dre polypeptides may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations, PCR amplification, and protein bioassay or immunoassay techniques that include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein sequences.
Host cells transformed with nucleotide sequences encoding Dre polypeptides may be cultured under conditions suitable for the expression and recovery of the protein from cell culture. The protein produced by a transformed cell may be secreted or retained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing the subject nucleotide sequence may be designed to contain signal sequences that direct secretion of the subject polypeptides through a prokaryotic or eukaryotic cell membrane.
In addition, a host cell strain may be chosen for its ability to modulate expression of the inserted nucleotide sequences or to process the expressed protein in the desired fashion. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation. Post-translational processing that cleaves a “prepro” or “pro” form of the protein may also be used to specify protein targeting, folding, and/or activity. Different host cells that have specific cellular machinery and characteristic mechanisms for post-translational activities (e.g., CHO, HeLa, MDCK, HEK293, and W138) are available from the American Type Culture Collection (ATCC, Manassas Va.) and may be chosen to ensure the correct modification and processing of the foreign protein.
Rox Site and Lox Site Nucleotide Sequences
The invention also encompasses a rox nucleotide sequence. The rox sites typically function as substrate sites for the Dre recombinase having SEQ ID NO. 1. The Dre recombinase of the invention catalyzes site specific recombination at a rox site that is not recognized by wild-type Cre or other Cre homologues of the invention having SEQ ID Nos. 2, 3, or 4. Conversely, Dre recombinase does not catalyze site specific recombination at a lox site. The rox site of the invention consists of two 14 base pair inverted repeats separated by a 4 base pair spacer region and has the following nucleotide sequence:




A further aspect of the invention encompasses the use of lox site nucleotide sequences. The lox sites typically function as a substrate for the Cre homlogues of the invention having SEQ ID Nos. 2, 3, or 4. In general, lox site nucleotide sequences will typically consist of two oppositely oriented perfect repeats that are separated by a spacer region. For example, the loxP site consists of two 13 base pair inverted repeats separated by an 8 base pair spacer region. Lox sites suitable for use in the practice of the invention include any of loxP, loxB, loxL, or loxR. In a preferred embodiment, the lox site will be a loxP site having the following nucleotide sequence:




The rox and lox sites may be produced by a number of methods generally known in the art or as described in the examples herein. For example, rox and lox sites can be produced by a variety of synthetic techniques that are known in the art, such as the synthetic techniques for producing lox sites described by Ito et al. (1982) Nuc. Acid Res., 10: 1755; and Ogilvie et al., (1981) Science, 214: 270.
Dre/rox and Cre/lox Systems
Another aspect of the invention encompasses a Dre/rox system. The system typically comprises the Dre recombinase having SEQ ID NO. 1 and at least one rox site. The novel Dre/rox system may be used alone or in combination with other Cre/lox systems currently known in the art. A number of methods utilizing the Dre/rox system of the invention are described in detail below.
An additional aspect of the invention encompasses a Cre homologue/lox system. The system generally comprises a Cre homologue of the invention having any of SEQ ID Nos. 2, 3, or 4 in combination with at least one lox site. The Cre homologue/lox system may be used in place of the wild-type Cre/lox system in any of the application detailed herein or otherwise known in the art.
Methods Using the Dre/rox System
The Dre/rox system of the invention may be utilized in several applications, including for conditional mutagenesis and gene expression, gene replacement and deletion, and chromosome engineering. These applications are described more fully below.
It is contemplated that the rox sites of the invention may be introduced into a nucleic acid in a number of different orientations in order to achieve a desired recombination result for any given application. Since a rox site is an asymmetrical nucleotide sequence, two rox sites on the same DNA molecule can have the same or opposite orientation with respect to each other. In one embodiment, recombination between rox sites in the same orientation results in a deletion of the DNA segment located between the two rox sites and a connection between the resulting ends of the original DNA molecule. The deleted DNA segment forms a circular molecule of DNA. The original DNA molecule and the resulting circular molecule each contain a single rox site. Alternatively, recombination between two rox sites in opposite orientations on the same DNA molecule result in an inversion of the nucleotide sequence of the DNA segment located between the two rox sites. In addition, reciprocal exchange of DNA segments proximate to rox sites located on two different DNA molecules can occur.
One embodiment encompasses use of the Dre/rox system of the invention in a method for producing a site-specific recombination in a nucleotide sequence having a target DNA segment. In this method, a first and second rox site of the invention is introduced into the nucleotide sequence such that the rox sites flank the target DNA segment. The nucleotide sequence may be either in vitro, such as a plasmid in a reaction tube, or it may be in vivo, such as in a cell. The target DNA segment can be a gene or a number of other sequences of deoxyribonucleotides of homologous, heterologous or synthetic origin. In an exemplary embodiment, the target DNA segment is a gene for a structural protein, an enzyme, a regulatory molecule; or a DNA sequence that influences gene expression in the cell such as a regulatory nucleotide sequence, a promoter, or a polyadenylation nucleotide sequence. The nucleotide sequence comprising the target DNA segment flanked by the first and second rox sites are then contacted with a Dre polypeptide of the invention. The contact may take place either in vitro or in vivo. In a preferred embodiment, the Dre polypeptide will be contacted with the rox sites as a Dre nucleotide sequence operably linked to an inducible regulatory sequence, such as any of the inducible promoters described above or otherwise generally known in the art, so that its expression can be triggered at a desired time. Alternatively, the Dre polypeptide can be contacted with the rox sites according to the methods described herein or generally known in the art. In one alternative of this embodiment, the first and second rox sites have the same orientation, and contact with Dre produces a deletion of the target DNA segment. Alternatively, in another embodiment the first and second rox sites have opposite orientation, and contact with Dre produces an inversion of the nucleotide sequence of the target DNA segment. In still another alternative of this embodiment, the first and second rox sites are introduced into two different nucleotide sequences and contact with the Dre produces a reciprocal exchange of nucleotide sequence proximate to the rox sites.
Yet another preferred embodiment encompasses use of the Dre/rox system of the invention in a method comprising a means to selectively produce site-specific recombination in a number of different nucleotide sequences. Because Dre and Cre are heterospecific recombinases, a Dre/rox system and a Cre/lox system may be used together in a method for selectively producing site-specific recombination. For example, the method may comprise producing site-specific recombination at multiple different nucleotide sequences or at one or more sites within the same nucleotide sequence. The nucleotide sequences may be either in vitro, such as in a test tube, or it may be in vivo, such as the same cell or in a combination of different cells. By way of non-limiting example, when the method has two nucleotide sequences it typically will employ one Dre polypeptide and one Cre polypeptide. The Dre polypeptide recognizes rox sites, but not lox sites. The Cre polypeptide recognizes lox sites but not rox sites. Advantageously, because Dre and Cre are heterospecific, the method provides a means to selectively catalyze site-specific recombination at the two target DNA segments either simultaneously or at different times. A method for producing site-specific recombination at two target DNA segments is described in detail below.
Accordingly, in one alternative of this embodiment site-specific recombination is selectively performed at a first and a second nucleotide sequence. The method employs two rox sites, two lox sites, a Dre recombinase and a Cre recombinase. In this embodiment, a first and second rox site is introduced into the first nucleotide sequence such that the rox sites flank a first target DNA segment. The method also encompasses introducing a first and a second lox site into a second nucleotide sequence such that the lox sites flank a second target DNA segment. The first and second lox sites comprise a wild-type lox site such as any of loxP, loxB, loxL, or loxR. In a typical embodiment, the first and second lox sites comprise wild-type loxP. Depending upon the embodiment, the lox sites may be introduced into either the same nucleotide sequence as the rox sites or into different nucleotide sequence. The method additionally comprises contacting the rox sites with Dre polypeptide and contacting the lox sites with Cre polypeptide. The Dre and Cre polypeptides typically will be contacted with the nucleotide sequence comprising either the rox sites or lox sites as a Dre nucleotide sequence operably linked to an inducible regulatory sequence or as a Cre nucleotide sequence operably linked to an inducible regulatory sequence, such as any of the inducible promoters described above or otherwise generally known in the art, so that recombinase expression can be triggered at a desired time. Alternatively, the Dre or Cre polypeptides can be contacted with the nucleotide sequence comprising the rox sites or lox sites according to the methods described herein or generally known in the art. Depending upon the particular embodiment, the rox sites may be contacted with the Dre polypeptide either before, simultaneously, or after the lox sites are contacted with the Cre polypeptide. In one alternative of this embodiment, the rox sites and lox sites have the same orientation relative to each other, and contact with the particular Dre or Cre polypeptide produces a deletion of the respective target DNA segment. Alternatively, in another embodiment the rox sites and the lox sites have opposite orientation relative to each other, and contact with the particular Dre or Cre polypeptide produces an inversion of the nucleotide sequence of the respective target DNA segment. In still another alternative of this embodiment, the rox sites are each introduced into two different nucleotide sequences and contact with the particular Dre polypeptide produces a reciprocal exchange of nucleotide sequence proximate to the rox sites. In an additional embodiment, the rox sites are introduced in opposite orientation and the pair of lox sites is introduced in the same orientation. In still another embodiment, the rox sites are introduced in opposite orientation and the lox sites are introduced on two separate nucleotide sequences. In yet another embodiment, the rox sites are introduced in the same orientation and the lox sites are introduced on two separate nucleotide sequences.
In one exemplary application, the methods of the invention will be utilized to knock-in a target DNA segment, such as a gene, by use of a site-specific recombination reaction that is catalyzed by a Dre polypeptide of the invention. One preferred use for the knock-in embodiment, is for introduction of a target DNA segment into a chromosome or into a transgenic animal, such as a mouse. In this method, a first nucleotide construct comprising a nucleotide sequence encoding a Dre polypeptide operably linked to a promoter is used to site-specifically recombine a second nucleotide construct comprising two rox sites, a target DNA segment to be knocked-in, and a promoter. In a typical embodiment, the promoter employed to express the Dre polypeptide will be an inducible promoter so that the target DNA segment can be knocked-in by the Dre at a time and location controlled manner. In a typical arrangement of the second nucleotide construct, the promoter is arranged upstream of a first rox site and the second rox site is downstream of the first rox site, with an intervening nucleotide sequence disposed between the first and second rox sites. The promoter is preferably arranged so as to induce the expression of the target DNA segment to be knocked-in. An exemplary second nucleotide construct has the following arrangement:




When the Dre polypeptide is contacted with the rox sites, it binds to the sites and removes the intervening nucleotide sequence disposed between the first and second rox sites (see diagram above). After the Dre polypeptide has excised the intervening nucleotide sequence, the first rox site is left behind and the target DNA segment is operably linked to the promoter in a manner such that the promoter can cause expression of the target DNA segment.
Alternatively, in yet another exemplary application, the methods of the invention will be utilized to knock-out a target DNA segment, such as a gene, by use of a site-specific recombination reaction that is catalyzed by a Dre polypeptide of the invention. The method is typically employed to terminate expression of a gene. In many respects, the knocking-out method is performed in a substantially similar manner as the knocking-in method except the position of the promoter sequence in relation to the target DNA segment in the second nucleotide construct is different. Because the knocking-out method is employed primarily as a means to terminate gene expression, it is satisfactory if either the target DNA segment or the promoter sequence are knocked-out, either in whole or in part, from the second nucleotide construct. Suitable examples of arrangements for the first and second rox sites, the promoter sequence, and the target DNA segment within the second nucleotide construct are included in examples (a), (b) or (c):

    
    
        (a) —promoter—first rox site—target DNA segment—second rox site—
        (b) —first rox site—promoter—target DNA segment—second rox site—
        (c) —first rox site—promoter—second rox site—target DNA segment—

The knock-out method also encompasses a first nucleotide construct comprising a nucleotide sequence encoding a Dre polypeptide operably linked to a promoter. In a typical embodiment, the promoter employed to express the Dre polypeptide will be an inducible promoter so that the target DNA segment can be knocked-out by the Dre at a time and location controlled manner. When the Dre polypeptide is contacted with the rox sites, it binds to the sites and removes the intervening nucleotide sequence disposed between the first and second rox sites. Depending upon the arrangement of the second nucleotide construct, the intervening nucleotide sequence may include all or a part of the promoter or the target DNA segment, or both. This nucleotide sequence excision results in a loss of target DNA segment function, or loss of promoter function or both. A schematic showing a typical embodiment of knock-out of a target DNA segment is as follows:

    
    






The knock-in and knock-out methods described above may be utilized to introduce or excise a target DNA segment in a variety of in vivo or in vitro applications and in several organisms. By way of non-limiting example, the methods may be employed as a tool for conditional mutagenesis and gene expression, gene replacement and deletion, and chromosome engineering.
In one exemplary embodiment, the knock-in and knock-out methods are employed to produce a variety of transgenic non-human organisms. The transgenic organisms may be produced by the methods described herein or methods that are generally known in the art, such as by using homologous recombination in embryonic stem cells (See, e.g., U.S. Pat. Nos. 5,175,383 and 5,767,337.). For example when utilizing a knock-out method, mouse embryonic stem (ES) cells, such as the mouse 129/SvJ cell line, are derived from the early mouse embryo and grown in culture. Homologous recombination takes place using the Dre/rox system of the invention to knock-out a gene of interest in a tissue- or developmental stage-specific manner, as described above or as known in the art (Marth, J. D. (1996) Clin. Invest. 97:1999-2002; Wagner, K. U. et al. (1997) Nucleic Acids Res. 25:4323-4330). Transformed ES cells are identified and microinjected into mouse cell blastocysts such as those from the C57BL/6 mouse strain. The blastocysts are surgically transferred to pseudopregnant dams, and the resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains. Alternatively, when utilizing a knock-in method, polynucleotides encoding a target DNA segment can be used to create transgenic animals (mice or rats). Typically, a region of a polynucleotide encoding a target DNA segment is injected into animal embryonic stem cells, and the injected sequence integrates into the animal cell genome. Transformed cells are injected into blastulae, and the blastulae are implanted as described above.
In one non limiting example of a transgenic animal that may be produced in the practice of the invention, a knock-out mouse that no longer has a target gene in a particular cell type can be produced. Referring to FIG. 8, a transgenic mouse containing a target gene flanked by rox sites is mated with a transgenic mouse that expresses a Dre recombinase gene in only one cell type. The mouse resulting from this breeding will have both the Dre gene and the rox-flanked gene. In cells of the mouse that does not express the Dre polypeptide, the target gene will function normally. Alternatively, in a cell where the Dre is expressed, the target gene will be deleted. In a preferred alternative of this embodiment, the target gene will be conditionally knocked-out. A conditional knock-out mouse can be produced if the Dre gene is operably linked to an inducible or tissue specific promoter. When conditions needed for promoter function are provided, Dre polypeptide is expressed and the target gene is knocked out. Alternatively, if conditions needed for promoter function are not provided, Dre polypeptide is not expressed and the target gene is not knocked-out.
Introduction of Dre and Cre Sequences and rox and lox Sequences
Irrespective of the particular use of the Dre/rox system of the invention, a number of methods are suitable for introducing rox or lox site nucleotide sequences and Dre or Cre nucleotide sequences into a nucleic acid molecule or a target cell. The method selected for such introduction can and will vary depending upon the particular sequence and target cell. Generally speaking, the cell may be an in vivo or in vitro cell. For example, the nucleotide sequences can be expressed by a recombinant cell, such as a bacterial cell, a cultured eukaryotic cell, or a cell disposed in a living organism, including a non-human transgenic organism, such as a transgenic animal. By way of non-limiting example, cultured cells available for use include Hela cells, HEK 293 cells and U937 cells, as well as other cells used to express proteins.
In one exemplary embodiment of the invention, a vector, such as a vector detailed above, can be employed to introduce a suitable rox or lox site or Dre or Cre polynucleotide into a host cell. Typically, in this aspect of the invention, the polynucleotide is incorporated into an expression vector, which subsequently is utilized to transfect a target cell. Depending upon the embodiment, the cell may be a cultured cell or a cell disposed within a living organism. Irrespective of the embodiment, the vector binds to the target cell membrane, and the subject nucleotide sequence is internalized into the cell. The vector comprising the nucleotide sequence (i.e., rox or lox site or Dre or Cre) may be either integrated into the target cell's nucleic acid sequence or may be a plasmid. Irrespective of its form, the vector employed results in Dre or Cre polypeptide expression and insertion of the rox or lox sites at a desired location.
In one embodiment, the transfer vector is a retrovirus. Retroviruses can package up to 5 Kb of exogenous nucleic acid material, and can efficiently infect dividing cells via a specific receptor, wherein the exogenous genetic information is integrated into the target cell genome. In the host cell cytoplasm, the reverse transcriptase enzyme carried by the vector converts the RNA into proviral DNA, which is then integrated into the target cell genome, thereby expressing the transgene product.
In another alternative embodiment, the transfer vector is an adenovirus. In general, adenoviruses are large, double-stranded DNA viruses which contain a 36 Kb genome that consists of genes encoding early regulatory proteins and a late structural protein gene. Adenoviruses, advantageously, can be grown in high titers of purified recombinant virus (up to 1012 infectious particles/ml), incorporate large amounts of exogenous genetic information, and can broadly infect a wide range of differentiated non-dividing cells in vivo.
In yet another alternative embodiment, the transfer vector is an adeno-associated virus (AAV). AAV is a human parvovirus that is a small, single-stranded DNA virus that can infect both dividing and non-dividing cells. AAV is relatively non-toxic and non-immunogenic and results in long-lasting expression. The packaging capacity of recombinant AAV is 4.9 kb. Successful AAV-mediated gene transfer into brain, muscle, heart, liver, and lung tissue has been reported.
Exemplary transfer vectors for transfer into eukaryotic cells include MSCV, Harvey murine sarcoma virus, pFastBac, pFastBac HT, pFastBac DUAL, pSFV, pTet-Splice, pEUK-Cl, pPUR, pMAM, pMAMneo, pBI101, pBI121, pDR2, pCMVEBNA, YACneo, pSVK3, pSVL, pMSG, pCH110, pKK232-8, p3'SS, pBlueBacIII, pCDM8, pcDNA1, pZeoSV, pcDNA3, pREP4, pET21b, pCEP4, and pEBVHis vectors.
In one embodiment and by way of non limiting example, the vector will be the ApR reporter plasmid. Briefly, the ApR plasmid carries two directly repeated rox sites flanking a rrn T1T2 transcription terminator (Term) interposed between the lac promoter and neo. Dre-mediated excision at the rox sites allows neo expression to give kanamycin resistance.
The transfected cells include isolated in vitro population of cells. In vivo, the vector can be delivered to selected cells, whereby the carrier for the vector is attracted to the selected cell population.
Activation of the gene in a transfected cell can be caused by an external stress factor. For example, the transfected cells can be contacted with an etoposide or a proteosome inhibitor. In the alternative, an activator can be included in the vector in accordance with the methods detailed above.
In another alternative embodiment, the rox site, lox site, Cre or Dre nucleotide sequences can be introduced into a target cell by mechanical, electrical or chemical procedures. Mechanical methods include microinjection, pressure, and particle bombardment. Electrical methods include electroporation. Chemical methods include liposomes, DEAE-dextran, calcium phosphate, artificial lipids, proteins, dendrimers, or other polymers, including controlled-release polymers.
In one aspect of this embodiment, accordingly, a mechanical method is employed to introduce the subject nucleotide sequences into the target cell. One such method is hydrodynamic force and other external pressure-mediated DNA transfection methods. Alternatively, ultrasonic nebulization can be utilized for DNA-lipid complex delivery. In other suitable embodiments, particle bombardment, also known as biolistical particle delivery, can be utilized to introduce DNA into several cells simultaneously. In still another alternative mechanical method, DNA-coated microparticles (e.g., gold, tungsten) are accelerated to high velocity to penetrate cell membranes or cell walls. This procedure is used predominantly in vitro for adherent cell culture transfection.
In a further aspect of this embodiment, an electrical method is employed to introduce subject nucleotide sequences into the target cell. In one alternative of this embodiment, electroporation is employed. Electroporation uses high-voltage electrical impulses to transiently permeabilize cell membranes, and thereby, permits cellular uptake of macromolecules, such as nucleic acid and polypeptide sequences.
In an additional aspect of this embodiment, a chemical method is employed to introduce a selected nucleotide sequences into the target cell. Chemical methods, using uptake-enhancing chemicals, are highly effective for delivering nucleic acids across cell membranes. For example, nucleotide sequences are typically negatively charged molecules. DEAE-dextran and calcium phosphate, which are positively charged molecules, interact with nucleotide sequences to form DEAE-dextran-DNA and calcium phosphate-DNA complexes, respectively. These complexes are subsequently internalized into the target cell by endocytosis.
In another alternative embodiment, the chemical enhancer is lipofectin-DNA. This complex comprises an artificial lipid-based DNA delivery system. In this embodiment, liposomes (either cationic, anionic, or neutral) are complexed with DNA. The liposomes can be used to enclose a subject nucleic acid for delivery to target cells, in part, because of increased transfection efficiency.
In yet another alternative chemical embodiment, protein-based methods for DNA introduction may also utilized. The cationic peptide poly-L-lysine (PLL) can condense DNA for more efficient uptake by cells. Protamine sulfate, polyamidoamine dendrimers, synthetic polymers, and pyridinium surfactants may also be utilized.
In still a further chemical embodiment for nucleotide introduction, biocompatible controlled-release polymers may be employed. Biodegradable poly (D,L-lactide-co-glycolide) microparticles and PLGA microspheres have been used for long-term controlled release of DNA molecules to cells. In a further embodiment, the subject nucleotide sequences may also be encapsulated into poly(ethylene-co-vinyl acetate) matrices, resulting in long term controlled, predictable release for several months.
Similarly, as for the introduction of Dre or Cre nucleotide sequences, the Dre or Cre polypeptide can also be introduced into target cells by any of the mechanical, electrical or chemical means detailed above. Mechanical methods include microinjection, pressure, and particle bombardment. Direct microinjection of Dre polypeptide into cells in vitro occurs directly and efficiently. As with DNA-injected cells, once cells are modified in vitro, they can be transferred to the in vivo host environment. In particle bombardment, Dre polypeptide-coated microparticles are physically hurled with force against cell membranes or cell walls to penetrate cells in vitro. Electroporation, particularly at low voltage, and high frequency electrical impulses, is suitable for introduction of Dre polypeptides with in vitro or in vivo. Moreover, any of the chemical means detailed above may also be employed.
The invention also encompasses nucleic acid constructs, cells and organisms having a Dre recombinase (i.e., nucleotide or polypeptide), rox or lox site, or both a Dre and rox site.
Production of Antibodies Specific for Dre Polypeptide
Yet a further aspect of the invention encompasses the use of Dre polypeptides or proteins to produce antibodies. The antibodies may be employed in in vitro and in vivo assays or to purify a Dre polypeptide. Antibodies to any of the polypeptides suitable for use in the invention may be generated using methods that are well known in the art. Such antibodies may include, but are not limited to, polyclonal, monoclonal, chimeric, and single chain antibodies, Fab fragments, and fragments produced by a Fab expression library.
For the production of antibodies, various hosts including goats, rabbits, rats, mice, humans, and others may be immunized by injection with a subject polypeptide that has immunogenic properties. Depending on the host species, various adjuvants may be used to increase immunological response. Such adjuvants include, but are not limited to, Freund's, mineral gels such as aluminum hydroxide, and surface-active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, KLH, and dinitrophenol. Among adjuvants used in humans, BCG (bacilli Calmette-Guerin) and Corynebacterium parvum are especially preferable.
It is preferred that the oligopeptides, peptides, or fragments used to induce antibodies to a selected polypeptide have an amino acid sequence consisting of at least about 5 amino acids, and generally will consist of at least about 10 amino acids. It is also preferable that these oligopeptides, peptides, or fragments are identical to a portion of the amino acid sequence of the natural protein. Short stretches of the selected polypeptide's amino acid may be fused with those of another protein, such as KLH, and antibodies to the chimeric molecule may be produced.
Monoclonal antibodies to a polypeptide may be prepared using a technique that provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique. (See, e.g., Kohler, G. et al. (1975) Nature 256:495-497; Kozbor, D. et al. (1985) J. Immunol. Methods 81:3142; Cote, R. J. et al. (1983) Proc. Natl. Acad. Sci. USA 80:2026-2030; and Cole, S. P. et al. (1984) Mol. Cell Biol. 62:109-120.)
In addition, techniques developed for the production of “chimeric antibodies,” such as the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity can be used. (See, e.g., Morrison, S. L. et al. (1984) Proc. Natl. Acad. Sci. USA 81:6851-6855; Neuberger, M. S. et al. (1984) Nature 312:604-608; and Takeda, S. et al. (1985) Nature 314:452-45). Alternatively, techniques described for the production of single chain antibodies may be adapted, using methods known in the art, to produce Dre polypeptide-specific single chain antibodies. Antibodies with related specificity, but of distinct idiotypic composition, may be generated by chain shuffling from random combinatorial immunoglobulin libraries. (See, e.g., Burton, D. R. (1991) Proc. Natl. Acad. Sci. USA 88:10134-10137.)
Antibodies may also be produced by inducing in vivo production in the lymphocyte population or by screening immunoglobulin libraries or panels of highly specific binding reagents as disclosed in the literature. (See, e.g., Orlandi, R. et al. (1989) Proc. Natl. Acad. Sci. USA 86:3833-3837; Winter, G. et al. (1991) Nature 349:293-299.)
Antibody fragments that contain specific binding sites for Dre polypeptides may also be generated. For example, such fragments include, but are not limited to, F(ab′)2 fragments produced by pepsin digestion of the antibody molecule and Fab fragments generated by reducing the disulfide bridges of the F(ab′)2 fragments. Alternatively, Fab expression libraries may be constructed to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity. (See, e.g., Huse, W. D. et al. (1989) Science 246:1275-1281.)
Various immunoassays may be used for screening to identify antibodies having the desired specificity. Numerous protocols for competitive binding or immunoradiometric assays using either polyclonal or monoclonal antibodies with established specificities are well known in the art. Such immunoassays typically involve the measurement of complex formation between the polypeptide and its specific antibody. A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering polypeptide epitopes is generally used, but a competitive binding assay may also be employed.
Various methods such as Scatchard analysis in conjunction with radioimmunoassay techniques may be used to assess the affinity of antibodies for the subject polypeptide. Affinity is expressed as an association constant, Ka, which is defined as the molar concentration of polypeptide-antibody complex divided by the molar concentrations of free antigen and free antibody under equilibrium conditions. The Ka is determined for a preparation of polyclonal antibodies, which are heterogeneous in their affinities for multiple polypeptide epitopes, represents the average affinity, or avidity, of the antibodies for the particular polypeptides. The Ka is determined for a preparation of monoclonal antibodies, which are monospecific for a particular polypeptide epitope, represents a true measure of affinity. High-affinity antibody preparations with Ka ranging from about 109 to 1012 L/mole are preferred for use in immunoassays in which the polypeptide-antibody complex must withstand rigorous manipulations. Low-affinity antibody preparations with Ka ranging from about 106 to 107 L/mole are preferred for use in immunopurification and similar procedures that ultimately require dissociation of polypeptides, preferably in active form, from the antibody (Catty, D. (1988) Antibodies, Volume I: A Practical Approach, IRL Press, Washington D.C.; Liddell, J. E. and A. Cryer (1991) A Practical Guide to Monoclonal Antibodies, John Wiley & Sons, New York N.Y.).
The titer and avidity of polyclonal antibody preparations may be further evaluated to determine the quality and suitability of such preparation for certain downstream applications. For example, a polyclonal antibody preparation containing at least 1-2 mg specific antibody/ml, preferably 5-10 mg specific antibody/ml, is generally employed in procedures requiring precipitation of a subject polypeptide-antibody complex. Procedures for evaluating antibody specificity, titer, and avidity, and guidelines for antibody quality and usage in various applications, are generally available. (See, e.g., Catty, supra, and Coligan et al. supra.)
Generally speaking, the antibodies of the invention may be utilized in a variety of applications such as for protein purification. Alternatively, the antibodies are also used as tools to mark the presence of the Dre protein. The marker antibodies include a marker, such as a fluorescent marker, and will bind to the Dre protein.
Kits
A further aspect of the invention encompasses kits that employ the Dre/rox system of the invention.
In one embodiment, the kit is for producing site-specific recombination of a target DNA segment. Typically, a kit in this embodiment will include a purified Dre polypeptide that can catalyze site specific recombination at a rox site. The kit also comprises two isolated mutant rox nucleotide sequences. The kit will also include instructions for producing site-specific recombination of a target DNA segment.
In yet another embodiment, the kit is for producing selective site-specific recombination of two or more different target DNA segments. The kit comprises a purified Dre polypeptide, a purified Cre polypeptide, an isolated pair of rox nucleotide sequences, and an isolated pair of lox nucleotide sequences. The kit will also include instructions for producing selective site-specific recombination in the target DNA segments.
All publications, patents, patent applications and other references cited in this application are herein incorporated by reference in their entirety as if each individual publication, patent, patent application or other reference were specifically and individually indicated to be incorporated by reference.
DEFINITIONS
Cell as used herein refers to either a prokaryotic cell or an eukaryotic cell. Examples of such cells include bacterial cells, yeast cells, mammalian cells, plant cells, insect cells or fungal cells.
Conservative amino acid substitutions are those substitutions that do not abolish the ability of a subject polypeptide to participate in the biological functions as described herein. Typically, a conservative substitution will involve a replacement of one amino acid residue with a different residue having similar biochemical characteristics such as size, charge, and polarity versus non polarity. A skilled artisan can readily determine such conservative amino acid substitutions.
DNA segment refers to a linear fragment of single- or double-stranded deoxyribonucleic acid (DNA), which can be derived from any source.
The term expression as used herein is intended to mean the synthesis of gene product from a gene coding for the sequence of the gene product. The gene product can be RNA or a protein.
A gene is a hereditary unit that has one or more specific effects upon the phenotype of the organism that can mutate to various allelic forms.
Homology describes the degree of similarity in nucleotide or protein sequences between individuals of the same species or among different species. As the term is employed herein, such as when referring to the homology between either two proteins or two nucleotide sequences, homology refers to molecules having substantially the same function, but differing in sequence. Most typically, the two homologous molecules will share substantially the same sequence, particularly in conserved regions, and will have sequence differences in regions of the sequence that does not impact function.
A host organism is an organism that receives a foreign biological molecule, including an antibody or genetic construct, such as a vector containing a gene. The organism may be either a prokaryote or an eukaryote. For example, the organism may be a bacteria, a yeast, a mammal, a plant, an insect, or a fungus.
As used herein the expression lox site means a nucleotide sequence at which the gene product of the cre gene, referred to herein as Cre, can catalyze a site-specific recombination. The loxP site is a 34 base pair nucleotide sequence that can be isolated from bacteriophage P1 by methods known in the art. One method for isolating a loxP site from bacteriophage P1 is disclosed by Hoess et al., Proc. Natl. Acad. Sci. USA, 79: 3398 (1982). The loxP site consists of two 13 base pair inverted repeats separated by an 8 base pair spacer region. Other suitable lox sites include loxB, loxL and loxR sites which are nucleotide sequences isolated from E. coli. These sequences are disclosed and described by Hoess et al., Proc. Natl. Acad. Sci. USA, 79: 3398 (1982). Lox sites can also be produced by a variety of synthetic techniques that are known in the art. For example, synthetic techniques for producing lox sites are disclosed by Ito et al., Nuc. Acid Res., 10: 1755 (1982) and Ogilvie et al., Science, 214: 270 (1981).
Mutation is defined as a phenotypic variant resulting from a changed or new gene. Mutant is an organism bearing a mutant gene that expresses itself in the phenotype of the organism. Mutants include both changes to a nucleic acid sequence, as well as elimination of a sequence or a part of a sequence. In addition polypeptides can be expressed from the mutants.
A nucleic acid is a nucleotide polymer better known as one of the monomeric units from which DNA or RNA polymers are constructed, it consists of a purine or pyrimidine base, a pentose, and a phosphoric acid group.
P1-related phage is typically a phage having a similar DNA structure, life-style and immuno-crossreactivity to E. coli bacteriophage P1. Typically, P1 phages have several unique characteristics that define them as a class including: 1) they are temperate phages that can exist as an extrachromosomal replicon in its host; 2) their genomes are large, such as from about 80 to about 100 kb; and 3) they have structural proteins (e.g., capsid, tail) that are related.
Peptide is defined as a compound formed of two or more amino acids, with an amino acid defined according to standard definitions, such as is found in the book “A Dictionary of Genetics” by King and Stansfield.
Plasmids are double-stranded, closed DNA molecules ranging in size from 1 to 200 kilobases. Plasmids are incorporated into vectors for transfecting a host with a nucleic acid molecule.
A polypeptide is a polymer made up of less than 350 amino acids.
Protein is defined as a molecule composed of one or more polypeptide chains, each composed of a linear chain of amino acids covalently linked by peptide bonds. Most proteins have a mass between 10 and 100 kilodaltons. A protein is often symbolized by its mass in kDa.
Polyadenylation nucleotide sequence or polyadenylation nucleotide region refers to a nucleotide sequence usually located 3′ to a coding region which controls the addition of polyadenylic acid to the RNA transcribed from the coding region in conjunction with the gene expression apparatus of the cell.
As used herein, the term promoter region refers to a sequence of DNA, usually upstream (5′) of the coding sequence, which controls the expression of the coding region by providing the recognition for RNA polymerase and/or other factors required for transcription to start at the correct site. A “promoter fragment” constitutes a DNA sequence consisting of the promoter region. A promoter region can include one or more regions that control the effectiveness of transcription initiation in response to physiological conditions, and a transcription initiation sequence.
Regulatory nucleotide sequence as used herein, refers to a nucleotide sequence located proximate to a coding region whose transcription is controlled by the regulatory nucleotide sequence in conjunction with the gene expression apparatus of the cell. Generally, the regulatory nucleotide sequence is located 5′ to the coding region. A promoter can include one or more regulatory nucleotide sequences.
As used herein, the expression site-specific recombination is intended to include the following three events: (1) deletion of a target DNA segment flanked by rox or lox sites, (2) inversion of the nucleotide sequence of a target DNA segment flanked by rox or lox sites, and (3) reciprocal exchange of DNA segments proximate to rox or lox sites located on different DNA molecules. It is to be understood that this reciprocal exchange of DNA segments can result in an integration event.
Substrate as used herein is a site within a nucleic acid sequence recognized by a particular recombinase, wherein the recombinase catalyzes site specific recombination. For example, the substrate for Dre recombinase is a rox site and the substrate for Cre recombinase is a lox site.
Target DNA segment as employed herein can be a gene or a number of other sequences of deoxyribonucleotides of homologous, heterologous or synthetic origin. In an exemplary embodiment, the target DNA segment is a gene for a structural protein, an enzyme, a regulatory molecule; or a DNA sequence that influences gene expression in the cell such as a regulatory nucleotide sequence, a promoter, or a polyadenylation nucleotide sequence.
A vector is a self-replication DNA molecule that transfers a DNA segment to a host cell.
Wild-type is the most frequently observed phenotype, or the one arbitrarily designated as “normal”. Often symbolized by “+” or “WT.”
As various changes could be made in the above compounds, products and methods without departing from the scope of the invention, it is intended that all matter contained in the above description and in the examples given below, shall be interpreted as illustrative and not in a limiting sense.
EXAMPLES
Examples 1-4 below detail the ability of Dre recombinase or Cre homologues to catalyze site specific recombination at either a rox site or at a lox site, depending upon the particular polypeptide.
In the examples below, where indicated, the following experimental procedures and reagents were employed:
Bacteria and Phage
Bacterial strains and lysogens used in these examples are listed in Table 1. Bacteria were propagated in Luria-Bertani broth (26) with appropriate antibiotics: streptomycin (10 μg/ml), ampicillin (100 μg/ml) and chloramphenicol (34 μg/ml). Zeocin (Invitrogen) was used at a concentration of 10 μg/ml in Lennox broth (27). Phage were titered, maintained and propagated in the presence of 5 mM CaCl2. Lysogenization of DH5ΔlacU169 by selection for CmR after infection with P1 CM (a gift from N. Sternberg) generated BS610.
In general, phage stocks were prepared and titered using the indicator strain Sh-16. Strains lysogenic for P1CM, P7 c1.9, φw39 and D6 (Table 1) all spontaneously released a low number of phage after culture overnight that gave small plaques on Sh-16, indicating that these P1-like phages were capable of both lysogenic and lytic growth. Phage plate stocks (9-10 hr at 37° C.) were prepared with a fresh overnight culture of the indicated donor strain (28), and used immediately. For transduction, 0.1 ml of a fresh overnight of the recipient strain DH5ΔlacU169 was infected with an aliquot of the transducing stock. After preadsorption for 5 min at room temperature, cells were diluted to 1 ml with Luria-Bertani broth +5 mM CaCl2, incubated 50 min at 37° C. and then plated on selective medium.
DNA Sequencing and Plasmid Construction
Circular plasmid DNA of bacteriophages P1 CM, P7 c1.9, φw39, p15B and D6 was prepared using the Qiagen Large Construct Kit (Valencia, Calif.). For phages PICM, P7 c1.9, φw39 and p15B PCR primers were based on the published sequences of the P1 genes between lpa (formerly gene 10) and ref. This region encompasses the DNA packaging genes pacA and pacB, the c1 gene along with several other immunity genes, and the gene for Cre recombinase. For all of these phages at least several P1 primer pairs were identified for amplification of this interval. PCR fragments generated from each phage were sequenced directly and the resulting sequence information was used to design additional primers. A combination of PCR fragment sequencing and primer walking by direct sequencing from phage DNA was then used to obtain the complete sequence for each phage of the  ̃7 kb region from pacA to the beginning of the ref gene.
For phage D6 none of the PCR primer pairs used for P 1 or the other P1-related phages produced an amplified product. A D6 library was constructed by partial Sau3A digestion of D6 DNA, cloning into the BamHI site of pUC19 and transformed into DH5α. To eliminate smaller clones from this library it was digested with EcoRI, size-selected by agarose gel electrophoresis to contain inserts of ≧1.5 kb and religated. Shotgun sequencing identified one clone having strong similarity to the P1 pacB gene. Specific primers were designed and were used to sequence directly from D6 DNA by primer walking in both directions to obtain  ̃7 kb of flanking sequence.
DNA sequences were assembled and analyzed using Vector NTI (Invitrogen) and then compared to the corresponding region of the P1 genome, GenBank accession number AF234172. The sequences of the immC regions of phages P7 c1.9 (6751 bp), φw39 (7208 bp), p15B (7094 bp) and D6 (7644 bp) have been assigned GenBank accession numbers AY751747, AY751748, AY751749 and AY753669, respectively.
Oligonucleotide sequencing primers and linkers were synthesized by Integrated DNA Technologies (Coralville, Iowa) and restriction enzymes were from New England Biolabs (Beverly, Mass.). Annealing of the oligo's 5′-CTA GAT AAC TTT AAA TAA TTG GCA TTA TTT AAA GTT AG-3′ (SEQ ID NO. 9) and 5′-GAT CCT AAC TTT AAA TAA TGC CAA TTA TTT AAA GTT AT-3′ (SEQ ID NO. 10) and cloning into the XbaI and BamHI sites of pUC19 generated the rox plasmid pBS1051 (D6 sequence underlined). Similarly, oligo's 5′-CTA GCT ATA ACT TCG TAT AAT GTA TGC TAT ACG AAG TTG-3′ (SEQ ID NO. 11) and 5′-TCG ACA ACT TCG TAT AGC ATA CAT TAT ACG AAG TTA TAG-3′ (SEQ ID NO. 12) were cloned into a pBluescript II KS (Stratagene) derivative using NheI and SalI to give the rox plasmid pBS516. The one nucleotide difference (double underline) of this rox site from rox does not affect Cre-mediated recombination (29). Digestion of pBS1051 with either XbaI+AlwNI or BamHI+AlwNI and ligation with the XbaI-BamHI zeo fragment from pZeoSV (Invitrogen) generated the rox2-zeo plasmid pBS1080. The analogous rox2 zeo plasmid pBS890 was constructed by blunt-ending the 600 bp FokI-SalI zeo fragment from pZeoSV and cloning it into the SmaI site of the rox2 vector pBS246 (30). The dre gene was amplified with Pfu DNA polymerase (Stratagene) from D6 DNA with the oligo's 5′-AGA TGG TAC CAG GAG GAT ATC AAT ATG AGT GAA TTA ATT ATC TCT GG-3′ (SEQ ID NO. 13) and 5′-CTT TAG TCT AGA TTC ATT ATG AAT CCA TCA AGC GGC-3′ (SEQ ID NO. 14) (D6 coding region underlined), digested with KpnI and XbaI and cloned into the CmR arabinose-inducible vector pBAD33 (31) to generate pBS1081. The analogous pBAD33-cre construct has been described previously (6). All cloned oligos and PCR products were confirmed by DNA sequencing.
The dre gene was placed under the control of the EF1α promoter for mammalian expression by replacing the KpnI-XbaI GFP fragment of pBS377 (32) with the KpnI-XbaI dre fragment from pBS1081. The EF1α-cre expression plasmid pBS513 (33) and the control CMV-lacZ plasmid p324 (34) have been described previously. To construct the EGFP expression vector pBS504 the following three DNA fragments were cloned between the unique HindIII and EcoRI sites of pBS397 (35): the EcoRI-KpnI EF1α fragment of pBS377, the KpnI-XbaI EGFP fragment of pEGFP-1 (Clontech, Palo Alto, Calif.) and the XbaI-EcoRI fragment from pBS377 carrying the polyA signal. The EcoRI-HindIII rox2 zeo cassette from pBS1080 was blunt-end ligated into the EcoRV site lying between the EF1α promoter and the EGFP gene in pBS504 to generate the rox recombination reporter plasmid pBS1083.
DNA Analysis
A PSI-BLAST search (36) was performed to determine closest homologs of identified genes. The bendability/curvature propensity plot were calculated with the bend it server, using DNase I-based bendability parameters (37) and the consensus bendability scale (38).
Site-Specific DNA Excision
Plasmids pBAD33, pBAD33-dre or pBAD33-cre were electroporated into DH5αcells containing either the reporter plasmid pBS890 or pBS1080, incubated for 1 hr at 37° C. in SOB media (6) and then plated, selecting for CmR ApR to ensure retention of both plasmids in the resulting transformants. To ensure that recombinase was not expressed at inordinately high levels the pBAD plasmids were used without overt arabinose induction (9). The next day colonies were individually tested for drug resistance markers by growth on appropriate antibiotic containing plates.
CHO-K1 cells were transfected using Polyfect (Qiagen, Valencia, Calif.) with 1.5 μg DNA per well of a 6-well dish as recommended by the manufacturer. Co-transfections used a 9:1 ratio of Cre, Dre or lacZ expression vector DNA to either pBS504 or pBS1083 as indicated. Fluorescence was monitored 2 days after transfection with a Leica DMR microscope mounted with an Optronics Magnafire digital camera, and DNA was then prepared for PCR analysis. Recombination was detected by PCR (31 cycles 30 s 94° C., 30 s 60° C., 60 s 72° C.) using the sense EF1 α primer KC315 5′ GCTTGGCACTTGATGTAATTCTCCTTG 3′ (SEQ ID NO. 15) and the antisense EGFP primer BSBS382 5′ GGTCAGCTTGCCGTAGGTGGC 3′(SEQ ID NO. 16). Predicted product sizes are 302 bp for pBS504, 1704 bp for pBS1083 (not observed because of the short cycling times used) and 389 bp for the Dre excision product of pBS1083.
Example 1
A comparison was performed of genes from Cre homologues. Even though the immC region of phage P1 does not cross-hybridize to phage D6 DNA it seemed likely that D6 would carry a site-specific DNA recombination system like that of P1, and that this recombinase/recombinase recognition site would lie in the D6 immC region. Presence of a recombinase activity was checked genetically. If there were a Cre-like D6 recombinase, then infection of the D6 clone plasmid library with phage D6 would identify relevant plasmid clones as a result of low level site-specific integrative recombination between phage DNA and plasmids carrying a D6 recombination site. Thus, D6 would be able to transduce relevant ApR clones to a new bacterial recipient where they would be excised from the phage genome by the D6 site-specific recombinase to take up plasmid residency. A similar strategy was used previously to pick-up rox plasmid clones using phage lambda carrying the rox-cre region of P1 (39). Table 2 shows that D6 could transduce the ApR marker from a library of D6 clones, but not from a strain having an anonymous randomly chosen D6 cloned insert or from a non-plasmid strain, Sh-16. These results indicate that, like P1, D6 carries a site-specific DNA recombinase that catalyzes both integrative and excisive recombination.
To compare the recombinase genes, as well as the adjacent c1 and pac genes, the  ̃7 kb immC region from four P1-related phages: P7 c1.9, φw39, p15B and D6 was sequenced. For the first three of these phages the gene organization of this region was identical to that of phage P1. That of phage D6 had a similar structure (FIG. 1). To confirm that this D6 region did indeed harbor the recombinase site that was detected previously, 6 randomly chosen plasmids transduced by D6 were sequenced, naming them Pick-Up clones PU-5, etc. All carried overlapping sequences from the same immC DNA region was sequenced (FIG. 1), strongly indicating that each carried a D6 DNA site for site-specific recombination.
The overall gene organization of the sequenced region from D6 is similar to the pac-ref region of P1 despite low sequence identity. On the left (FIG. 1) there is a gene showing 24% similarity to P1's lpa (late promoter activating protein) or gene 10. This is followed by DNA packaging genes (pacA and pacB), a c1 repressor gene and a D6 recombinase “dre” similar to the P1 cre gene. There are also several non-conserved ORFs in this region of the D6 genome, and an insertion of a gene similar to the deoxyuridine 5′-triphosphate nucleotidohydrolase of the photosynthetic bacterium Rubrivivax gelatinosus (dut; FIG. 1).
Example 2
P1 packages its DNA using a terminase composed of the PacA small subunit and the PacB large subunit. Table 3 compares the PacA's and PacB's for each of the 5 P1 family phages. Although PacA was very similar (97-100%) for phages P1, P7, φw39 and p15B, the PacA protein of D6 was 57 amino acids longer and showed only 18% similarity to PacA from any of the other phages. D6 PacB was somewhat more similar to the PacB proteins of the other P1 family members (53-54%) and was slightly larger. Interestingly, the other four phages form two clear subgroups: P1 and P7 are nearly identical to each other, likewise φw39 and p15B are nearly identical, with the two subgroups 89% similar to each other. In addition, the defective phage p15B carried a nonsense mutation that truncates the C-terminus of PacB.
P1 headful DNA packaging proceeds from a specific 162 bp pac site located within the 5′ end of the pacA structural gene (FIG. 3). The site consists of two clusters of hexanucleotide repeats flanking a central region where DNA cleavage occurs (40). Each of the hexamer repeats has a core 5′-GATC dam methylation site. PacA protein binds to the hexamer repeats in a DNA methylation-dependent manner and then associates with PacB to loop the two binding domains in an IHF and HU-dependent manner prior to DNA cleavage (41,42). In phages P7, φw39 and p15B this 162 bp region differed from that of P1 by 4, 9 and 2 bp, respectively, but the integrity of the seven hexamer repeats was completely preserved, suggesting that all four of these phages package DNA in the a similar manner. Similarly, the IHF binding site adjacent to the region of DNA cleavage was identical in φw39 and P1, although in P7 and p15B this site displayed a one nucleotide change from 5′-AAACAAAGAGTTA (SEQ ID NO. 17) to 5′-AAACAGAGAGTTA (SEQ ID NO. 18) (change underlined).
The low degree of similarity between D6 and P1 PacA proteins suggests that their DNA binding specificities may differ. In addition there was no region of clustered dam sites characteristic of the P1 pac site and no consensus IHF binding site in the D6 pacA gene (FIG. 3), further suggesting a difference in the DNA recognition specificities of the P1 and D6 terminases. Interestingly, though, there was a potentially curved DNA sequence in the 5′ region off the D6 pacA gene (asterisk, FIG. 3). The curvature-propensity plot, calculated with DNase I-based trinucleotide parameters, contained one peculiar maximum in this region, whose magnitude (14.7°/helical turn) exceeded the value calculated for Columba risoria bent satellite DNA (13.5°/helical turn). No such potentially curved DNA was detected in the pacA genes of P1, P7, φw39 or p15B.
Example 3
The C1 repressor and immunity genes were examined for each phage. There was little difference in the immunity genes of the immC region for the four phages P1, P7, φw39 and p15B (FIG. 1). The C1 repressors of P1 and P7 had previously been shown to be identical (43), so the three amino acid changes (A110V, P190L and D277S) in P7 c1.9 are likely specific to this P7 temperature-sensitive repressor. Aside from a K268R change in φw39, the p15B and φw39 C1 repressors were identical to that of P1. The Coi (c one inactivator) protein sequence was identical for all four of these phages except for an A62T substitution in p15B. The predicted imcA and imcB gene products were also identical except for an A27T difference in P1. Interestingly these two genes were fused in P7. Some variation was seen for C8 among phages P1, P7, φw39 and p15B but all showed ≧85% similarity. On the other hand, the D6 C1 protein was only 16% similar to P1 C1. Moreover, in phage D6 the distance between c1 and the recombinase gene dre was much shorter than the corresponding region in P1, and the coi and imcA/imcB genes were missing.
Example 4
Dre and Cre homologue recombination activity was examined. Among the four phages P1, P7, φw39 and p15B the 343 amino acid Cre recombinase was highly conserved (FIG. 1). The φw39 Cre differed from P1 Cre by the single amino acid change T206A, P7 Cre differed from P1 Cre by the two changes A178S and G280D, and the p15B Cre differed from P1 Cre by three changes: P107L, A249S and A252P. Similarly conserved among these four phages was cra (putative cre associated function), an open reading frame of unknown function adjacent to cre originally designated orfl (44). The putative P1 Cra protein differed from that of P7, φw39 and p15B by 3, 1 and 2 amino acids respectively. In accord with the nearly identical Cre recombinases of these four phages all of them carried an identical 34 bp rox site located midway between c1 and cre.
In contrast, D6 displayed a recombinase gene only 39% similar to the P1 cre gene and no 34 bp rox site anywhere in this 7.6 kb region of DNA (FIG. 1). This suggested that the D6 recombinase (dre) might recognize a recombination site distinct from rox. As noted above, the interval between c1 and dre was much shorter in D6 than the corresponding region in P1, and no open reading frame corresponding to cra was found. From the D6 pick-up experiments it was deduced that a recombination site must lie within the D6 sequence present in the PU7 clone (FIG. 1), a 2.1 kb fragment that includes both dre and the interval between c1 and dre.
The P1 rox site consists of two 13 bp inverted repeats flanking an asymmetrical 8 bp spacer region that imparts an overall directionality to the recombination site. In the c1-dre interval from D6 two DNA sequences were detected resembling this structure. FIG. 3 shows a 69 bp portion of the c1-dre interval within which is a 32 bp sequence having two perfect 14 bp inverted repeats (solid arrows) separated by 4 bp. Just abutting this potential Dre recombination site was a similarly configured 18 bp DNA sequence with less perfect inverted repeats (dashed line arrows).
To determine the involvement of either of these DNA sequences in Dre-mediated recombination several test plasmids were constructed and evaluated for their ability to recombine with D6 using the D6 plasmid transduction assay. Table 4 shows that D6 transduces PU7, but not pUC19, from a recA host to a recA recipient at high frequency. Taking advantage of a fortuitous DraI site present in each 14 bp inverted repeat (FIG. 3, lower case) the 32 bp candidate site was mutated by deleting the 12 bp between the DraI sites site to generate a PU7 derivative, PU7-ΔDra1. The lack of D6 transduction of this plasmid (Table 4) indicated that the integrity of the 32 bp region was necessary for recombination and suggested that the adjacent shorter imperfect inverted repeat region was not a recombination site. The 32 bp region might thus be the region of crossover (X-over) recombination or rox site for Dre recombinase. To test this sequence was placed on pUC19 and tested for its ability to undergo recombination with D6. Transduction of pUC19 carrying the putative rox site occurred at high frequency (Table 4), confirming that the rox sequence was sufficient for recombination. Moreover, no transduction of a pUC19-rox plasmid was obtained, indicating that D6 can not recombine with the P1 rox site.
To establish whether the Dre recombinase was the only D6-encoded protein required for recombination at rox, as a first step in this direction, the dre structural gene was placed under the control of the arabinose-inducible promoter in plasmid pBAD33. SDS-PAGE and Western blot analysis showed that this construct expressed a Cre-sized protein of  ̃36 kDa that cross-reacted with a polyclonal antibody to Cre (FIG. 5).
Dre-mediated recombination was assayed using a rox2 zeo construct (FIG. 6) that carries two directly repeated rox sites flanking zeo, a gene that confers resistance to the antibiotic zeocin. Cells carrying this construct become sensitive to zeocin upon loss of zeo by excisive recombination at the rox sites. Table 5 shows that transformation of the rox2 zeo strain with the compatible CmR plasmid pBAD33-dre resulted in loss of zeocin resistance in all transformants. No loss of zeo was seen with a control plasmid having no insert or with a construct expressing Cre recombinase. Conversely, a strain carrying a rox2 zeo construct was refractory to excisive recombination by the Dre-expressing construct but readily underwent excisive recombination with loss of zeo when tranformed with the Cre-expressing construct. Sequencing of the rox plasmid from several zeocin sensitive colonies confirmed that precise excisive recombination had occurred at the rox site. Thus Dre mimicked Cre's ability to perform excisive recombination but the two recombinases were heterospecific, that is, Cre did not catalyze recombination at rox and Dre did not catalyze recombination at rox.
Unlike many members of the tyrosine recombinase family, Cre recombinase of phage P1 requires no accessory phage or bacterial proteins for recombination. This characteristic of Cre is illustrated by Cre's ability to catalyze DNA recombination in a variety of eukaryotic cells (45,46). To determine whether Dre also had no requirement for accessory bacterial proteins, and thus would be able to catalyze DNA recombination in a mammalian cell, Dre's ability to recombine rox sites in CHO cells was tested. Dre recombination was assayed by using a reporter plasmid that would express EGFP in transfected cells only if activated by recombination between two directly repeated rox sites (FIG. 7A). In the reporter plasmid a rox2 zeo cassette is inserted between the EF1α promoter and the EGFP gene, positioning both an upstream zeo gene and a polyadenylation site act to block EGFP expression. Dre-mediated recombination at the flanking rox sites would remove these blocks. To express Dre, a second plasmid vector was constructed in which the dre gene was placed under the control of the EF1α promoter. FIG. 7B shows that co-transfection of CHO cells with the rox reporter construct and the Dre expression vector produced a significant number of green fluorescent cells (panel i), whereas there was no detectable fluorescence was when the reporter was co-transfected with a Cre expression plasmid (panel ii). he frequency of fluorescent cells from Dre-mediated activation of the EGFP gene was similar to the transfection efficiency of an EGFP reporter plasmid having no rox2 zeo cassette (panel iii). PCR confirmed that recombination at the rox sites in cells co-transfected with the Dre expression plasmid and that no recombination occurred at the rox sites in cells co-transfected with the Cre expression plasmid (FIG. 7C). Thus, Dre-mediated recombination requires no bacterial proteins for efficient DNA recombination at rox.
The tables referenced in the examples are shown below.







TABLE 1







Bacterial strains









Strain
Relevant Genotype
Source/Description





Sh-16 (Shigella
StrR
J. Scott (52)


dysenteriae)


Escherichia coli:


DH5ΔlacU169
recA lacU169
M. Berman


DH5α
recA lacU169
Invitrogen



(φ80dlacΔM15)


BS610
DH5ΔlacU169
this work



(P1 CM r− m−)


BR231
(P7 c1.9)
M. Yarmolinsky (53)


39W (CCUG#11425)
(φw39)
Univ. of Göteborg,




Sweden (22)


15 (CGSC#4905)
(p15B)
E. coli Genetic Stock




Center (21)


C600(D6)
(D6)
J. Scott (25)


BS1379
DH5α [pBS516]
this work/rox plasmid


BS1478
DH5α [pUC19]
this work


BS2060
DH5α [pBS1051]
this work/rox plasmid


BS2061
DH5α [PU-7]
this work


BS2080
DH5α [PU-7 ΔDra]
this work


BS2089
DH5α [pBS1080]
this work/pUC-rox2-zeo


BS1850
DH5α [pBS890]
this work/pUC-rox2-zeo
















TABLE 2







D6 “pick-up” identification of a D6 recombination site











D6 Transducing stock
ApR colonies
Frequency (ApR/pfu)















D6.Sh-16
0
<2.5 × 10−8



D6.Lib1000a
32
 1.7 × 10−5



D6.clone#3b
0
<8.3 × 10−7







aThe donor strain was a pool of 1000 colonies from the EcoRI-sized D6 library.



bThe donor strain was a randomly chosen clone from the EcoRI-sized D6 library.













TABLE 3







DNA packaging genes









Similarity













Protein/phage
Size (aa)
P1
P7
φw39
p15B
D6
















PacA








P1
397
100
99
96
97
18


P7
397

100
96
97
18


φw39
397


100
98
18


p15B
397



100
18


D6
454




100


PacB


P1
494
100
100
89
89
53


P7
494

100
89
89
53


φw39
494


100
100
54


p15B
 494*



100
54


D6
502




100





*Amber mutation at aa position 473.













TABLE 4







Plasmid transduction by phage D6










Plasmid (donor strain)
D6 Transduction Frequency (ApR/pfu)














pUC19
<0.00004



PU7
0.08



PU7-ΔDra
<0.001



pUC-rox
0.09



pUC-rox
<0.00004

















TABLE 5







Dre-mediated excision in E. coli











Resident Reporter
Transformants tested












Plasmid
Construct
CmR ApR
ZeoR
% Excision














pBAD33
rox2 zeo
152
152
0


pBAD33-dre
rox2 zeo
152
0
100


pBAD33-cre
rox2 zeo
152
152
0


pBAD33
rox2 zeo
152
152
0


pBAD33-dre
rox2 zeo
152
152
0


pBAD33-cre
rox2 zeo
152
0
100









CONCLUSION
Comparison of the pac-c1 regions of P1 and four other P1-related phages showed that the gene organization of this region is conserved, and that the gene products of this region are nearly identical for all phages with the exception of D6. From sequence comparisons the specificity of the D6 DNA packaging, immunity and site-specific DNA recombinase functions are likely to be different from those of P1. The heterospecificity for the DNA recombinase Dre of D6 has been confirmed and it has also been shown that Dre can catalyze site-specific DNA recombination in mammalian cells.
All references cited in the preceding text of the patent application or in the following reference list, to the extent that they provide exemplary, procedural, or other details supplementary to those set forth herein, are specifically incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
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## Claims

1. A purified Dre recombinase, the amino acid sequence of which comprises a sequence at least 95% identical to SEQ ID NO. 1, which recombinase catalyzes site specific recombination at a rox site.

2. The purified Dre recombinase of claim 1, the amino acid sequence of which comprises a sequence at least 99% identical to SEQ ID NO. 1, which recombinase catalyzes site specific recombination at a rox site.

3. The purified Dre recombinase of claim 1, the amino acid sequence of which comprises SEQ ID NO. 1 with 1 to 15 conservative amino acid substitutions, which recombinase catalyzes site specific recombination at a rox site.

4. The purified Dre recombinase of claim 1, the amino acid sequence of which comprises SEQ ID NO. 1 with 1 to 10 conservative amino acid substitutions, which recombinase catalyzes site specific recombination at a rox site.

5. The purified Dre recombinase of claim 1, the amino acid sequence of which comprises SEQ ID NO. 1.

6. The purified Dre recombinase of claim 1, the amino acid sequence of which consists of SEQ ID NO. 1.

7. An isolated polypeptide, the amino acid sequence of which comprises SEQ ID NO:1.

8. An isolated polypeptide, the amino acid sequence of which consists of SEQ ID NO:1.