WO2005123923A2

WO2005123923A2 - Inducer specific tetracycline repressor proteins and methods of use thereof

Info

Publication number: WO2005123923A2
Application number: PCT/EP2005/006551
Authority: WO
Inventors: Wolfgang Hillen; Eva Henssler
Original assignee: Wolfgang Hillen; Eva Henssler
Priority date: 2004-06-17
Filing date: 2005-06-17
Publication date: 2005-12-29
Also published as: WO2005123923A3

Abstract

The present invention relates to polynucleotides encoding inducer-specific tetracycline repressor proteins which are specifically induced by a tetracycline analog lacking a 4-dimethylamino grouping, vectors or host cells comprising said polynucleotides, or polypeptides being encoded thereby. Moreover, the present invention encompasses antibodies against the polypeptides, non-human transgenic animals comprising the polynucleotides or vectors or pharmaceutical compositions or uses. Finally, the present to invention pertains to methods for producing polypeptides or polynucleotides or for regulating transcription of a tet-operator-linked gene.

Description

Inducer Specific Tetracycline Repressor Proteins And Methods Of Use Thereof

The present invention relates to polynucleotides encoding inducer-specific tetracycline repressor proteins which are specifically induced by a tetracycline analog lacking a 4- dimethylamino grouping, vectors or host cells comprising said polynucleotides, or polypeptides being encoded thereby. Moreover, the present invention encompasses antibodies against the polypeptides, non-human transgenic animals comprising the polynucleotides or vectors or pharmaceutical compositions or uses. Finally, the present invention pertains to methods for producing polypeptides or polynucleotides or for regulating transcription of a tet-operator-linked gene.

The transcriptional regulator protein Tet repressor (TetR) combines high affinity for its cognate DNA sequence (tetO) with sensitive induction by tetracycline (tc) and especially the more potent analogs doxycycline (dox) and anhydrotetracycline (ate) (1). TetR is a homodirneric protein built up of 10 α-helices in each subunit, and is one of the best investigated prokaryotic effector dependent regulatory proteins. The TetR protein regulates the expression of tetracycline resistance genes in gram negative bacteria, e.g., Escherichia coli, in a tc dependent fashion (reviewed in Hillen & Berens, 1994). In the absence of tc, a TetR protein dimer binds to operator sequences (tetO) and inhibits expression of the tetracyline resistance gene (tetA). When the inducer Tc enters the cell and binds to TetR, the affinity for tetO is reduced and TetR dissociates from tetO, allowing expression of tetA. Since inducers can penetrate most cells by passive diffusion, there is widespread use of TetR based gene regulation in pro- and eukaryotes (2).

The crystal structures of the [tc-Mg]⁺ bound, the operator boxmd and free TetR have been solved (3, 4). TetR is an all α-helical protein with ten α-helices composing a monomeric unit, and two subunits forming the homodimer. It contains two N-terminal DNA binding domains build of helices αl to α3 of each subunit. Helix α4 connects the N-terminal domain with the C-terminal domain consisting of helices α5 to αlO of both subunits. The inducer binding region is located inside the C-terminal domain where each chemical function of tc is contacted by the protein (see Figure 2), leading to the nM affinity of the drug for TetR. Despite of this intimate interaction, TetR shows an unexpected plasticity for induction by tc variants (5). A TetR H64K S135L mutant has been described, wherein inducer specificity was modified such that TetR was induced by cmt3, a sancycline derivative lacking the 4-dma grouping (see Figxire 1 for chemical structures), instead of tc (7). However, in the TetR H64K S135L mutant, TetR also responded to high affinity inducers ate and dox classifying it as a relaxed specificity mutant (7).

The technical problem xinderlying the present invention must be seen in the provision of means and methods for allowing independent expression control of different genes in the same cell. The technical problem is solved by the embodiments characterized in the claims and herein below.

Accordingly, the present invention relates to a polynucleotide comprising a nucleic acid molecule selected from the group consisting of a) a nucleic acid molecule having a nucleic acid sequence as shown in 9, 13, 21, 23, 29, 35, 37, 47, 49, 63 or 65; b) a nucleic acid molecule encoding a polypeptide having an amino acid sequence as shown in 10, 14, 22, 24, 30, 36, 38, 48, 50, 64 or 66; c) a nucleic acid molecule having a nucleic acid sequence which is at least 70 % identical to the nucleic acid sequence of a) or b), wherein the polypeptide encoded by said nucleic acid molecule is specifically induced by a tetracycline analog lacking a 4-dma (4-dimethylamino) grouping, d) a nucleic acid molecule encoding a polypeptide having an amino acid sequence which is at least 70 % identical to the amino acid sequence of a polypeptide encoded by the nucleic acid molecule of any one of a) to c), wherein the polypeptide encoded by said nucleic acid molecule is specifically induced by a tetracycline analog lacking a 4-dma grouping, and e) a nucleic acid molecule comprising a biologically active fragment comprising at least 100 contiguous nucleotides of the nucleic acid molecules of any one of a) to d), wherein said fragment encodes a polypeptide which is specifically induced by a tetracycline analog lacking a 4-dma grouping; f) a nucleic acid molecule comprising a biologically active fragment comprising at least 30 contiguous amino acids of the amino acid sequence encoded by the nucleic acid molecules of any one of a) to d), wherein the polypeptide encoded by said nucleic acid molecule is specifically induced by a tetracycline analog lacking a 4-dma grouping. The polynucleotides referred to above encode polypeptides which are specifically induced by a tetracycline analog lacking a 4-dma grouping. More preferably, the polynucleotides are polynucleotides encoding a tet-repressor which is specifically induced by 4-ddma (4- dedimethylamino-anhydrotetracyline) derivatives of tetracycline (referred to herein sometimes as 4-ddma derivatives), but not by ate (anhydrotetracycline) or doxycycline.

A nucleic acid molecule as referred to above, which is at least 70 % identical to a specific nucleic acid sequence, is more preferably at least 75 %, 80 %, 85 %, 90 %, 95 %, 98 % or 99 % identical on the nucleotide level to the said specific nucleic acid sequence. These nucleic acid molecules encode tet-repressor polypeptides which can be specifically induced by a tetracycline analog lacking a 4-dma grouping. More preferably, the said tet-repressor is inducible by 4-ddma derivatives, but not by ate or doxycycline. Moreover, the nucleic acid molecules encoding a polypeptide having an amino acid sequence, which is at least 70 % identical to the specific amino acid sequences referred to above, encode more preferably a polypeptide which is specifically inducible a tetracycline analog lacking a 4-dma grouping and which is at least 75 %, 80 %, 85 %, 90 %, 95 %, 98 % or 99 % identical on the amino acid level to the specific acid amino sequences referred to above. Most preferably, the polypeptides encoded by said nucleic acid molecules are inducible by 4- ddma derivatives, but not by ate or doxycycline.

The biologically active fragments referred to above are fragments which when comprised by a polypeptide are sufficient to contribute inducibility by a tetracycline analog lacking a 4-dma grouping. Most preferably, the polypeptide comprising the biologically active fragment will be specifically inducible by 4-ddma derivatives, but not by ate or doxycycline.

More preferably, said polynucleotide of the present invention further encodes a polypeptide domain which directly or indirectly activates transcription in the exikaryotic cell. Most preferably, said polypeptide domain which directly or indirectly activates transcription in the eukaryotic cell consists of at least one, at least two or at least three copies of the NP-16 minimal activator domain, the structure of which is further described below. Most preferably, said polynucleotides encode cTA2 5 or cTA2^D4c-5 as described in Example 4. In another preferred embodiment, the polynucleotides of the invention referred to above encode a TetR which specifically recognizes a modified tetO, preferably tetO-4c as described in Helbel and Hillen, 1998.

The present invention also relates to a vector containing the aforementioned polynucleotides of the present invention. Preferably, the vector is selected from the group consisting of pCM190GFP+, pUHD15-l, pREP9, pUHD and baculovirus expression vectors.

The present invention furthermore relates to a host cell comprising the polynucleotide or the vector of the present invention referred to above. Preferably, said host cell is a plant cell, an insect cell, a fungal cell, a bacterial cell or mammalian cell. Most preferably, said host cell further comprises a expressible polynucleotide under the control of the tet operator (tetO). The structure of the tetO is well known in the art and described below. The term "expressible polynucleotide under the control of the tet operator" encompasses endogenous and exogenous polynucleotides, e.g. endogenous genes or exogenous transgenes, which are operatively linked to the tet operator as to allow control of the expression by the tet system as specified in detail below.

The present invention further encompasses a polypeptide encoded by the polynucleotide or the vector of the present invention or which is obtainable by the host cell of the present invention. It is to be understood that a polypeptide which is obtainable by the host cell of the present invention as used herein refers to a polypeptide which is encoded by the polynucleotide of the present invention. However, said polypeptide obtainable by the host cell of the present invention may differ from the polypeptide encoded by the polynucleotide of the present invention in that it may contain modifications due to posttranslational modifications. Posttranslational modifications include proteolytic cleavage of one or more amino acid residues from the polypeptide, phosphorylation of the polypeptide, glykosylation of the polypeptide or other known modifications.

The invention also relates to an antibody which specifically recognizes the polypeptide of the present invention. Suitable antibodies and techniques how to develop those antibodies are described in detail below. Preferably, the antibody is a polyclonal or monoclonal antibody. Moreover, the present invention relates to a non-human transgenic animal comprising the polynucleotide or the vector of the present invention. Transgenic animals and techniques for producing them are described in detail below. In a preferred embodiment, the transgenic animal comprises the polynucleotide or the vector of the present invention homologously recombined with an endogeneous gene. In another preferred embodiment, the non-human transgenic animal is selected from the group consisting of monkey, cow, goat, sheep, dog, cat, rabbit, rat, mouse.

The present invention furthermore encompasses a pharmaceutical composition comprising the polynucleotide, the vector, the host cell, the polypeptide or the antibody of the present invention. The pharmaceutical composition may be applied in gene therapy. The present invention also includes the use of the polynucleotide, vector, polypeptide, host cell or antibody of the present invention for the manufacture of a pharmaceutical composition to be applied in gene therapy. The term "pharmaceutical composition" as used herein is described in detail below.

Moreover, the present invention relates to a method for producing a polypeptide comprising a) culturing a host cell of the invention further comprising a polynucleotide encoding the polypeptide to be produced (i.e. the polypeptide of interest) operatively linked to a tet operator sequence; and b) isolating the polypeptide to be produced from said host cells or from the cell culture medium.

The present invention in a further embodiment relates to a method for regulating transcription of a tet operator-linked gene in a host cell comprising providing a host cell of the invention; and modulating the concentration of a tetracycline analog lacking a 4-dma grouping in contact with the host cell.

In a further embodiment, the present invention relates to a method for producing a polynucleotide encoding a polypeptide which is specifically induced by a tetracycline analog lacking 4-dma grouping comprising mutating the codons for amino acids 82 and 138 of the mutated tet repressor H64K S135L. Mutating the aforementioned codons can be done by basic molecular biology techniques well known to ther person skilled in the art. Preferably, the codons may be mutated by site-directed mutagenesis as described in the accompanied Examples. A polynucleotide encoding a polypeptide which is specifically induced by a tetracycline analog lacking a 4-dma grouping can be done by determining the inducibility of a reporter gene which is under the control of the tet operator in the presence of a polypeptide encoded by the polynucleotide to be screened and in the presence and/or absence of a tetracycline analog lacking a 4-dma grouping. An example for a suitable screening procedure is given in the accompanied Examples. The method referred to above, may not only comprise the identification of a suitable polynucleotide, but also preferably includes the production of said polynucleotide, once identified, by techniques well known in the art.

Isolation of a TetR mutant specifically induced by tc analogs lacking the 4-dimethylamino grouping (4-ddma) such as 4-dedimethylaminoanhydrotetracycline (4-ddma-atc) may be useful for gene regulation in prokaryotes and eukaryotes. In combination with specific operator binding and different dimerization specificities (20, 21, 22), TetR mutants with inducer affinity distinction will allow fully independent expression control of more than one gene by the Tet system in the same cell. Thus, there is a need for inducer specific TetR mutants which can be specifically induced by tc derivatives lacking the 4-dma grouping.

The invention provides an inducer specific modified tetracycline repressor (TetR) characterized by having inducer affinity distinction between tetracycline (tc) analogs, wherein the modified TetR is induced by a tetracycline (tc) analog lacking a 4- dimethylamino (4-dma) grouping. In one embodiment, the modified TetR binds to tetracycline operator (tetO) in the absence of the tc analog. In another embodiment, the modified TetR binds to tetracycline operator (tetO) in the presence of the tc analog.

The invention also provides an inducer specific modified TetR comprising the following mutations: H64K, S135L, and SI 381. In one embodiment of the invention, the inducer specific modified TetR further comprises a transcriptional activator. In another embodiment of the invention, the inducer specific modified TetR further comprises a transcriptional inhibitor.

The invention provides an inducer specific modified tetracycline repressor (TetR) characterized by having inducer affinity distinction between tetracycline (tc) analogs, wherein the modified TetR is induced by dedimethylamino-anhydrotetracycline (4-ddma- atc). The invention describes modified TetR that is induced by a tetracycline (tc) analog lacking a 4-dimethylamino (4-dma) grouping and has decreased affinity for tetracycline (tc) and tc analogs containing a 4-dma grouping. In one embodiment, the modified TetR binds to tetracycline operator (tetO) in the absence of the tc analog lacking a 4-dma grouping. In another embodiment, the modified TetR binds to tetracycline operator (tetO) in the presence of the tc analog lacking a 4-dma grouping.

In still another embodiment, the modified TetR comprises the following mutations: H64K, S135L, and SI 381. In one embodiment, the modified TetR further comprises a transcriptional activator. In still another embodiment, the modified TetR further comprises a transcriptional inhibitor. In one embodiment of the invention, the modified TetR binds the tc analog dedimethylamino-anhydrotetracycline (4-ddma-atc).

The invention provides a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 59, and 61. Also included in the invention is a nucleic acid molecule comprising a nucleotide sequence which encodes an amino acid sequence selected from the group consisting of SEQ ID NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62.

The invention also describes an isolated nucleic acid molecule that encodes an inducer specific modified tetracycline repressor (TetR) that: (i) has inducer affinity distinction between tetracycline (tc) analogs, wherein the modified TetR is induced by a tc analog lacking a 4-dimethylamino (4-dma) grouping; (ii) comprises at least one amino acid substitution that corresponds to an amino acid substitution present in an amino acid sequence selected from the group consisting of SEQ ID NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62; and wherein said nucleic acid (iii) hybridizes under high stringency over substantially the entire length to a nucleic acid molecule comprising SEQ ID NO: 35 or (iv) has at least 60 % nucleotide sequence identity to SEQ ID NO: 35.

In addition, the invention provides a nucleic acid molecule that encodes an inducer specific modified tetracycline repressor (TetR) that: (i) has inducer affinity distinction between tetracycline (tc) analogs, wherein the modified TetR is induced by a tc analog lacking a 4- dimethylamino (4-dma) grouping; and (ii) comprises at least one amino acid substitution that corresponds to an amino acid substitutions present in an amino acid sequence selected from the group consisting of SEQ ED NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62 as compared to an unmodified TetR of any one of tet(A), tet(B), tet(C), tet(D), Tet(E), tet(G), tet(H), tet(J), or tet(Z) family.

The invention also includes a polypeptide comprising the amino acid sequence of SEQ ID NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62.

In one embodiment, the invention describes a eukaryotic host cell comprising a recombinant expression vector, said vector comprising a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 59, and 61. The invention also describes an isolated nucleic acid molecule encoding a fusion protein which regulates transcription in eukaryotic cells, the fusion protein comprising an inducer specific mutant Tet repressor (TetR) comprising at least one amino acid substitution that corresponds to an amino acid substitution present in an amino acid sequence selected from the group consisting of SEQ ID NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62, operatively linked to a polypeptide which regulates transcription in eukaryotic cells.

In one embodiment, the nucleic acid molecule of the invention encodes a polypeptide which activates transcription in eukaryotic cells. In another embodiment, the nucleic acid molecule of the invention encodes a polypeptide which inhibits transcription in eukaryotic cells.

In one embodiment, the invention provides a recombinant vector comprising a nucleic acid encoding a modified inducer specific TetR. In another embodiment, the invention provides a host cell comprising the recombinant vector of containing the nucleic acid encoding a modified inducer specific TetR.

The invention describes a method for regulating transcription of a gene in a cell, comprising introducing into the cell a nucleic acid molecule encoding a fusion protein which regulates transcription, the fusion protein comprising an inducer specific mutant Tet repressor (TetR) comprising at least one amino acid substitution that corresponds to an amino acid substitution present in an amino acid sequence selected from the group consisting of SEQ ED NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62, operatively linked to a polypeptide which regulates transcription in eukaryotic cells; and modulating the concentration of a tetracycline (tc) analog lacking a 4-dimethylamino (4-dma) grouping in contact with the cell. In one embodiment, the polypeptide of the invention which regulates transcription is a tetracycline transactivator. In another embodiment of the invention, the polypeptide which regulates transcription is a transcriptional silencer. In still another embodiment, the polypeptide of the invention activates transcription in eukaryotic cells. In still another embodiment, the polypeptide of the invention inhibits transcription in eukaryotic cells.

The invention provides a method for regulating transcription of a tet operator-linked gene in a cell of a subject, comprising introducing into the cell a first nucleic acid molecule comprising the tet operator-linked gene; introducing into the cell a second nucleic acid molecule encoding a fusion protein which regulates transcription, the fusion protein comprising an inducer specific mutant Tet repressor comprising at least one amino acid substitution that corresponds to an amino acid substitution present in an amino acid sequence selected from the group consisting of SEQ ED NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62, operatively linked to a polypeptide which regulates transcription in exikaryotic cells; and modulating the concentration of a tetracycline (tc) analog lacking a 4-dimethylamino (4-dma) grouping in the subject.

In addition, the invention describes a method for regulating expression of a tet operator- linked gene is a cell of a subject comprising, introducing into the cell a single nucleic acid molecule encoding tet operator-linked gene and also encoding a fusion protein which regulates transcription, the fusion protein comprising a mutant Tet repressor comprising at least one amino acid substitution that corresponds to an amino acid substitution present in an amino acid sequence selected from the group consisting of SEQ ED NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62, operatively linked to a polypeptide which regulates transcription in eukaryotic cells; and modulating the concentration of a tetracycline (tc) analog lacking a 4-dimethylamino (4- dma) grouping in the subject. In one embodiment, the polypeptide of the invention which regulates transcription is a tetracycline transactivator. In another embodiment of the invention, the polypeptide which regulates transcription is a transcriptional silencer. In still another embodiment of the invention, the polypeptide activates transcription in the cell of a subject. In yet another embodiment, the polypeptide of the invention inhibits transcription in the cell of a subject. The invention also includes an antibody that binds to a polypeptide of the invention.

The invention also includes a non-human transgenic animal having a transgene comprising a polynucleotide sequence encoding a fusion protein which regulates transcription, the fusion protein comprising an inducer specific mutant Tet repressor comprising at least one amino acid substitution that corresponds to an amino acid substitution present in an amino acid sequence selected from the group consisting of SEQ ID NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62, operatively linked to a polypeptide which regulates transcription in eukaryotic cells. In one embodiment, the fusion protein of the invention further comprises a tetracycline transactivator. In another embodiment, the fusion protein of the invention further comprises a tetracycline transcriptional silencer.

In a further embodiment, the animal of the invention has a second transgene comprising a gene of interest operably linked to at least one tet operator sequence. In one embodiment of the invention, the animal is a non-human animal. In another embodiment, the animal of the invention is selected from a group consisting of a mouse, a cow, a goat, a sheep and a pig. In one embodiment, the invention provides a method for modulating transcription of the second transgene in the transgenic animal of the invention, comprising administering a tetracycline (tc) analog lacking a 4-dimemylamino (4-dma) grouping.

The invention also describes host cell comprising at least two nucleic acid molecules comprising at least one nucleic acid encoding a tet operator-linked gene and also encoding an inducer specific modified tetracycline repressor (TetR) characterized by having inducer affinity distinction between tetracycline (tc) analogs, wherein the modified TetR is induced by a tetracycline (tc) analog lacking a 4-dimethylamino (4-dma) grouping; and at least one nucleic acid encoding a tet operator-linked gene and also encoding a tetracycline repressor (TetR) which is not induced by a tetracycline (tc) analog lacking a 4-dimethylamino (4- dma) grouping.

The instant invention provides TetR variants with unique inducer specificity. The invention describes methods for achieving such mutants by changing residues located in proximity of the 4-dma moiety in the TetR-[tc-Mg]⁺2 complex. The present invention is based, at least in part, on conversion of the TetR protein such that TetR is induced by tetracycline (tc) derivatives lacking the 4-dimethylamino grouping, e.g., 4-dedimethylamino- anhydrotetracycline (4-ddma-atc) and 4-dedimethylamino-6-demethyl-6-deoxytetracycline (cmt3), while showing reduced specificity for tc and tc derivatives. The TetR mutants set forth herein specifically require tc derivatives lacking the 4-dimethylamino grouping for tetO binding, as compared to wild-type TetR proteins, which require tc or an analog thereof for induction (see Henssler et al. (2004) "Structure Based Design of Tet Repressor To Optimize A New Inducer Specificity" Biochemistry, In Press, incorporated by reference herein).

In an advantageous embodiment, the invention provides a TetR mutant with specificity for the tc analog 4-ddma-atc which is neither an antibiotic or an inducer for the wild-type TetR. Previously described TetR mutants, such as the H64K. S135L mutant, show relaxed specificity as they display reduced induction by tc but full induction by doxycycline (dox), anhydrotetracycline (ate) and 4-dedimethylarnino-6-demethyl-6-deoxytetracycline (cmt3). In one embodiment, the invention provides the mutant TetR H64K S135L S138I which can be induced by 4-ddma-atc, yet with pronounced reduction of affinity for ate and dox.

Before further description of the invention, certain terms employed in the specification, examples and appended claims are, for convenience, collected here.

As used herein, "nucleotide sequence" refers to a heteropolymer of nucleotides, including but not limited to ribonucleotides and deoxyribonucleotides, or the sequence of these nucleotides. "Nucleic acid molecule" and "polynucleotide" are also used interchangeably herein to refer to a heteropolymer of nucleotides, which may be xinmodified or modified DNA or FINA. For example, polynucleotides can be single-stranded or double-stranded DNA, DNA that is a mixture of single-stranded and double-stranded regions, hybrid molecules comprising DNA and RNA with a mixture of single-stranded and double- stranded regions. In addition, the polynucleotide can be composed of triple-stranded regions comprising DNA, RNA, or both. A polynucleotide can also contain one or more modified bases, or DNA or RNA backbones modified for nuclease resistance or other reasons. Generally, nucleic acid segments provided by this invention can be assembled from fragments of the genome and short oligonucleotides, or from a series of oligonucleotides, or from individual nucleotides, to provide a synthetic nucleic acid molecule.

As used herein, a "probe", "primer", or "fragment" is single-stranded DNA or RNA that has a sequence of nucleotides that includes at least 10 contiguous bases that are the same as

(or the complement of) any 14 bases set forth in any of SEQ ID NOs: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 59, and 61. Preferred regions from which to construct probes and primers include 5' and/or 3' coding sequences, sequences predicted to confer the reverse phenotype in an organism, e.g., a eukaryotic organism. Particularly preferred nucleic acid fragments are those containing at least one mutation conferring an inducer specific phenotype in eukaryotic organisms.

As used herein, "polypeptide" refers to the molecule formed by joining amino acids to each other by peptide bonds, and may contain amino acids other than the twenty commonly used gene-encoded amino acids. The term "active polypeptide" refers to those forms of the polypeptide which retain the biologic and/or immxmologic activities of any naturally occurring polypeptide. The term "naturally occurring polypeptide" refers to polypeptides produced by cells that have not been genetically engineered and specifically contemplates various polypeptides arising from post-translational modifications of the polypeptide including, but not limited to, proteolytic processing, acetylation, carboxylation, glycosylation, phosphorylation, lipidation and acylation.

The term "derived from" is intended to mean that a sequence is identical to or modified from another sequence. Polypeptide or protein derivatives include polypeptide or protein sequences that differ from the sequences described or known in amino acid sequence, or in ways that do not involve sequence, or both, and still preserve the activity of the polypeptide or protein. Derivatives in amino acid sequence are produced when one or more amino acids are substituted with a different natural amino acid, an amino acid derivative or non-native amino acid. In certain embodiments protein derivatives include naturally occurring polypeptides or proteins, or biologically active fragments thereof, whose sequences differ from the wild type sequence by one or more conservative amino acid substitutions, which typically have minimal influence on the secondary structure and hydrophobic nature of the protein or peptide. Derivatives may also have sequences which differ by one or more non-conservative amino acid substitutions, deletions or insertions which do not abolish the biological activity of the polypeptide or protein.

Conservative substitutions (substituents) typically include the substitution of one amino acid for another with similar characteristics (e.g., charge, size, shape, and other biological properties) such as substitutions within the following groups: valine, glycine; glycine, alanine; valine, isoleucine; aspartic acid, glutamic acid; asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. The non-polar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine. The positively charged (basic) amino acids include argjnine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid.

The polypeptides and proteins of this invention may also be modified by various changes such as insertions, deletions and substitutions, either conservative or nonconservative where such changes might provide for certain advantages in their use.

In other embodiments, derivatives with amino acid substitutions which are less conservative may also result in desired derivatives, e.g., by causing changes in charge, conformation and other biological properties. Such substitutions would include, for example, substitution of hydrophilic residue for a hydrophobic residue, substitution of a cysteine or proline for another residue, substitution of a residue having a small side chain for a residue having a bulky side chain or substitution of a residue having a net positive charge for a residue having a net negative charge. When the result of a given substitution cannot be predicted with certainty, the derivatives may be readily assayed according to the methods disclosed herein to determine the presence or absence of the desired characteristics.

Derivatives within the scope of the invention also include polynucleotide derivatives. Polynucleotide or nucleic acid derivatives differ from the sequences described or known in nucleotide sequence. For example, a polynucleotide derivative may be characterized by one or more nucleotide substitutions, insertions, or deletions.

As used herein, "isolated" refers to a nucleic acid molecule or polypeptide separated from at least one macromolecular component (e.g., nucleic acid molecule or polypeptide) present with the nucleic acid molecule or polypeptide of the invention in its natural source. In one embodiment, the polynucleotide or polypeptide of the invention is purified such that it constitutes at least 95% by weight, more preferably at least 99.8% by weight, of the indicated biological macromolecules present (but water, buffers, and other small molecules, especially molecules having a molecular weight of less than 1000 daltons, can be present).

As used herein, "recombinant" refers to a polypeptide or protein, means that is derived from recombinant (e.g., microbial or mammalian) expression systems. "Microbial" refers to recombinant polypeptides or proteins made in bacterial or fungal (e.g., yeast) expression systems. As a product, "recombinant microbial" refers to a polypeptide or protein essentially unaccompanied by associated native glycosylation. Polypeptides or proteins expressed in most bacterial cultures, e.g., E. coli, will be free of glycosylation modifications; polypeptides or proteins expressed in yeast will be glycosylated.

As used herein, "substantially" varies with the context as understood by those skilled in the relevant art and generally means at least 70%, preferably means at least 80%, more preferably at least 90%, and still more preferably 95%, and most preferably at least 98%.

As used herein, a "sub-inhibitory" concentration of e.g. tetracycline or a tetracycline analog refers to a concentration that does not significantly affect the growth rate of a specific organism, e.g., a exikaryotic organism. That is, the growth rate of the organism cultured in the presence of a sub-inhibitory concentration of tetracycline or a tetracyline analog is substantially the same as that of the same organism cultured in the absence of tetracycline or the tetracyline analog. A sub-inhibitory level of tetracycline or a tetracycline analog is also referred to herein as a "non-antibiotic" concentration of tetracycline or a tetracycline analog.

As used herein, "substantial sequence homology" as used in reference to the nucleotide sequence of DNA, the ribonucleotide sequence of RNA, or the amino acid sequence of protein, that have slight and non-consequential sequence variations from the actual sequences disclosed herein. Species having substantial sequence homology are considered to be equivalent to the disclosed sequences and as such are within the scope of the appended claims. In this regard, "slight and non-consequential sequence variations" mean that "homologous" sequences, i.e., sequences that have substantial similarity with the DNA, RNA, or proteins disclosed and claimed herein, are functionally equivalent to the sequences disclosed and claimed herein. Functionally equivalent sequences will function in substantially the same manner to produce substantially the same compositions as the nucleic acid molecule and amino acid compositions disclosed and claimed herein. In particular, functionally equivalent DNAs encode proteins that are the same as those disclosed herein or that have conservative amino acid variations, such as substitution of a non-polar residue for another non-polar residue or a charged residue for a similarly charged residue. These changes include those recognized by those of skill in the art as those that do not substantially alter the tertiary structure of the protein. As used herein, "substantially pure" means sufficiently homogeneous to appear free of readily detectable impurities as determined by standard methods of analysis, such as thin layer chromatography (TLC), gel electrophoresis and high performance liquid chromatography (HPLC), used by those of skill in the art to assess such purity, or sufficiently pure such that further purification would not detectably alter the physical and chemical properties, such as enzymatic and biological activities, of the substance. Methods for purification of the compounds to produce substantially chemically pure compoxinds are known to those of skill in the art. A substantially chemically pure compound may, however, be a mixture of stereoisomers. In such instances, further purification might increase the specific activity of the compoxind.

As used herein, "biological activity" refers to the in vivo activities of a compoxind or physiological responses that result upon administration of a compoxind, composition or other mixture. Biological activities may be observed in in vitro systems designed to test or use such activities.

A preferred biological activity in accordance with the present invention is the capability of a polypeptide to be induced by a tetracycline analog lacking a 4-dma grouping. Most preferably, said biological activity is the capability to be induced by 4-ddma derivatives, but not by ate or doxycycline.

As used herein, "functionally equivalent," refers to a polypeptide capable of exhibiting a substantially similar in vivo activity as the modified inducer specific TetR repressors encoded by one or more of the nucleotide sequences described herein.

As used herein, the term "hybridizes under stringent conditions" is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 60% (65%, 70%, preferably 75%) identical to each other typically remain hybridized to each other. Such stringent conditions are known to those skilled in the art and can be found in sections 6.3.1-6.3.6 of Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989). A preferred, non-limiting example of stringent hybridization conditions are hybridization in 6X sodium chloride/sodixim citrate (SSC) at about 45°C, followed by one or more washes in 0.2X SSC, 0.1% SDS at 50-65°C. It is understood that equivalent stringencies may be achieved using alternative buffers, salts and temperatures (e.g., see Maniatis (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor, N.Y.; Cxirrent Protocols in Molecular Biology (Ausubel et al, eds) Vol. 1, Chapter 2 (John Wiley & Sons, Inc.)).

As used herein, "expression" refers to the process by which a nucleic acid molecule is transcribed into mRNA and translated into peptides, polypeptides, or proteins.

As used herein, "vector" or "plasmid" refers to discrete elements that are used to introduce heterologous DNA into cells for either expression of the heterologous DNA or for replication of the cloned heterologous DNA. Selection and use of such vectors and plasmids are well within the level of skill of the art.

As used herein, "transformation/transfection" refers to the process by which DNA or RNA is introduced into cells. Transfection refers to the taking up of exogenous nucleic acid molecules, e.g., an expression vector, by a host cell whether any coding sequences are in fact expressed or not. Numerous methods of transfection are known to the ordinarily skilled artisan, for example polyethylene glycol [PEG] -mediated DNA uptake, electroporation, lipofection [see, e.g., Strauss (1996) Meth. Mol. Biol. 54:307-327], microcell fusion [see, Lambert (1991) Proc. Natl. Acad. Sci. U.S.A. 88:5907-5911; U.S. Pat. No. 5,396,767, Sawford et al. (1987) Somatic Cell Mol. Genet. 13:279-284; Dhar et al. (1984) Somatic Cell Mol. Genet. 10:547-559; and McNeill-Killary et al (1995) Meth. Enzymol. 254:133-152], lipid-mediated carrier systems [see, e.g., Teifel et al. (1995) Biotechniques 19:79-80; Albrecht et al. (1996) Ann. Hematol. 72:73-79; Holmen et al. (1995) In Vitro Cell Dev. Biol. Anim. 31:347-351; Remy et al. (1994) Bioconjug. Chem. 5:647-654; Le Bolch et al. (1995) Tetrahedron Lett. 36:6681-6684; Loeffler et al. (1993) Meth. Enzymol. 217:599-618] or other suitable method. Transformation means introducing DNA into an organism so that the DNA is replicable, either as an extrachromosomal element or by chromosomal integration. Transformation include various processes of DNA transfer that occur between organisms, such as but not limited to conjugation. Successful transformation/transfection is generally recognized by detection of the presence of the heterologous nucleic acid molecule within the transformed/transfected cell, such as any indication of the operation of a vector within the host cell.

As used herein, "recombinant host cells" refers to cultured cells which have stably integrated a recombinant transcriptional unit into chromosomal DNA or carry stably the recombinant transcriptional unit extrachromosomally. Recombinant host cells as defined herein will express heterologous polypeptides or proteins, particularly inducer specific TetR repressors of the present invention, and RNA encoded by the DNA segment or synthetic gene in the recombinant transcriptional unit. This term also means host cells which have stably integrated a recombinant genetic element or elements having a regulatory role in gene expression, for example, promoters or enhancers. Recombinant expression systems as defined herein will express RNA, polypeptides or proteins endogenous to the cell upon induction of the regulatory elements linked to the endogenous DNA segment or gene to be expressed. The cells can be prokaryotic or eukaryotic.

As used herein, the one letter and three letter abbreviations for amino acids are in accord with their common usage and the IUPAC-IUB Commission on Biochemical Nomenclature, see, (1972) Biochem. 11 : 1726. Each naturally occurring L- amino acid is identified by the standard three letter code or the standard three letter code with or without the prefix "L-"; the prefix "D-" indicates that the stereoisomeric form of the amino acid is D.

As used herein, mutations within the class B-class D chimeric modified repressor are indicated by the wild type amino acid residue, the amino acid position corresponding to SEQ ID NO: 2, and the mutant amino acid residue. For example, H64K shall mean a mutation from histidine to lysine at position 64 in the modified repressor. Mutations in other classes of repressor will be indicated by the gene, its classification, the wild type amino acid residue, the amino acid position corresponding to the representative of the class as indicated above, and the mutant amino acid residue.

As used herein, "tetracycline analog" or "tc analog" is intended to include compounds which are structurally related to tetracycline and which bind to the Tet repressor with a K_a of at least about 10 M. Preferably, the tetracycline analog binds with an affinity of about

10^"9 M or greater. Examples of such tetracycline analogs include, but are not limited to, anhydrotetracycline (ate), doxycycline (dox), chlorotetracycline, oxytetracycline, deoxytetracycline and others disclosed by Hlavka and Boothe, "The Tetracyclines," in Handbook of Experimental Pharmacology 78, R. K. Blackwood et al. (eds.), Springer-

Nerlag, Berlin, Ν.Y., 1985; Mitscher, "The Chemistry of the Tetracycline Antibiotics",

Medicinal Research 9, Dekker, N.Y., 1978; Noyee Development Coφoration,

"Tetracycline Manufacturing Processes" Chemical Process Reviews, Park Ridge, N.J., 2 volumes, 1969; Evans, "The Technology of the Tetracyclines," Biochemical Reference Series 1, Quadrangle Press, New York, 1968; and Dowling, "Tetracycline," Antibiotic

Monographs, no. 3, Medical Encyclopedia, New York, 1955. For use in prokaryotic or eukaryotic organisms, a tc analog can be chosen which has reduced antibiotic activity as compared to tc, such as, but not limited to, anhydrotetracycline (ate). In one embodiment of the invention, the tc analog lacks the 4-dimethylamino (4-ddma) grouping. Examples of tc analogs lacking the 4-ddma grouping include, but are not limited to, cmt3 and 4-ddma- ate.

As used herein, "wild-type Tet repressor" or "wild-type TetR" is intended to describe a protein occxirring in nature which represses transcription via binding to a tet operator sequence in a cell in the absence of tc. The difference(s) between a modified Tet repressor and a wild-type Tet repressor may be substitution of one or more amino acids, deletion of one or more amino acids or addition of one or more amino acids. The term is intended to include repressors of different class types, such as but not limited to, TetR(A), TetR(B), TetR(C), TetR(D), TetR(E), TetR(G), TetR(H), TetR(J), and TetR(Z).

In light of the high degree of sequence conservation (at least 80%) among members of each class of Tet repressor, a single member of each class of Tet repressor is used herein as representative of the entire class. Accordingly, the teaching of the present invention with respect to a specific member of a Tet repressor class is directly applicable to all members of that class.

As used herein, the TetR(A) class is represented by the Tet repressor carried on the Tnl721 transposon (Allmeir et al. (1992) Gene 111: 11-20; NCBI (National Library of Medicine, National Center for Biotechnology Information) accession number X61367 and database cross reference number (Gl:) for encoded protein sequence GL48198).

The TetR(B) class is represented by a Tet repressor encoded by a TnlO tetracycline resistance determinant (Postle et al. (1984) Nucleic Acids Research 12(12): 4849-63, Accession No. X00694, G 43052).

The TetR(C) class is represented by the tetracycline repressor of the plasmid pSCIOl (Brow et al. (1985) Mol. Biol. Evol 2(1): 1-12, Accession No. M36272, GL150496).

The TetR(D) class is represented by the Tet repressor identified in Salmonella ordonez (Allard et al. (1993) Mol. Gen. Genet. 237: 301-5, Accession No. X65876, GL49075). The TetR(E) class is represented by a Tet repressor isolated from a member of Enterobacteriaceae (Tovar et al. (1988) Mol Gen. Genet. 215(1): 76-80, Accession No. M34933, GI: 155020).

The TetR(G) class is represented by a Tet repressor identified in Nibrio anguillarum (Zhao et al. (1992) Microbiol Immunol 36: 1051-60, Accession No. S52438, GT.262929).

The TetR(H) class is represented by a Tet repressor encoded by plasmid pMNl 11 isolated from Pasteurella multocida (Hansen et al. (1993) Antimicrob. Agents. Chemother. 37(12): 2699-705, Accession No. U00792, G 392872).

The TetR(J) class is represented by a Tet repressor cloned from Proteus mirabilis (Magalhaes et al. (1998) Biochim. Biophys. Acta. 1443(1-2): 262-66, Accession No. AF038993, GL4104706).

The TetR(Z) class is represented by a Tet repressor encoded by the pAGl plasmid isolated from the gram-positive organism Corynebacterium glutamicum (Tauch et al. (2000) Plasmid 44(3): 285-91, Accession No. AAD25064, G 4583400).

As used herein, "modified tetracycline repressor" or "mutant Tet repressor (TetR)," is intended to include polypeptides having an amino acid sequence which is similar to or derived from one or more wild-type Tet repressor but which has at least one amino acid difference from a wild-type Tet repressor. In one embodiment, the invention describes modified TetR molecules which are characterized in that they can distinguish between different tc analogs, i.e., have inducer affinity distinction.

As used herein, "inducer specific modified tetracycline repressor", "inducer specific modified Tet repressor (TetR)" is intended to include TetR polypeptides having an amino acid sequence which is similar to or derived from one or more wild-type Tet repressor but which has at least one amino acid difference from a wild-type Tet repressor that confers the ability of the inducer specific TetR to preferentially bind to a certain tc analog or type of tc analog. An inducer specific modified TetR has inducer affinity distinction between tc analogs, wherein the modified TetR binds certain tc analogs but not others. In a preferred embodiment of the invention, the inducer specific modified TetR binds to tc analogs lacking the 4-dma grouping and does not bind tc or tc analogs with a 4-dma grouping. As used herein, "modified tetracycline repressor exhibiting a reverse phenotype," "revTetR," or "revTetR protein" is intended to include polypeptides having an amino acid sequence which is similar to or derived from one or more wild-type Tet repressor but which has at least one amino acid difference from a wild-type Tet repressor that confers greater binding affinity to a tet operator (tetO) sequence in a cell in the presence of tetracycline or a tc analog than in the absence of tetracycline or its analog. A revTetR provided herein has the following functional properties: 1) the polypeptide can bind to a tetO sequence, i.e., it retains the DNA binding specificity of a wild-type Tet repressor; and 2) it is regxilated in a reverse manner by tetracycline than a wild-type Tet repressor, i.e., the modified Tet repressor binds to a tetO sequence with a greater binding affinity (or a lower dissociation constant, K_d) in the presence of tc or tc analog, than in the absence of tc or its analog. Moreover, the affinity of a revTetR protein of the present invention for a tetO sequence is substantially proportional to the concentration of tetracyline; that is, as the concentration of tetracycline or analog thereof increases, the binding affinity of the revTetR protein for the tet operator sequence increases. The term modified tetracycline repressor or revTetR is intended to include modified TetR of different class types, such as but not limited to TetR(A), TetR(B), TetR(C), TetR(D), TetR(E), TetR(G), TetR(H), TetR(J), and TetR(Z), as well as "chimeric tetracycline repressor" or "chimeric revTetR".

As used herein, "chimeric tetracycline repressor" is intended to include polypeptides having an amino acid sequence comprising amino acid residues derived from more than one type of tetracycline repressor. The term is intended to include chimeric tetracycline repressors constructed from different class types, such as but not limited to, TetR(A), TetR(B), TetR(C), TetR(D), TetR(E), TetR(G), TetR(H), TetR(J), and TetR(Z). In certain embodiments, the chimeric tetracycline repressors of the present invention comprise an ammo-terminal DNA-binding domain and a carboxy-terminal tetracycline binding domain, including but not limited to the corresponding domains of the TetR(A), TetR(B), TetR(C), TetR(D), TetR(E), TetR(G), TetR(H), TetR(J), and TetR(Z). Such chimeric tetracycline repressors further comprise at least one amino acid substitution that confers the reverse phenotype. A chimeric revTetR retains the DNA binding specificity of the DNA binding domain of a wild-type Tet repressor. Preferably, this reverse phenotype of the chimeric revTetR is displayed a eukaryote.

In one embodiment of the invention, the term "modified tetracycline repressor" or "revTetR" further include Tet repressors wherein the amino-terminal DNA-binding domain is derived from a DNA-binding protein other than a TetR repressor protein, and the DNA sequence to which such a chimeric tetracycline repressor protein binds corresponds to the DNA sequence recognized and bound by the non-TetR repressor, DNA-binding protein. Non-limiting examples of such DNA-binding proteins include, but are not limited to, the cro repressor, 454 repressor and CI repressor of bacteriophageλ, as well as the hin, gin, cin, and pin recombinase proteins (see, Feng et al. (1994) Science 263: 348-55).

In a preferred embodiment, the parent Tet repressors from which the chimeric repressors of the present invention are constructed are TetR of classes B and D (see Schnappinger et al, (1998,) EMBO J. 17:535-543), and the tet operator sequence is a class B tet operator sequence.

In another embodiment, the inducer specific Tet repressor of the invention contains a combination of different types of modifications which confer distinct phenotypes to TetR. For example, the inducer specific Tet repressor may contain mutations which confer the ability of the TetR to preferentially bind a certain class of tc analog and mutations which allow TetR to bind the tetO in the presence of the inducer molecules (revTetR phenotype).

As described in detail below, it has been discovered that certain mutations within TetR confer the ability of TetR to have inducer affinity distinction between different types of tc analogs. In particular, it has been discovered that nucleotide substitutions that result in at least one codon change in amino acid residues from positions 64, 135, and 138 of SEQ ED NO: 2 appear to be important for the inducer specific phenotype.

The crystal structure of a Tet repressor-tetracycline complex, as described in Hinrichs, W. et al. (1994) Science 264: 418-420, can be used for the rational design of mutant Tet repressors, including, for example, inducer specific TetR. The polypeptide folds into 10a helices, αl to αlO. Helices α7 to αlO are apparently involved in the dimerization of the repressor. More specifically, Hinrichs (1994) further described the tetracycline repressor protein as made up of a "protein core" and DNA binding domains. The core domain consists of helices α5 to αlO from both subunits and harbors two tetracycline binding pockets as well as the dimer interface. The two DNA binding domains are each connected to that core domain via helix α4. The DNA binding domains are formed with α- helices αl- α3 of both repressor proteins of the dimer and the DNA-binding domains are connected to the core through the α4 helix. Helices αl to α3 include an HTH motif. Based on the comparison of operator- bound and induced conformations of TetR, a model for the conformational transition accompanying induction has been proposed (Orth et al, 2000). The induction signal needs to be conducted over a 33 Angstrom distance through the TetR protein from the tetracycline binding pocket to the tetO binding surface. The structural changes affect helices α4 and α6 and result in a pendulum like motion of the DNA binding domain relative to the core domain. As a consequence, the tetO affinity drops about eight orders of magnitude (Lederer et al, 1996).

The amino sequence of each of the ten α helices of the TetR(B) and TetR(D) are provided in Schnappinger et al. (1998) EMBO J. 17(2): 535-543. Accordingly, each of these ten helices appears to include the following indicated amino acid residues as provided in SEQ ED NO: 1: αl, amino acid residues 5-21; α 2, amino acid residues 27-34; α3, amino acid residues 38-44; α4, amino acid residues 48-64; α5, amino acid residues 74-92; α6, amino acid residues 95-100; α7, amino acid residues 110-123; α8, amino acid residues 128-154; α9, amino acid residues 167-178; and αlO, amino acid residues 183-203. Therefore, based upon the crystal structure, amino acid positions 70 and 71 are located prior to α5 of the tetracycline-binding pocket and yet amino acid substitutions at this site appear to contribute to the desired functional properties of a revTetR. Amino acid positions which can be mutated to confer a reverse phenotype on TetR are described in U.S. Provisional Appln. No. 60/574169.

Furthermore, preferred tet repressors exhibiting a reverse phenotype (rtTAs) are those which are disclosed in WO 00/75347 A2. In particular, a reverse phenotype of the tet repressor may be obtained by modifying the amino acids at position 19 and 56 and, optionally, at positions 148 and 179. Most preferably, a reverse tet repressor contains a G at position 19 and a T at position 56.

The term "compound" as used herein (e.g., as in "modulator compound," or "test compound") is meant to include both exogenously added test compounds and peptides endogenously expressed from a peptide library. For example, in certain embodiments, the host cell also produces the test compound which is being screened. For instance, the host cell can produce, e.g., a test polypeptide, a test nucleic acid molecule and/or a test carbohydrate which is screened for its ability to modulate the activity of the transcriptional regulatory protein. In such embodiments, a culture of such reagent cells will collectively provide a library of potential effector molecules and those members of the library which either stimulate or inhibit the activity of the transcriptional regulatory protein can be selected and identified. "Tetracycline controlled transactivators (tTA)" are fusions between TetR transcriptional activators, e.g., proper domains thereof. In one such fusion protein, a major portion of the Herpes simplex virus protein 16 (NP16) was fused at the level of DΝA to TetR. Yet, other xTA's demonstrate a graded transactivation potential resulting from connecting different combinations of minimal activation domains to the C-terminus of TetR (Baron et al, 1997). These TetR fusion proteins allow one to regulate the expression of genes placed downstream of minimal promoter-tetO fusions (Ptet)- En absence of tetracycline P_tet is activated whereas in presence of the antibiotic activation of P_tet is prevented. In one embodiment of the invention, an inducer specific modified TetR is fused to a transcriptional activator, such as, but not limited to, NP16.

As used herein, a "reverse tetracycline controlled transactivator" or (rtTA)" is intended to include a fusion protein comprising a TetR mutant (a revTetR protein) which binds operator DΝA only in the presence of some tefracycline or an analogue thereof, such as anhydrotefracycline (ate), operatively linked to a transcription activation domain, such that transcription is activated, e.g., in a exikaryotic cell.

A "tetracycline controlled transcriptional silencer (tTS)" is intended to include a fusion protein comprising TetR and a transcriptional silencer or inhibitor. As used herein, a "reverse tetracycline controlled transcriptional silencer" or (rtTS)" is intended to include a fusion protein comprising a TetR mutant (a revTetR protein) which binds operator DΝA only in the presence of some tetracycline or an analog thereof, such as dedimethylamino- anhydrotetracycline (4-ddma-atc), operatively linked to a transcription silencing domain, such that transcription is silenced, e.g., in a eukaryotic cell. In one embodiment of the invention, an inducer specific modified TetR is fused to a transcriptional silencer.

The term "DΝA binding protein" is intended to include any protein, or functional domain thereof, that specifically interacts with a cognate DΝA sequence, or response element, within the regulatory sequences of a gene. The DΝA binding domains of transcriptional regulatory proteins can be classified into structural families which include, but are not limited to, basic helix-loop-helix domains, leucine zipper domains, zinc finger domains, and helix-turn-helix domains/homeodomains. A fusion protein of the present invention includes a polypeptide comprising a DΝA binding protein, or a functional DΝA binding domain thereof. The recognition and binding of a DΝA binding protein to its cognate DΝA sequence can be regulated by conformational changes in the DΝA binding protein itself conferred by the binding of a modulator molecule or ligand. Similarly, the conformation of the cognate DNA sequence within the chromatin, e.g., organized into nucleosome, also influences the binding of a DNA binding protein to its cognate DNA sequence.

The term "gene regulatory sequences" is intended to include the DNA sequences that control the transcription of an adjacent gene. Gene regulatory sequences include, but are not limited to, promoter sequences that are found in the 5' region of a gene proximal to the transcription start site which bind RNA polymerase to initiate transcription. Gene regulatory sequences also include enhancer sequences which can function in either orientation and in any location with respect to a promoter, to modulate the utilization of a promoter. Transcriptional control elements include, but are not limited to, promoters, enhancers, and repressor and activator binding sites. The gene regulatory sequences of the present invention contain binding sites for transcriptional regulatory proteins. In a preferred embodiment, gene regulatory sequences comprise sequences derived from the tet operator (tetO) which bind tet repressor proteins.

As used herein, "tet operator," "tet operator sequence," or "tetO", is intended to encompass all classes of tet operator sequences, such as but not limited to tetO(A), tetO (B), tetO (C), tetO (D), tetO (E), tetO (G), tetO (H), tetO (J) and tetO (Z). The nucleotide sequences of Tet repressors of members of the A, B, C, D, E, G, H, J and Z classes, and their corresponding tet operator sequences are known, and can be used in the present invention. See, for example, Waters et al. (1983) Nucl Acids Res 11:6089-6105, Hillen and Schollmeier (1983) Nucl. Acids Res. 11:525-539 and Postie et al. (1984) Nucl. Acids Res. 12:4849-4863, Unger et al. (1984) Gene 31: 103-108, Unger et al. (1984) Nucl Acids Res. 12:7693-7703 and Tovar et al (1988) Mol. Gen. Genet. 215:76-80, which are incoφorated herein by reference in their entireties.

As used herein, a "host cell" includes any cultivatable cell that can be modified by the introduction of heterologous DNA. Preferably, a host cell is one in which a transcriptional regulatory protein can be stably expressed, post-translationally modified, localized to the appropriate subcellular compartment, and made to engage the appropriate transcription machinery. The choice of an appropriate host cell will also be influenced by the choice of detection signal. For example, reporter constructs, as described above, can provide a selectable or screenable trait upon activation or inhibition of gene transcription in response to a transcriptional regulatory protein; in order to achieve optimal selection or screening, the host cell phenotype will be considered. A host cell of the present invention includes prokaryotic cells and eukaryotic cells. Prokaryotes include gram negative or gram positive organisms, for example, E. coli or Bacilli. Suitable prokaryotic host cells for transformation include, for example, E. coli, Bacillus subtilis, Salmonella typhimurium, and various other species within the genera Pseudomonas, Streptomyces, and Staphylococcus. Eukaryotic cells include, but are not limited to, yeast cells, plant cells, fungal cells, insect cells (e.g., bacxilovirus), mammalian cells, and the cells of parasitic organisms, e.g., trypanosomes.

As used herein, the term "yeast" includes not only yeast in a strict taxonomic sense, i.e., unicellular organisms, but also yeast-like multicellular fungi of filamentous fungi. Exemplary species include Kluyverei lactis, Schizosaccharomyces pombe, and Ustilaqo maydis, with Saccharomyces cerevisiae being preferred. Other yeast which can be used in practicing the present invention are Neurospora crassa, Aspergillus niger, Aspergillus nidulans, Pichia pastoris, Candida tropicalis, and Hansenula polymorpha.

Mammalian host cell culture systems include established cell lines such as COS cells, L cells, 3T3 cells, Chinese hamster ovary (CHO) cells, embryonic stem cells, with HeLa cells being preferred.

The term "indicator gene" or "reporter gene" generically refers to an expressible (e.g., able to transcribed and (optionally) translated) DNA sequence which is expressed in response to the activity of a transcriptional regulatory protein. Indicator genes include unmodified endogenous genes of the host cell, modified endogenous genes, or a reporter gene of a heterologous construct, e.g., as part of a reporter gene construct. In a preferred embodiment, the level of expression of an indicator gene produces a detectable signal.

Reporter gene constructs are prepared by operatively linking an indicator gene with at least one transcriptional regulatory element. If only one transcriptional regulatory element is included it must be a regulatable promoter. In a preferred embodiment at least one of the selected transcriptional regulatory elements is indirectly or directly regulated by the activity of a transcriptional regulatory protein of the present invention, whereby activity of the transcriptional regulatory protein can be monitored via transcription of the reporter genes.

Many reporter genes and transcriptional regulatory elements are known to those of skill in the art and others may be identified or synthesized by methods known to those of skill in the art. Reporter genes include any gene that expresses a detectable gene product, which may be RNA or protein. Preferred reporter genes are those that are readily detectable. In one embodiment an indicator gene of the present invention is comprised in the nucleic acid molecule in the form of a fusion gene with a polynucleotide that includes desired transcriptional regulatory sequences.

Examples of reporter genes include, but are not limited to CAT (chloramphenicol acetyl transferase) (Alton and Napnek (1979), Nature 282: 864-869) luciferase, and other enzyme detection systems, such as beta-galactosidase; firefly luciferase (deWet et al. (1987), Mol. Cell Biol. 7:725-737); bacterial luciferase (Engebrecht and Silverman (1984), PNAS 1 : 4154-4158; Baldwin et al. (1984), Biochemistry 23: 3663-3667); alkaline phosphatase (Toh et al. (1989) Eur. J. Biochem. 182: 231-238, Hall et al. (1983) J. Mol. Appl Gen. 2: 101), hximan placental secreted alkaline phosphatase (Cullen and Malim (1992) Methods in Enzymol. 216:362-368), and horseradish peroxidase. In a preferred embodiment, the indicator gene is green fluorescent protein (U.S. patent 5,491,084; WO96/23898).

The term "detecting a signal produced by an indicator gene" is intended to include the detection of alterations in gene transcription of an indicator or reporter gene induced upon alterations in the activity of a transcriptional regulatory protein. In certain embodiments, the reporter gene may provide a selection method such that cells in which the transcriptional regulatory protein activates transcription have a growth advantage. For example the reporter could enhance cell viability, relieve a cell nutritional requirement, and/or provide resistance to a drug. In other preferred embodiments, the detection of an alteration in a signal produced by an indicator gene encompass assaying general, global changes to the cell such as changes in second messenger generation.

The amount of transcription from the reporter gene may be measured using any method known to those of skill in the art. For example, specific mR A expression may be detected using Northern blots or specific protein product may be identified by a characteristic stain or an intrinsic activity. In preferred embodiments, the gene product of the reporter is detected by an intrinsic activity associated with that product. For instance, the reporter gene may encode a gene product that, by enzymatic activity, gives rise to a detection signal based on color, fluorescence, or luminescence.

The amount of activation of the indicator gene, e.g., expression of a reporter gene, is then compared to the amount of expression in a control cell. Control cells include cells that are substantially identical to the recombinant cells, but do not express one or more of the proteins encoded by the heterologous DNA, e.g., do not include or express a reporter gene construct, transcriptional regulatory protein, or selectable marker gene. Similarly, the amount of transcription of an indicator gene may be compared between a cell in the absence of a test modulator molecule and an identical cell in the presence of a test modulator molecule.

A "minimal activation domain" as used herein is intended to include a polypeptide sequence or fragment that comprises the transactivation potential of a transcriptional regulatory protein. A polypeptide encoding a minimal activation domain can be a naturally occxirring polypeptide, e.g., it can be found within a protein that exists in nature, or it can be a polypeptide that has a composition that does not exist within a naturally occurring protein. In the context of the present invention a minimal activation domain is sufficient to confer upon a heterologous protein the ability to activate gene transcription. In a preferred embodiment, a niinimal activation domain is derived from a 12 amino acid segment, residues 436 to 447, comprising the "acidic activation domain" of VP16. The minimal activation domain may also be mutated and/or used in tandem, as described in U.S. Patent Nos. 6,087,166 and 6,271,341.

The term "modulator", as in "modulator of the transcription of a gene of interest" and "modulator of a transcriptional regulatory protein" is intended to encompass, in its various grammatical forms, induction and/or potentiation, as well as inhibition and/or downregulation of gene transcription and/or the activity of a transcriptional regulatory protein. In one embodiment, a method of the present invention encompasses the modulation of the transcription of an indicator gene in response to the activity of a transcriptional regulatory protein. In another embodiment, a method of the present invention encompasses the modulation of the activity of a transcriptional regulatory protein by a test compound which then results in a change in the transcription of a gene, preferably an indicator gene.

The term "operatively linked" or "operably linked" is intended to mean that molecules are functionally coupled to each other in that the change of activity or state of one molecule is affected by the activity or state of the other molecule. Nucleotide sequences are "operably linked" when the regulatory sequence functionally relates to the DNA sequence encoding the polypeptide or protein of interest. For example, a promoter nucleotide sequence is operably linked to a DNA sequence encoding the protein or polypeptide of interest if the promoter nucleotide sequence controls the transcription of the DNA sequence encoding the protein of interest. Typically, two polypeptides that are operatively linked are covalently attached through peptide bonds.

The term "selectable marker gene" or "selectable marker" is intended to include genes that encode a protein product that confers upon the cell expressing the protein product a phenotype that is distinguishable from cells that are not expressing the selectable marker gene. Selectable marker genes of the present invention include genes that confer amino acid or nucleotide prototrophy, antibiotic resistance, and metabolic drug resistance.

In the case of yeast, exemplary positively selectable (beneficial) genes include the following: URA3, LYS2, HIS3, LEU2, TRP1; ADE1, 2, 3, 4, 5, 7, 8; ARGl, 3, 4, 5, 6, 8; HIS1, 4, 5; ILV1, 2, 5; THR1, 4; TRP2, 3, 4, 5; LEU1, 4; MET2 3, 4, 8, 9, 14, 16, 19; URA1, 2, 4, 5, 10; H0M3, 6; ASP3; CHOI; ARO 2, 7; CYS3; OLE1; IN01, 2, 4; PR01, 3. Coxmtless other genes are potential selectable markers. The above genes are involved in well-characterized biosynthetic pathways. In a preferred embodiment, a selectable marker gene is URA3 which encodes orotidine-5'-phosphate decarboxylase. URA3 expression can be used to confer growth in the absence of uracil. Conversely, URA3 is also a counterselectable or negatively selectable gene; loss of URA3 expression confers resistance to 5-fluoroorotic acid.

The term "transcriptional regulatory domain" is intended to include the discrete domain of a transcriptional regulatory protein that modulates transcription of a gene. The mechanism by which a transcriptional regulatory domain modulates transcription includes, but is not limited to, direct or indirect interaction with elements of the basal transcription complex, e.g., RNA polymerase and TATA binding protein, direct or indirect interaction with other transcriptional regulatory proteins, and alteration of the conformation of the gene regulatory sequences. A transcriptional regulatory domain can either activate or inhibit transcription.

The Heφes simplex virion protein 16 contains two distinct transcriptional activation domains characterized by bulky, hydrophobic amino acids positioned in a highly negatively charged surroxinding (Regier et al. (1993) Proc. Natl. Acad. Sci. U. S. A. 90, 883). Each domain was shown to activate transcription when fused to a heterologous DNA binding domain, such as the one of GAL4 (Seipel et „/.(1992) EMBO-J 11, 4961-4968). In one embodiment, a transcriptional regulatory domain of the present invention is a polypeptide derived from the Herpes simplex virion protein 16 (VP16). In another embodiment, a transcriptional regulatory domain includes at least one copy of a minimal activation domain of NP16. In a preferred embodiment, a transcriptional regulatory domain comprises an acidic region comprising amino acid residues 436 to 447 of the NP16.

The terms "transcriptional regulatory protein" and "transcriptional regulator" are used interchangeably and are intended to include any protein that is capable of modulating the transcription of a gene by contact, either directly or indirectly, with the gene regulatory sequences of the gene. Typically, the DΝA binding and transcriptional activation or repression functions of a transcriptional regulatory protein, or transcription factor, are contained within discrete, modular domains of the protein. A transcriptional regulatory protein of the present invention includes a fusion protein comprising a polypeptide comprising a DΝA binding protein operatively linked, e.g., functionally coupled, to a polypeptide comprising amino acid sequences derived from a transcriptional regulatory domain.

The term "variant allele" or "sequence variant" is intended to include a polynucleotide encoding a polypeptide or protein that comprises at least one mutation relative to the wild type allele. A mutation in a polynucleotide sequence is transferred to a mutation in the amino acid sequence encoded by said polynucleotide, and may thus affect protein structure and function. Types of mutations include silent, missense and nonsense mutations, as well as insertion and deletion mutations.

The present invention pertains to nucleic acid molecules and proteins which can be used to regulate the expression of genes in vitro or in vivo in a highly controlled manner, (i.e. which encode Inducer specific TetR Fusion proteins). Narious aspects of the invention pertain to fusion proteins which are capable of activating or silencing gene transcription when bound to tet operator (tetO) sequences. The invention includes fusion proteins which bind to tet operator sequences only in the presence of specific tetracycline analogs (revTetR), as well as fusion proteins which bind to tet operator sequences only in the absence of specific tetracycline analogs. Thus, in a host cell, e.g., a eukaryotic cell, transcription of a gene operatively linked to a tet operator sequence(s) is stimulated or inhibited by a fusion protein of the invention by altering the concentration of certain tetracycline or tetracycline analogs in contact with the host cell (e.g., adding or removing tetracycline from a culture medium, or aάministering or ceasing to administer tetracycline to a host organism, etc.).

The transcriptional regulatory proteins of the invention include transactivators which stimulate or transcriptional silencers which repress the transcription of a gene under the control of sequences derived from the tet operator. The transactivators and transcriptional silencers of the invention may be fusion proteins. One aspect of the invention thus pertains to fusion proteins and nucleic acid molecules (e.g., DNA) encoding fusion proteins. The term "fusion protein" is intended to describe at least two polypeptides, typically from different sources, which are operatively linked. Typically, the two polypeptides are covalently attached through peptide bonds. The fusion protein is preferably produced by standard recombinant DNA techniques. For example, a DNA molecule encoding the first polypeptide is ligated to another DNA molecule encoding the second polypeptide, and the resultant hybrid DNA molecule is expressed in a host cell to produce the fusion protein. The DNA molecules are ligated to each other in a 5' to 3' orientation such that, after ligation, the translational frame of the encoded polypeptides is not altered (i.e., the DNA molecules are ligated to each other in-frame).

The transactivator fusion proteins of the invention are composed, in part, of a first, mutant Tet repressor polypeptide which binds to a tet operator sequence in a cell in the absence of certain tetracycline analogs, including, for example, tetracycline analogs lacking the 4-dma grouping. The invention also includes inducer specific modified Tet repressor polypeptides which contain additional mutations which reverse the binding phenotype of the TetR, such that the mutant Tet repressor polypeptide binds to a tet operator sequence in a cell in the presence of certain tetracycline analogs. The mutated Tet repressor of the invention is intended to include polypeptides having an amino acid sequence which is similar to a wild- type Tet repressor but which has at least one amino acid difference from the wild-type Tet repressor. The amino acid difference(s) between a mutated Tet repressor and a wild-type Tet repressor may be substitution of one or more amino acids, deletion of one or more amino acids or addition of one or more amino acids.

A first polypeptide of the transactivator fusion protein (e.g., the Tet repressor) has the property of binding specifically to a tet operator sequence. Each class of Tet repressor has a corresponding target tet operator sequence. Accordingly, the term "tet operator sequence" is intended to encompass all classes of tet operator sequences, e.g. class A, B, C, D, E, or G. In a preferred embodiment, the mutated Tet repressor is a TnlO-encoded repressor (i.e., class B) and the tet operator sequence is a class B tet operator sequence. Alternatively, a mutated class A Tet repressor can be used with a class A tet operator sequence, and so on for the other classes of Tet repressor/operators.

The first polypeptide of the transactivator fusion protein is operatively linked to a second polypeptide which directly or indirectly activates transcription in eukaryotic cells. To operatively link the first and second polypeptides, typically nucleotide sequences encoding the first and second polypeptides are ligated to each other in-frame to create a chimeric gene encoding a fusion protein, although the first and second polypeptides can be operatively linked by other means that preserve the function of each polypeptide (e.g., chemically crosslinked). In a preferred embodiment, the second polypeptide of the transactivator itself possesses transcriptional activation activity (i.e., the second polypeptide directly activates transcription). In another embodiment, the second polypeptide activates transcription by indirect mechanisms, through recruitment of a transcriptional activation protein to interact with the fusion protein. Accordingly, the term "a polypeptide which activates transcription in eukaryotic cells" as used herein is intended to include polypeptides which either directly or indirectly activate transcription.

Polypeptides which can function to activate transcription in exikaryotic cells are well known in the art. In particular, transcriptional activation domains of many DNA binding proteins have been described and have been shown to retain their activation function when the domain is transferred to a heterologous protein. A preferred polypeptide for use in the fusion protein of the invention is the heφes simplex virus virion protein 16 (referred to herein as VP16, the amino acid sequence of which is disclosed in Triezenberg et al. (1988) Genes Dev. 2:718-729). In one embodiment, the second polypeptide of the fusion protein is a polypeptide derived from the Herpes simplex virus protein 16 (NP16). In another embodiment the second polypeptide of the fusion protein comprises at least one copy of a minimal activation domain of Herpes simplex NP16. In a further embodiment, the second polypeptide of the fusion protein comprises at least one copy of an acidic region comprising amino acid residues 436 to 447 of Herpes simplex NP16. In still another embodiment, the minimal activation domain can contain mutations and/or be used in tandem to achieve graded transcription levels (see U.S. Patent Νos. 6,087,166 and 6,271,341).

As referred to already before, in a more preferred embodiment of the present invention the second polypeptide which directly or indirectly activates transcription in exikaryotic cells essentially consists of one or more repeats of the aforementioned minimal activation domain of VP-16. Preferably, it essentially consists of at least two, at least three, at least four copies of the said minimal activation domain.

Other polypeptides with transcriptional activation ability in eukaryotic cells can be used in the fusion protein of the invention. Transcriptional activation domains found within various proteins have been grouped into categories based upon similar structural features. Types of transcriptional activation domains include acidic transcription activation domains, proline-rich transcription activation domains, serine/threonine-rich transcription activation domains and glutamine-rich transcription activation domains. Examples of acidic transcriptional activation domains include the NP16 regions already described and amino acid residues 753-881 of GAL4. Examples of proline-rich activation domains include amino acid residues 399-499 of CTF/ΝF1 and amino acid residues 31-76 of AP2. Examples of serme/threonine-rich transcription activation domains include amino acid residues 1-427 of ITF1 and amino acid residues 2-451 of ITF2. Examples of glutamine- rich activation domains include amino acid residues 175-269 of Octl and amino acid residues 132-243 of Spl. The amino acid sequences of each of the above described regions, and of other useful transcriptional activation domains, are disclosed in Seipel et al. (EMBOJ. (1992) 13:4961-4968).

In addition to previously described transcriptional activation domains, novel transcriptional activation domains, which can be identified by standard techniques, are within the scope of the invention. The transcriptional activation ability of a polypeptide can be assayed by linking the polypeptide to another polypeptide having DΝA binding activity and determining the amoxint of transcription of a target sequence that is stimulated by the fusion protein. For example, a standard assay used in the art utilizes a fusion protein of a putative transcriptional activation domain and a GAL4 DΝA binding domain (e.g. , amino acid residues 1-93). This fusion protein is then used to stimulate expression of a reporter gene linked to GAL4 binding sites (see e.g., Seipel et al. (1992) EMBO J. 11:4961-4968 and references cited therein).

In another embodiment, the second polypeptide of the fusion protein indirectly activates transcription by recruiting a transcriptional activator to interact with the fusion protein. For example, a tetR of the invention can be fused to a polypeptide domain (e.g., a dimerization domain) capable of mediating a protein-protein interaction with a transcriptional activator protein, such as an endogenous activator present in a host cell. It has been demonstrated that functional associations between DNA binding domains and transactivation domains need not be covalent (see e.g., Fields and Song (1989) Nature 340:245-247; Chien et al. (1991) Proc. Natl. Acad. Sci. USA 88:9578; Gyuris et al. (1993) Cell 75:791-803; and Zervos (1993) Cell 72:223-232). Accordingly, the second polypeptide of the fusion protein may not directly activate transcription but rather may form a stable interaction with an endogenous polypeptide bearing a compatible protein-protein interaction domain and transactivation domain. Examples of suitable interaction (or dimerization) domains include leucine zippers (Landschulz et al. (1989) Science 243:1681-1688), helix-loop-helix domains (Murre et al. (1989) Cell 58:537-544) and zinc finger domains (Frankel et al. (1988) Science 240:70-73). Interaction of a dimerization domain present in the fusion protein with an endogenous nuclear factor results in recruitment of the transactivation domain of the nuclear factor to the fusion protein, and thereby to a tet operator sequence to which the fusion protein is boxmd.

It is understood to one skilled in the art that the nucleotide sequence determined from the sequencing of the mutant transactivator fusion protein genes allows for the generation of comparable transactivator fusion protein mutations within homologous genes.

In addition to an inducer specific mutated Tet repressor and a transcriptional activation domain, a fusion protein of the invention can contain an operatively linked third polypeptide which promotes transport of the fusion protein to a cell nucleus. Amino acid sequences which, when included in a protein, function to promote transport of the protein to the nucleus are known in the art and are termed nuclear localization signals (NLS).

Nuclear localization signals typically are composed of a stretch of basic amino acids. When attached to a heterologous protein (e.g., a fusion protein of the invention), the nuclear localization signal promotes transport of the protein to a cell nucleus. The nuclear localization signal is attached to a heterologous protein such that it is exposed on the protein surface and does not interfere with the function of the protein. Preferably, the NLS is attached to one end of the protein, e.g. the N-terminus. Preferably, a nucleic acid encoding the nuclear localization signal is spliced by standard recombinant DNA techniques in-frame to the nucleic acid encoding the fusion protein (e.g., at the 5' end).

Another aspect of the invention pertains to transcriptional inhibitor or silencer fusion proteins. The inhibitor fusion proteins of the invention are constructed similarly to the transactivator fusion proteins of the invention (see Subsection A above) but instead of containing a polypeptide domain that stimulates transcription in eukaryotic cells, the inhibitor fusion proteins contain a polypeptide domain that inhibits transcription in eukaryotic cells. The inhibitor fusion proteins are used to downregulate the expression of genes operably linked to tetO sequences. For example, when a tetO-linked gene is introduced into a host cell or animal, the level of basal, constitutive expression of the gene may vary depending upon the type of cell or tissue in which the gene is introduced and on the site of integration of the gene. Alternatively, constitutive expression of endogenous genes into which tetO sequences have been introduced may vary depending upon the strength of additional endogenous regulatory sequences in the vicinity. The inhibitor fusion proteins described herein provide compositions that can be used to inhibit the expression of such tetO-linked genes in a controlled manner.

In one embodiment, the inhibitor fusion protein comprises a first polypeptide that binds to tet operator sequences in the absence, but not the presence, of tetracycline operatively linked to a heterologous second polypeptide that inhibits transcription in exikaryotic cells. In another embodiment, the inhibitor fusion protein comprises a first polypeptide that binds to tet operator sequences in the presence, but not the absence, of tetracycline operatively linked to a heterologous second polypeptide that inhibits transcription in eukaryotic cells. The term "heterologous" is intended to mean that the second polypeptide is derived from a different protein than the first polypeptide. Like the transactivator fusion proteins, the transcriptional inhibitor fusion proteins can be prepared using standard recombinant DNA techniques as described herein.

As described above, the transcriptional inhibitor fusion protein of the invention may be composed, in part, of a first polypeptide which binds to a tet operator sequence in the presence, but not the absence of Tc or an analogue thereof. In another embodiment, the transcriptional inhibitor fusion protein may be composed, in part, of a first polypeptide which binds to a tet operator sequence in the absence, but not the presence of Tc or an analogue thereof. A mutated Tet repressor of any class (e.g., A, B, C, D or E) may be used as the first polypeptide.

The first polypeptide of the transcriptional inhibitor fusion protein is operatively linked to a second polypeptide which directly or indirectly inhibits transcription in eukaryotic cells. As described in Section A, above, to operatively link the first and second polypeptides of a fusion protein, typically nucleotide sequences encoding the first and second polypeptides are ligated to each other in-frame to create a chimeric gene encoding the fusion protein. However, the first and second polypeptides can be operatively linked by other means that preserve the function of each polypeptide (e.g., chemically crosslinked). Although the fusion proteins are typically described herein as having the first polypeptide at the amino- terminal end of the fusion protein and the second polypeptide at the carboxy-terminal end of the fusion protein, it will be appreciated by those skilled in the art that the opposite orientation (i.e., the second polypeptide at the amino-terminal end and the first polypeptide at the carboxy-terminal end) is also contemplated by the invention.

Proteins and polypeptide domains within proteins which can function to inhibit transcription in eukaryotic cells have been described in the art (for reviews see, e.g., Renkawitz (1990) Trends in Genetics 6:192-197; and Herschbach and Johnson, (1993) Annu. Rev. Cell. Biol. 9:479-509). Such transcriptional inhibitor domains have been referred to in the art as "silencing domains" or "repressor domains." Although the precise mechanism by which many of these polypeptide domains inhibit transcription is not known (and the invention is not intended to be limited by mechanism), there are several possible means by which repressor domains may inhibit franscription, including: 1) competitive inhibition of binding of either activator proteins or the general transcriptional machinery,

^' 2) prevention of the activity of a DNA boxmd activator and 3) negative interference with the assembly of a functional preinitiation complex of the general transcription machinery. Thus, a repressor domain may have a direct inhibitory effect on the franscriptional machinery or may inhibit franscription indirectly by inhibiting the activity of activator proteins. Accordingly, the term "a polypeptide that inhibits transcription in eukaryotic cells" as used herein is intended to include polypeptides which act either directly or indirectly to inhibit transcription. As used herein, "inhibition" of transcription is intended to mean a diminution in the level or amount of franscription of a target gene compared to the level or amount of transcription prior to regulation by the transcriptional inhibitor protein. Transcriptional inhibition may be partial or complete. The terms "silencer", "repressor" and "inhibitor" are used interchangeably herein to describe a regulatory protein, or domains thereof, that can inhibit transcription. A transcriptional "repressor" or "silencer" domain as described herein is a polypeptide domain that retains its transcriptional repressor function when the domain is transferred to a heterologous protein. Proteins which have been demonstrated to have repressor domains that can function when transferred to a heterologous protein include the v-erbA oncogene product (Baniahmad. et al. (1992) EMBO J. 11:1015-1023), the thyroid hormone receptor (Baniahmad, supra), the retinoic acid receptor (Baniahmad, supra), and the Drosophila Krueppel (Kr) protein (Licht et al. (1990) Nature 346:76-79; Sauer and Jackie (1991) Nature 353:563-566; Licht et al. (1994) Mol Cell Biol. 14:4057-4066). Non-limiting examples of other proteins which have franscriptional repressor activity in eukaryotic cells include the Drosophila homeodomain protein even-skipped (eve), the S. cerevisiae Ssn6/Tupl protein complex (see Herschbach and Johnson, supra), the yeast SER1 protein (see Chien, et al. (1993) Cell 75:531-541), NePl (see Kohne, et al. (1993) J. Mol. Biol. 232:747-755), the Drosophila dorsal protein (see Kirov, et al. (1994) Mol. Cell. Biol. 14:713-722; Jiang, et al. (1993) EMBO J. 12:3201-3209), TSF3 (see Chen, et al. (1993) Mol Cell. Biol. 75:831-840), SF1 (see Targa, et al (1992) Biochem. Biophys. Res. Comm. 188:416-423), the Drosophila hunchback protein (see Zhang et al. (1992) Proc. Natl. Acad. Sci. USA 89:7511-7515), the Drosophila knfrps protein (see Gerwin et al. ( 1994) Mol. Cell Biol. 14:7899-7908), the WT1 protein (Wilm's tumor gene product) (see Anant, et al. (1994) Oncogene 9:3113-3126; Madden et al, (1993) Oncogene 8:1713-1720), Oct-2.1 (see Lillycrop, et al. (1994) Mol Cell. Biol. 14:7633-7642), the Drosophila engrailed protein (see Badiani et al. (1994) Genes Dev. 8:770-782; Han and Manley, (1993) EMBO J. 12:2723-2733), E4BP4 (see Cowell and Hurst, (1994) Nucleic Acids Res. 22:59-65) and ZF5 (see Numoto et al. (1993) Nucleic Acids Res. 21:3767-3775).

In a preferred embodiment, the second polypeptide of the transcriptional inhibitor fusion protein of the invention is a transcriptional silencer domain of the Drosophila Krueppel protein. A C-terminal region having repressor activity can be used, such as amino acids 403-466 of the native protein (see Sauer and Jackie supra). This region is referred to as C64KR. Alternatively, an alanine-rich amino terminal region of Kr that also has repressor activity can be used as the second polypeptide of the fusion protein. For example, amino acids 26-110 of Kr (see Licht et al, (1990) supra) can be used as the second polypeptide. Alternatively, shorter or longer polypeptide fragments encompassing either of the Kr silencer domains that still retain full or partial inhibitor activity are also contemplated (e.g., amino acids 62 to 92 of the N-terminal silencer domain; see Licht et al. (1994) supra).

In another preferred embodiment, the second polypeptide of the transcriptional inhibitor fusion protein of the invention is a franscriptional silencer domain of the v-erbA oncogene product. The silencer domain of v-erbA has been mapped to approximately amino acid residues 362-632 of the native v-erbA oncogene product (see Baniahmad, et al. supra). Accordingly, a fragment encompassing this region is used as the second polypeptide of the silencer domain. In one embodiment, amino acid residues 364-635 of the native v-erbA protein are used. Alternatively, shorter or longer polypeptide fragments encompassing the v-erbA silencer region that still retain full or partial inhibitor activity are also contemplated. For example, amino acid residues 346-639, 362-639, 346-632, 346-616 and 362-616 of v-erbA may be used. Additionally, polypeptide fragments encompassing these regions that have internal deletions yet still retain full or partial inhibitor activity are encompassed by the invention, such as amino acid residues 362-468/508-639 of v-erbA. Fxirthermore, two or more copies of the silencer domain may be included in the fusion protein, such as two copies of a.a. residues 362-616 of v-erbA. Suitable silencer polypeptide domains of v-erbA are described further in Baniahmad et al. (supra).

In other embodiments, other silencer domains are used. Non-limiting examples of polypeptide domains that can be used include: amino acid residues 120-410 of the thyroid hormone receptor alpha (THRα), amino acid residues 143-403 of the retinoic acid receptor alpha (RARα), amino acid residues 186-232 of kniφs, the N-terminal region of WT 1 (see Anant, supra), the N-terminal region of Oct-2.1 (see Lillycrop, supra), a 65 amino acid domain of E4BP4 (see Cowell and Hurst, supra) and the N-terminal zinc finger domain of ZF5 (see Numoto, supra). Moreover, shorter or longer polypeptide fragments encompassing these regions that still retain full or partial inhibitor activity are also contemplated.

In addition to previously described transcriptional inhibitor domains, novel transcriptional inhibitor domains, which can be identified by standard techniques, are within the scope of the invention. The transcriptional inhibitor ability of a polypeptide can be assayed by: 1) constructing an expression vector that encodes the test silencer polypeptide linked to another polypeptide having DNA binding activity (i.e., constructing a DNA binding domain-silencer domain fusion protein), 2) cofransfecting this expression vector into host cells together with a reporter gene construct that is normally constitutively expressed in the host cell and also contains binding sites for the DNA binding domain and 3) determining the amount of transcription of the reporter gene construct that is inhibited by expression of the fusion protein in the host cell. For example, a standard assay used in the art utilizes a fusion protein of a GAL4 DNA binding domain (e.g., amino acid residues 1-147) and a test silencer domain. This fusion protein is then used to inhibit expression of a reporter gene construct that contains positive regulatory sequences (that normally stimulate constitutive franscription) and GAL4 binding sites (see e.g., Baniahmad, supra).

In addition to a Tet repressor and a transcriptional silencer domain, a transcriptional inhibitor fusion protein of the invention can contain an operatively linked third polypeptide which promotes transport of the fusion protein to a cell nucleus. As described for the transactivator fusion proteins (see Subsection A, Part 3, above), a nuclear localization signal can be incoφorated into the franscriptional inhibitor fusion protein.

The inducer specific modified tetracycline repressor polypeptide of the invention is the TetR(BD) (SEQ ED NO: 1) further comprising at least one amino acid substitution which confers the ability of the TetR molecule to distinguish between tefracycline analogs. Presently preferred amino acid substitutions that confer inducer affinity distinction between tetracycline analogs at amino acid positions include, but are not limited to, H64, S135, and S138. Additional amino acid substitutions that confer an inducer specific phenotype in a TetR(BD) include those amino acid substitutions provided in Tables 1, 2, and 3. Accordingly, inducer specific polypeptides of the present invention are also selected from those comprising an amino acid sequence selected from the group consisting of SEQ ID NOs.: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62.

In addition, the methods and compositions of the invention also use and encompass proteins and polypeptides that represent functionally equivalent gene products. Such functionally equivalent gene products include, but are not limited to, natural variants of the polypeptides having an amino acid sequence set forth in SEQ ID NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62. Such equivalent inducer specific TetR repressors can contain, e.g., deletions, additions or substitutions of amino acid residues within the amino acid sequences encoded by the target gene sequences described above, but which result in a silent change, thus producing a functionally equivalent inducer specific TetR repressor product. As described above, nucleotide substitutions in the coding region of inducer specific TetR repressors that did not result in a corresponding codon change were identified using a cell-based assay as described herein.

Amino acid substitutions can be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophihcity size, nucleophilicity, and/or the amphipathic nature of the residues involved. Examples of such classifications, some of which overlap include, nonpolar (i.e., hydrophobic) amino acid residues can include alanine (Ala or A), leucine (Leu or L), isoleucine (He or I), valine (Nal or N), proline (Pro or P), phenylalanine (Phe or F), tryptophan (Tφ or W) and methionine (Met or M); polar neutral amino acid residues can include glycine (Gly or G), serine (Ser or S), threonine (Thr or T), cysteine (Cys or C), tyrosine (Tyr or Y), asparagine (Asn or Ν) and glutamine (Gin or Q); small arnino acids include glycine (Gly or G), and alanine (Ala or A); hydrophobic amino acid residues can include valine (Val or N), leucine (Leu or L), isoleucine (De or I), methionine (Met or M), and proline (Pro or P); nucleophilic amino acids can include serine (Ser or S), threonine (Thr or T), and cysteine (Cys or C); aromatic amino acids can include phenylalanine (Phe or F), tyrosine (Tyr or Y), and tryptophan (Tφ or W); amide amino acids can include asparagine (Asn or Ν), and glutamine (Gin or Q); positively charged (i.e., basic) amino acid residues can include arginine (Arg or R), lysine (Lys or K) and histidine (His or H); and negatively charged (i.e., acidic) amino acid residues can include aspartic acid (Asp or D) and glutamic acid (Glu or E). Thus, other amino acid substitutions, deletions or additions at these or other amino acid positions that retain the desired functional properties of the inducer specific TetR repressors are within the scope of the invention.

In light of the demonstrated sequence conservation between and among the TetR repressor proteins previously characterized, such an analysis can be performed with any TetR repressor protein including, but not limited to, other known members of these nine classes of TetR proteins. For instance, based on the information provided in Table 3, one of skill in the art can introduce the same substitution or substitutions as provided for TetR(BD) into any one of the listed TetR repressor classes.

Therefore, once the corresponding amino acid(s) have been identified, they, or their functional equivalents can be introduced into another TetR protein, or tetracycline-binding domain thereof, of each of the nine classes of TetR proteins, to provide a novel inducer specific Tet repressor protein, using recombinant DΝA techniques that are disclosed below and that are well known in the art. Accordingly, in another embodiment, the present invention is directed toward chimeric tefracycline repressor proteins that comprise, for example, a tetracycline-binding domain derived from a TetR protein of any of the TetR(A), TetR(B), TetR(C), TetR(D), TetR(E), TetR(G), TetR(H), TetR(J), and TetR(Z) classes of TetR binding proteins as disclosed above, that is operatively associated with a DΝA- binding domain, which may be derived from another TetR repressor protein or from a non- TetR repressor, DΝA-binding protein.

As used herein, the term "DΝA-binding domain" generally encompasses, for example, approximately the first 50 ammo-terminal residues of each TetR protein, which includes the helix-turn-helix structural motif known to be involved in the DΝA recognition and binding. As used herein, the term "tetracycline-binding domain" is generally intended to encompass that portion of a TetR protein other than the amino-terminal DNA-binding domain, and therefore, includes not only the tetracycline-binding portion but also those portions of the Tet repressor molecule that may be required for dimer formation. In other aspects of this embodiment, the tetracycline-binding domain of a chimeric revTetR protein comprises the carboxy terminal part of the polypeptide.

The modified tetracycline repressors of the present invention are useful for regulating gene expression in a wide variety of organisms including eukaryotic organisms using specific tetracycline analogs. While it is anticipated that each identified inducer specific TetR repressor will be broadly applicable across a number of organisms, it is possible that any given inducer specific TetR repressor may have slightly different activities from organism to organism, including little to undetectable activity. It is contemplated that one of skill in the art following the teachings provided herein will be able to determine the relative activity of any given inducer specific TetR repressor in view of the desired amount of regulation without undue experimentation.

As shown in Table 1, 2, and 3, the exemplary inducer specific TetR repressors (e.g., those set forth in SEQ ID NOs.: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62) exhibit the inducer specific phenotype in a representative prokaryotic organism, Escherichia coli, compared to wild-type repressor, although the absolute level of non-repressed and repressed transcription varies amongst the revTetR repressors. The varied levels of transcriptional regulation advantageously increase the flexibility and range of repressed versus non-repressed levels of regulated gene product. By selecting the appropriate inducer specific TetR and tet sequence for use in the methods described herein, levels of the regulated gene may be varied over a wide range as well as the overall ratio of inducer affinity distinction.

One of skill in the art can introduce similar mutations at the corresponding positions in the other classes of tefracycline repressor, or chimera, thereof, based on the teachings herein and the amino acid sequences of the positions provided in Tables 1 ,2, and 3 to generate inducer specific TetR repressors in these classes that are useful in the methods described herein. Described herein are methods for the production of antibodies capable of specifically recognizing epitopes of one or more of the inducer specific TetR proteins or the transactivator fusion proteins described herein. Such antibodies can include, but are not limited to, polyclonal antibodies, monoclonal antibodies (mAbs), human, humanized or chimeric antibodies, single chain antibodies, Fab fragments, F(ab')₂ fragments, fragments produced by a Fab expression library, anti-idiotypic (anti-Id) antibodies, and epitope- binding fragments of any of the above.

It is presumed that a nximber of the modified inducer specific TetR repressors of the present invention will have a conformation that is different from that of wild-type TetR. For the production of antibodies to the altered conformation of the inducer specific TetR repressors, various host animals can be immunized by injection with a inducer specific TetR protein, or a portion thereof containing one of the amino acid substitutions set forth herein. Such host animals can include but are not limited to rabbits, mice, and rats, to name but a few. Various adjuvants can be used to increase the immxmological response, depending on the host species, including but not limited to Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, plxironic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parvum. Accordingly, a method of eliciting an immxine response in an animal, comprising introducing into the animal an immunogenic composition comprising an isolated inducer specific TetR polypeptide, the amino acid sequence of which comprises at least one inducer specific TetR substitution and 9 consecutive residues of one of SEQ ID NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 56, 60, and 62.

Polyclonal antibodies are heterogeneous populations of antibody molecules derived from the sera of animals immiinized with an antigen, such as a inducer specific TetR repressor polypeptide, or an antigenic functional derivative thereof containing one of the amino acid substitutions set forth herein are provided. For the production of polyclonal antibodies, host animals such as those described above, can be immunized by injection with a inducer specific TetR repressor polypeptide or transactivator fusion protein supplemented with adjuvants as also described above. The antibody titer in the immxinized animal can be monitored over time by standard techniques, such as with an enzyme linked immxmosorbent assay (ELISA) using immobilized polypeptide. If desired, the antibody molecules can be isolated from the animal (e.g., from the blood) and further purified by well-known techniques, such as protein A chromatography to obtain the IgG fraction.

Monoclonal antibodies, which are homogeneous populations of antibodies to a particular antigen, can be obtained by any 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 of Kohler and Milstein, (1975, Nature 256: 495-97; and U.S. Pat. No. 4,376,110), the human B-cell hybridoma technique (Kosbor et al., 1983, Immunology Today 4:72; Cole et al, 1983, Proc. Natl. Acad. Sci. USA 80: 2026-30), and the EBN- hybridoma technique (Cole et al., 1985, Monoclonal Antibodies And Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). Such antibodies can be of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD and any subclass thereof. The hybridoma producing the mAb of this invention can be cultivated in vitro or in vivo. Production of high titers of mAbs in vivo makes this the presently preferred method of production.

Alternative to preparing monoclonal antibody-secreting hybridomas, a monoclonal antibody directed against a inducer specific TetR polypeptide or transactivator fusion protein of the invention can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with the polypeptide of interest. Kits for generating and screening phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SurfZAP J Phage Display Kit, Catalog No. 240612). Additionally, examples of methods and reagents particularly amenable for use in generating and screening antibody display library can be found in, for example, U.S. Pat. No. 5,223,409; PCT Publication No. WO 92/18619; PCT Publication No. WO 91/17271; PCT Publication No. WO 92/20791; PCT Publication No. WO 92/15679; PCT Publication No. WO 93/01288; PCT Publication No. WO 92/01047; PCT Publication No. WO 92/09690; PCT Publication No. WO 90/02809; Fuchs et al. (1991) Bio Technology 9:1370-1372; Hay et al. (1992) Hum. Antibod. Hybridomas 3:81-85; Huse et al. (1989) Science 246:1275-1281; Griffiths et al. (1993) EMBOJ. 12:725-734.

Additionally, recombinant antibodies, such as chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, which can be made using standard recombinant DNA techniques, are within the scope of the invention. A chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine mAb and a human immxrαoglobulin constant region. (See, e.g., Cabilly et al, U.S. Pat. No. 4,816,567; and Boss et al, U.S. Pat. No. 4,816397, which are incoφorated herein by reference in their entirety.) Humanized antibodies are antibody molecules from non-human species having one or more complementarily deterrnining regions (CDRs) from the non-human species and a framework region from a human immxmoglobulin molecule. (See, e.g., Queen, U.S. Pat. No. 5,585,089, which is incoφorated herein by reference in its entirety.) Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in PCT Publication No. WO 87/02671; European Patent Application 184,187; European Patent Application 171,496; European Patent Application 173,494; PCT Publication No. WO 86/01533; U.S. Pat. No. 4,816,567; European Patent Application 125,023; Better et al. (1988) Science 240:1041-1043; Liu et al. (1987) Proc. Natl. Acad. Sci. USA 84:3439-3443; Liu et al. (1987) J Immunol. 139:3521-3526; Sun et al. (1987) Proc. Natl. Acad. Sci. USA 84:214- 218; Nishimura et al. (1987) Cane. Res. 47:999-1005; Wood et al. (1985) Nature 314:446- 449; and Shaw et al. (1988) J. Natl. Cancer Inst. 80:1553-1559); Morrison (1985) Science 229:1202-1207; Oi et al. (1986) Bio/Techniques 4:214; U.S. Pat. No. 5,225,539; Jones et al. (1986) Nature 321:552-525; Nerhoeyan et al. (1988) Science 239:1534; and Beidler et al. (1988) J. Immunol. 141 :4053-4060.

Completely human antibodies are particularly desirable for therapeutic treatment of human patients. Such antibodies can be produced using transgenic mice which are incapable of expressing endogenous immunoglobulin heavy and light chains genes, but which can express human heavy and light chain genes. The transgenic mice are immunized in the normal fashion with a selected antigen, e.g., all or a portion of a polypeptide of the invention. Monoclonal antibodies directed against the antigen can be obtained using conventional hybridoma technology. The human immxmoglobulin transgenes harbored by the transgenic mice rearrange during B cell differentiation, and subsequently undergo class switching and somatic mutation. Thus, using such a technique, it is possible to produce therapeutically useful IgG, IgA and IgE antibodies. For an overview of this technology for producing human antibodies, see Lonberg and Huszar (1995, Int. Rev. Immunol. 13:65-93). For a detailed discussion of this technology for producing human antibodies and human monoclonal antibodies and protocols for producing such antibodies, see, e.g., U.S. Pat. 5,625,126; U.S. Pat. No. 5,633,425; U.S. Pat. No. 5,569,825; U.S. Pat. No. 5,661,016; and U.S. Pat. No. 5,545,806. Completely human antibodies which recognize a selected epitope can be generated using a technique referred to as "guided selection." In this approach a selected non-human monoclonal antibody, e.g., a mouse antibody, is used to guide the selection of a completely human antibody recognizing the same epitope. (Jespers et al. (1994) Bio/technology 12:899-903). For example, hximan antibodies specific to epitopes responsible for the reverse phenotype of these repressors would be highly desirable for monitoring revTetR in vivo expression levels.

Antibody fragments which recognize specific epitopes can be generated by known techniques. For example, such fragments include but are not limited to: the F(ab')₂ fragments which can be produced by pepsin digestion of the antibody molecule and the Fab fragments which can be generated by reducing the disulfide bridges of the F(ab')₂ fragments. Alternatively, Fab expression libraries can be constructed (Huse et al, 1989, Science 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity.

Antibodies provided herein may also be described or specified in terms of their binding affinity to a target gene product. Preferred binding affinities include those with a dissociation constant or K_d less than 5 x 10^"6M, 10^"6M, 5 x 10^"7M, 10^"7M, 5 x 10^"8M, 10^" ⁸M, 5 x 10^"9M, 10^"9M, 5 x 10^"10M, 10^"10M, 5 x 10^"πM, 10^"nM, 5 x 10^"12M, 10^"12M, 5 x 10^" ¹³M, 10^"13M, 5 x 10^"14M, 10^"14M, 5 x 10^"15M, or 10^"15M.

Antibodies directed against an inducer specific TetR repressor polypeptide, transactivator fusion protein, or fragment thereof containing one of the amino acid substitutions set forth herein can be used diagnostically to monitor levels of a revTetR repressor polypeptide or transactivator fusion protein in the tissue of an host as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given freatment regimen. Detection can be facilitated by coupling the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include 1251, 1311, 35S or 3H.

Described herein are nucleic acid molecules of the invention which encode the modified inducer specific tetracycline repressors and chimeric tetracycline repressors of the invention, such as those described herein.

In one embodiment, the isolated nucleic acid molecules of the invention comprise nucleotide substitutions that result in codon changes in the TetR (BD) chimera (SEQ ED NO. 2) at amino acid positions 64, 135, and/or 138. These nucleic acid molecules encode modified tetracycline repressors that display the inducer specific phenotype. These nucleic acid molecules can be prepared by modifying a nucleotide sequence that encode the TetR (BD) chimera, such as the nucleotide sequence set forth in SEQ ED NO: 1. The relative activity of these exemplary inducer specific TetR repressors encoded by the nucleotide sequences of the invention and wild type TetR repressor is illustrated in Table 1 to 5, and discussed in detail herein.

To isolate homologous inducer specific TetR repressors, the inducer specific TetR nucleotide sequences and fragments thereof described above can be labeled and used as probes to screen a library of DNA encoding mutant TetR sequences. Hybridization conditions should be of a lower stringency when the cDNA library was derived from a Tet repressor class or chimera different from the class of TetR from which the labeled sequence was derived. For guidance regarding such conditions see, for example, Sambrook et al, 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, N.Y.; and Ausubel et al, 1989, Current Protocols in Molecular Biology, (Green Publishing Associates and Wiley Interscience, N.Y.). In particular, oligonucleotide probes, primers or fragments that comprise nucleotide sequences encompassing the specified nucleotide substitutions described above that confer the reverse phenotype in one class of tetracycline repressor may be used in hybridization reactions or DNA amplification methods to specifically identify those members of the library containing the desired substitutions.

Alternatively, a modified inducer specific TetR repressor can be created by site-directed mutagenesis by substitution of amino acid residues in the sequence of a wild type Tet repressor, or chimera thereof. Tables 1 to 3 list the positions of amino acid residues present in various tetracycline repressor classes at which desirable substitutions can be made. In still further embodiments, the isolated nucleic acid molecules encode an inducer specific TetR repressor comprising a sequence of nucleotides containing a mutation or mutations that confers an inducer specific phenotype in eukaryotic organisms and preferably having at least 70%, 75%, 80%, 85%, 90%, 95%, 98% or 99% nucleotide sequence identity, more preferably at least 90%, 95%, 98% or 99% sequence identity, to any of the nucleotide sequences set forth in SEQ ID NOS. 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 59, and 61.

To determine the percent identity of two sequences, e.g., nucleotide or amino acid, the sequences are aligned for optimal comparison puφoses (e.g., gaps can be introduced in the sequence of a first amino acid or nucleotide sequence for optimal alignment with a second amino acid or nucleotide sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the nximber of identical positions shared by the sequences (i.e., % identity=number of identical overlapping positions/total nximber of positions xl00%). In one embodiment, the two sequences are the same length.

The determination of percent identity between two sequences can also be accomplished using a mathematical algorithm. A preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. U.S.A. 87: 2264-68, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. U.S.A. 90: 5873-77. Such an algorithm is incoφorated into the NBLAST and XBLAST programs of Altschul et al, 1990, J. Mol. Biol. 215: 403. BLAST nucleotide searches can be performed with the NBLAST nucleotide program parameters set, e.g., for score=100, wordlength=12 to obtain nucleotide sequences homologous to a nucleic acid molecules of the present invention. BLAST protein searches can be performed with the XBLAST program parameters set, e.g., to score-50, wordlength=3 to obtain amino acid sequences homologous to a protein molecule of the present invention. To obtain gapped alignments for comparison puφoses, Gapped BLAST can be utilized as described in Altschul et al, 1997, Nucleic Acids Res. 25: 3389-3402. Alternatively, PSI-BLAST can be used to perform an iterated search which detects distant relationships between molecules (Id.). When utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default parameters of the respective programs (e.g., of XBLAST and NBLAST) can be used (see, e.g., http://www.ncbi.nlm.nih.gov). Another preferred, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, (1988) CABIOS 4: 11-17. Such an algorithm is incoφorated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used.

The present invention also includes polynucleotides, preferably DNA molecules, that hybridize to the complement of the nucleic acid sequences encoding the modified tetracycline repressors. Such hybridization conditions can be highly stringent or less highly stringent, as described above and known in the art. The nucleic acid molecules of the invention that hybridize to the above described DNA sequences include oligodeoxynucleotides ("oligos") which hybridize to the nucleotide sequence encoding the inducer specific TetR repressor under highly stringent or stringent conditions. In general, for oligos between 14 and 70 nucleotides in length the melting temperature (Tm) is calculated using the formula:

Tm(°C.)=81.5+16.6 (log[monovalent cations (molar)]+0.41 (% G+C)-(500/N)

where N is the length of the probe. If the hybridization is carried out in a solution containing formamide, the melting temperature may be calculated using the equation:

Tm(°C.)=81.5+16.6 (log[monovalent cations (molar)])+0.41 (% G+C)-(0.61) (% formamide)-(500/N)

where N is the length of the probe. In general, hybridization is carried out at about 20-25 degrees below Tm (for DNA-DNA hybrids) or about 10-15 degrees below Tm (for RNA- DNA hybrids). Other exemplary highly stringent conditions may refer, e.g., to washing in 6 x SSC/0.05% sodium pyrophosphate at 37° C. (for 14-base oligos), 48° C. (for 17-base oligos), 55°. C. (for 20-base oligos), and 60° C. (for 23-base oligos).

In one embodiment, the isolated nucleic acid molecules comprise a sequence of nucleotides containing a revTetR mutation or mutations that hybridize under moderate stringency conditions to the entire length any of the nucleotide sequences set forth in SEQ ID NOS. 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 59, and 61. In still yet another embodiment, the isolated nucleic acid molecules comprise a sequence of nucleotides containing a revTetR mutation or mutations that hybridize under high stringency conditions to the entire length of any of the nucleotide sequences set forth in SEQ ED NOS. 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 59, and 61 are provided. Isolated nucleic acid molecules encoding a full-length complement of the nucleotide sequence any of these nucleic acid molecules are also provided.

In another embodiment, isolated nucleic acid fragments of the inducer specific TetR repressor proteins comprising at least 10, 15, 20, 25, 30, 35, 40, 45 or 50 contiguous nucleotides containing at least one mutation encoding conferring a reverse phenotype in eukaryotes, or the complement thereof, are also provided.

En another embodiment, the invention also encompasses (a) DNA vectors that comprise a nucleotide sequence comprising any of the foregoing sequences encoding a inducer specific TetR and or their complements (including antisense molecules); (b) DNA expression constructs that comprise a nucleotide sequence comprising any of the foregoing sequences encoding a inducer specific TetR operably linked with a regulatory element that directs the expression of the coding sequences; and (c) genetically engineered host cells that comprise any of the foregoing sequences of the inducer specific TetR gene, including the inducer specific TetR gene operably linked with a regulatory element that directs the expression of the coding sequences in the host cells.

Recombinant DNA methods which are well known to those skilled in the art can be used to construct vectors comprising nucleotide sequences encoding an inducer specific TetR, and appropriate transcriptional/translational confrol signals. The various sequences may be joined in accordance with known techniques, such as restriction, joining complementary restriction sites and ligating, blunt ending by filling in overhangs and blunt ligation, Bal31 resection, primer repair, in vitro mutagenesis, or the like. Polylinkers and adapters may be employed, when appropriate, and introduced or removed by known techniques to allow for ease of assembly of the DNA vectors and expression constructs. These methods may also include in vivo recombination/genetic recombination. At each stage of the manipulation of the enzyme gene sequences, the fragment(s) may be cloned, analyzed by restriction enzyme, sequencing or hybridization, or the like. A large nximber of vectors are available for cloning and genetic manipulation. Normally, cloning can be performed in E. coli. See, for example, the techniques described in Sambrook et al, 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, N.Y.; Ausubel, 1989, supra; Methods in Enzymology: Gxiide to Molecular Cloning Techniques, Academic Press, Berger, S. L. and A. R. Kirnmel eds., 1987; Pla et al, Yeast 12:1677-1702 (1996); Kinghorn and Unkles in Aspergillus, ed. by J. E. Smith, Plenum Press, New York, 1994, Chapter 4, p.65- 100; which are incoφorated by reference herein in their entireties.

In various embodiments of the invention, DNA vectors that comprise a nucleotide sequence encoding an inducer specific TetR of the invention, may further comprise replication functions that enable the transfer, maintenance and propagation of the DNA vectors in one or more species of host cells, including but not limited to E. coli cells, Gram positive bacteria, and Gram negative bacteria. The choice of the vector will typically depend on the compatibility of the vector with the host cell into which the vector is to be introduced. The vectors may be linear or closed circular plasmids, cosmid, or phagemids. The vector may be an autonomously replicating vector, i.e., a vector which exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a plasmid, an extrachromosomal element, a minichromosome, or an artificial chromosome. The vector may contain any means for assuring self-replication. Alternatively, the vector may be one which, when introduced into the host cell, is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated.

In specific embodiments of the present invention, expression of an inducer specific TetR- encoding gene is modulated so as to provide different levels of inducer specific TetR protein in a particular host. The level of expression of a gene encoding a particular inducer specific TetR protein may be manipulated by the choice of promoters with different transcription rates to which the inducer specific TetR coding sequence is operably associated, the inclusion of one or more positive and or negative regulatory sequences which control the rate of transcription from that promoter, and the copy number of the vector carrying the inducer specific TetR coding sequence. Representative, but not limiting examples of each of these elements is provided supra. Therefore, by manipulating each of these elements independently or in a concerted manner, the level of an inducer specific TetR protein within the eukaryotic host cell can be precisely established over a wide range.

Isolated nucleic acid molecules of the present invention comprising nucleotide sequences encoding modified tetracycline repressors that exhibit the desired reverse phenotype in exikaryotic organisms may be identified, for example, from amongst a collection of mutated wild type tefracycline repressors using a number of in vitro or cell-based screening techniques, including those described herein. Any method known to those of skill in the art may be used to introduce nucleotide substitutions into the coding sequence of gene encoding a tetracycline repressor protein to create the pool of mutated repressors or portions thereof comprising at least one substitution including, but not limited to, spontaneous mutations, error-prone PCR (Leung et al, (1989) Technique 1: 11-15), chemical mutagenesis (Eckert et al, Mutat. Res. (1987) 178: 1-10), site-directed mutagenesis (Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-92; Oliphant et al, (1986) Gene 44: 177-83) or DNA shuffling (Stemmer, (1994), Proc. Natl. Acad. Sci. USA 91 : 10747-51).

In one example, an isolated nucleic acid molecule comprising the nucleotide sequence encoding the C-terminal portion of TetR(D) can be subjected to DNA shuffling with a nucleic acid molecule encoding the N-terminal portion of TetR(B) to create a pool of isolated nucleic acid molecules encoding modified chimeric TetR(BD) repressors. The pool encoding the modified chimeric TetR(BD) repressors can be cloned and screened in a representative eukaryotic cell, for those clones comprising at least one mutation encoding an amino acid substitution and conferring an inducer specific phenotype. Analogous methods may be employed to create a pool of modified tetracycline repressors for screening using isolated nucleic acid molecules encoding a member of any class of TetR repressor. The inducer specific phenotype may be identified or confirmed using a number of methods well known to those of skill in the art including, but not limited to, in vitro transcription assays and cell-based assays using reporter systems that are regulated by tetracycline.

A modified inducer specific TetR repressor of the present invention can be selected, for example, by incoφorating an isolated nucleic acid molecule of the present invention into an expression vector and introduced into a cell, e.g., a eukaryotic cell, for screening. A screening assay is used which allows for selection of an inducer specific TetR repressor which binds to a tet operator sequence in the cell only in the presence of tefracycline. For example, a pool of mutated nucleic acid molecules in an expression vector can be introduced into the organism in which tet operator sequences confrol the expression of a reporter gene, e.g., a gene encoding a Lac repressor and the Lac repressor controls the expression of a gene encoding an selectable marker (e.g., drug resistance). Binding of a Tet repressor to tet operator sequences in the bacteria will inhibit expression of the Lac repressor, thereby inducing expression of the selectable marker gene. Cells expressing the marker gene are selected based upon the selectable phenotype (e.g., drug resistance). For wild-type Tet repressors, expression of the selectable marker gene will occur in the absence of tetracycline. A modified inducer specific TetR repressor is selected using this system based upon the ability to induce expression of the selectable marker gene in the bacteria only in the presence of a certain type of tetracycline or analog thereof.

In another embodiment, methods for identifying modified tetracycline repressors that exhibit an inducer specific phenotype in eukaryotes are provided. In one aspect, the method comprises introducing into a eukaryotic cell a nucleic acid molecule comprising a reporter gene operatively linked to a promoter regulated by tetracycline or tetracycline analog, transforming a culture of cells with a collection of expression vectors, each comprising a nucleotide sequence encoding a modified tefracycline repressor containing at least one amino acid substitution, expressing the modified tefracycline repressor proteins in the organism in the presence or absence of tetracycline or tetracycline analog, and identifying those transformants that express or express at a higher level the reporter gene in the absence, but not the presence, of the tetracycline or tetracycline analog.

Described here are methods for preparing recombinant, modified tetracycline repressors that exhibit an inducer specific phenotype in eukaryotes. Methods of making the modified repressor in a gene regulation system are described in below.

The modified tefracycline repressors or peptides thereof that exhibit an inducer specific phenotype in eukaryotes of the present invention can be readily prepared, e.g., by synthetic techniques or by methods of recombinant DNA technology using techniques that are well known in the art. Thus, methods for preparing the target gene products of the invention are discussed herein. First, the polypeptides and peptides of the invention can be synthesized or prepared by techniques well known in the art. See, for example, Creighton, 1983, Proteins: Structures and Molecular Principles, W. H. Freeman and Co., N.Y., which is incoφorated herein by reference in its entirety. Peptides can, for example, be synthesized on a solid support or in solution.

Alternatively, recombinant DNA methods which are well known to those skilled in the art can be used to construct expressible nucleic acid molecules that encode a modified tefracycline repressor coding sequence such as those set forth in SEQ ED NOS. 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 59, and 61, to which are operably linked the appropriate transcriptional/ translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques and in vivo recombination/genetic recombination. See, for example, the techniques described in Sambrook et al, 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, N.Y., Pla et al, Yeast 12:1677- 1702 (1996), and Ausubel, 1989, supra. Alternatively, RNA capable of encoding target gene protein sequences can be chemically synthesized using, for example, synthesizers. See, for example, the techniques described in Oligonucleotide Synthesis, 1984, Gait, M. J. ed., ERL Press, Oxford, which is incoφorated herein by reference in its entirety.

Accordingly, the method for preparing these modified inducer specific tetracycline repressors comprises introducing into an organism an expressible nucleic acid molecule encoding a modified tetracycline repressor that exhibits an inducer specific phenotype in the eukaryotic cell, expressing the modified tefracycline repressor in the eukaryotic cell, and purifying the expressed modified tetracycline repressor. In one preferred embodiment, the expressible nucleic acid molecule is an expression vector comprising the nucleotide sequence encoding the modified tefracycline repressor. In another preferred embodiment, the nucleotide sequence encoding the modified tetracycline repressor is selected from nucleotide sequence encoding any of the amino acid sequences of SEQ ID NOS. 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 59, and 61.

A variety of host-expression vector systems can be utilized to express the modified inducer specific TetR repressor coding sequences of the invention. Such host-expression systems represent vehicles by which the coding sequences of interest can be produced and subsequently purified, but also represent cells which can, when transformed or transfected with the appropriate nucleotide coding sequences, exhibit the target gene protein of the invention in situ. These include but are not limited to microorganisms such as bacteria (e.g., E. coli, B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing target gene protein coding sequences; yeast (e.g., Saccharomyces, Aspergillus, Candida, Pichia) transformed with recombinant yeast expression vectors containing the target gene protein coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing the target gene protein coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing target gene protein coding sequences; or mammalian cell systems (e.g. COS, CHO, BHK, 293, 3T3) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter). If necessary, the nucleotide sequences of coding regions may be modified according to the codon usage of the host such that the translated product has the correct amino acid sequence.

In bacterial systems, a number of expression vectors can be advantageously selected depending upon the use intended for the modified repressor being expressed. For example, when a large quantity of such a protein is to be produced, for the generation of antibodies or to screen for binding to DNA, for example, vectors which direct the expression of high levels of fusion protein products that are readily purified can be desirable. Such vectors include, but are not limited, to the E. coli expression vector pUR278 (Ruther et al., 1983, EMBO J. 2: 1791), in which the target gene protein coding sequence can be ligated individually into the vector in frame with the lacZ coding region so that a fusion protein is produced; pIN vectors (Inouye & Inouye, 1985, Nucleic Acids Res. 13: 3101-09; Van Heeke & Schuster, 1989, J. Biol. Chem. 264: 5503-09); and the like. pGEX vectors can also be used to express foreign polypeptides as fusion proteins with glutathione S- transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsoφtion to glutathione-agarose beads followed by elution in the presence of free glutathione. The pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene protein can be released from the GST moiety.

Following expression of a modified inducer specific TetR repressor, the resulting protein is substantially purified (e.g., see Ettner et al, (1996) J. Chromatogr. 742: 95-105). For example, the expressed proteins may be enriched from culture medium or a cell lysate by salt precipitation (e.g., ammonium sulfate) or gel filtration. The enriched fractions may be further purified using, for example, chromatographic methods, such as affinity chromatography using 1) tet operator sequences bound to solid supports or 2) antibodies directed against revTetR; ion-exchange chromatography or electrophoretic methods such as one- and two-dimensional gel electrophoresis, or isoelectric focusing gels. Such methods for the enrichment or purification of proteins are well known to those of skill in the art (e.g., Sambrook et al, (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, N.Y.). For example, revTetR genes are cloned into an expression plasmid such as, but not limited to, pWH1950 (Ettner et al, (1996) J. Chromatogr. 742: 95-105) under the control of a tac promoter, and the recombinant plasmid is used to transform a suitable E. coli host such as E. coli strain RB791. Cells are grown in 3-6 liters of LB medium at 22° C. in flasks on a rotary shaker to a density corresponding to an OD of 0.6 to 1.0. Expression of the recombinant revTetR gene is then initiated by addition of the gratuitous inducer isopropyl-. beta. -D-galact- opyranoside to a final concentration of 1 mM. Incubation is continued for 3 to 12 hours and the cells are then collected by centrifugation, resuspended in buffer A (0.05 M NaCl, 2 mM DTT, and 20 mM sodium phosphate, pH 6.8). The resuspended cells are broken by sonication and the inducer specific TetR protein purified by cation-exchange chromatography using POROS.TM. HS/M Medium (Applied Biosystems, Foster City, Calif.) and gel filtration as described, for example by Ettner et al. (Ettner et al., (1996) J. Chromatogr. 742: 95-105). Protein concentration is determined by UN-spectroscopy and saturating fluorescence titrations with anhydrotefracycline. In a specific embodiment, the yield of inducer specific TetR is increased by using a richer production medium such as TB-medium, (which is formulated as follows: 12 g tryptone, 24 g yeast extract, and 4 g glycerol are dissolved in distilled water and the volume adjusted to 900 ml. The solution is sterilized by autoclaving and then cooled to 60°C. or less and 100 ml of 0.17 M KH₂PO₄-0.72 M K₂HPO₄, pH 7.4 added), to which 0.4μM tefracycline is added upon inoculation with the recombinant expression host strain.

Another aspect of the invention pertains to vectors, preferably expression vectors, containing a nucleic acid molecule encoding an inducer specific TetR or a reverse inducer specific transactivator fusion protein (or a portion thereof).

A recombinant expression vector of the invention can be a virus, or portion thereof, which allows for expression of a nucleic acid molecule introduced into the viral nucleic acid molecule. For example, replication defective refroviruses, adenoviruses and adeno- associated viruses can be used. Protocols for producing recombinant refroviruses and for infecting cells in vitro or in vivo with such viruses can be found in Current Protocols in Molecular Biology, Ausubel, F.M. et al. (eds.) Greene Publishing Associates, (1989), Sections 9.10-9.14 and other standard laboratory manuals. Examples of suitable refroviruses include pLJ, pZIP, pWE and pEM which are well known to those skilled in the art. Examples of suitable packaging virus lines include ψCrip, ψCre, ψ2 and ψAm. The genome of adenovirus can be manipulated such that it encodes and expresses a transcriptional regulatory protein but is inactivated in terms of its ability to replicate in a normal lytic viral life cycle. See for example Berkner et al. (1988) BioTechniques 6:616; Rosenfeld et al. (1991) Science 252:431-434; and Rosenfeld et al. (1992) Cell 68:143-155. Suitable adenoviral vectors derived from the adenovirus strain Ad type 5 dl324 or other sfrains of adenovirus (e.g., Ad2, Ad3, Ad7 etc.) are well known to those skilled in the art. Alternatively, an adeno-associated virus vector such as that described in Tratschin et al. (1985) Mol. Cell. Biol. 5:3251-3260 can be used to express a transactivator protein of the present invention.

The recombinant expression vectors of the invention comprise a nucleic acid molecule of the invention in a form suitable for expression of the nucleic acid molecule in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid molecule sequence to be expressed. Within a recombinant expression vector, "operably linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/ translation system or in a host cell when the vector is introduced into the host cell). The term "regulatory sequence" is intended to include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cells and those which direct expression of the nucleotide sequence only in certain host cells (e.g., tissue- specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, and the like. The expression vectors of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acid molecules as described herein (e.g., reverse transactivator fusion proteins, fusion proteins and the like).

The recombinant expression vectors of the invention can be designed for expression of transactivator fusion proteins in prokaryotic or eukaryotic cells. For example, reverse transactivator fusion proteins can be expressed in bacterial cells such as E. coli, insect cells (using baculovirus expression vectors) yeast cells, mammalian cells, or plant cells. Appropriate cloning and expression vectors for use with bacterial, fungal, yeast, plant, and mammalian cellular hosts are known in the art, and are described in, for example, Powels et al. (Cloning Vectors: A Laboratory Manual, Elsevier, New York, 1985). For other suitable expression systems for both prokaryotic and exikaryotic cells see chapters 16 and 17 of Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.

Expression of proteins in prokaryotes is most often carried out in E. coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, usually to the a ino terminus of the recombinant protein. Such fusion vectors typically serve three puφoses: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the px rification of the recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D.B. and Johnson, K.S. (1988) Gene 67:31-40), pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein. Pxirified chimeric proteins can be utilized in transactivator fusion protein activity assays, or to generate antibodies specific for transactivator fusion proteins, for example.

One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 119-128). Another strategy is to alter the nucleic acid sequence of the nucleic acid molecule to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (Wada et al, (1992) Nucleic Acids Res. 20:2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.

A number of vectors exist for the expression of recombinant proteins in yeast. Examples of vectors for expression in yeast S. cerivisae include pYepSecl (Baldari. et al, (1987) Embo J. 6:229-234), pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al, (1987) Gene 54:113-123), and pYES2 (Invitrogen Coφoration, San Diego, CA). In addition, YEP24, YEP5, YEP51, YEP52, pYES2, and YRP17 are cloning and expression vehicles useful in the introduction of genetic constructs into S. cerevisiae (see, for example, Broach et al. (1983) in Experimental Manipulation of Gene Expression, ed. M. Inouye Academic Press, p. 83, incoφorated by reference herein). These vectors can replicate in E. coli due to the presence of the pBR322 ori, and in S. cerevisiae due to the replication determinant of the yeast 2 micron plasmid. In addition, drug resistance markers, e.g., antibiotics which confer resistance in fungal systems, can be used. Suitable promoters for function in yeast include the promoters for metallothionein, 3-phosphoglycerate kinase (Hitzeman et al, J. Biol. Chem. 255, 2073 (1980) or other glycolytic enzymes (Hess et al, J. Adv. Enzyme Req. 1, 149 (1968); and Holland et al. Biochemistry 17, 4900 (1978)), such as enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phospho-fructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phospho-glucose isomerase, and glucokinase. Suitable vectors and promoters for use in yeast expression are further described in R. Hitzeman et al, EPO Publication. No. 73,657. Other promoters, which have the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nifrogen metabolism, and the aforementioned metallothionein and glyceraldehyde-3 -phosphate dehydrogenase, as well as enzymes responsible for maltose and galactose utilization. Finally, promoters that are active in only one of the two haploid mating types may be appropriate in certain circumstances. Among these haploid-specific promoters, the pheromone promoters MFal and MFαl are of particular interest.

In a preferred embodiment, the recombinant expression vector of the invention is a plasmid selected from the group consisting of: pCM190GFP+, pUHD 15-1, pREP9, and pUHD.

Alternatively, transactivator fusion proteins can be expressed in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells (e.g., Sf 9 cells) include the pAc series (Smith et al. (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers (1989) Virology 170:31- 39). In yet another embodiment, a nucleic acid molecule of the invention is expressed in mammalian cells using a mammalian expression vector. Mammalian expression vectors may comprise non-transcribed elements such as an origin of replication, a suitable promoter and enhancer linked to the gene to be expressed, and other 5' or 3' flanking nontranscribed sequences, and 5' or 3' nonfranslated sequences, such as necessary ribosome binding sites, a poly-adenylation site, splice donor and acceptor sites, and transcriptional termination sequences. When used in mammalian cells, a recombinant expression vector's control functions are often provided by viral genetic material. For example, commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Nirus 40. Use of viral regulatory elements to direct expression of the fusion protein can allow for high level constitutive expression of the fusion protein in a variety of host cells. Examples of mammalian expression vectors include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC (Kaufman et al (1987) EMBO J. 6:187-195).

In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid molecule preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid molecule). Tissue-specific regulatory elements are known in the art. Νon-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1 :268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43:235-275), in particular promoters of T cell receptors (Winoto and Baltimore (1989) EMBO J. 8:729-733) and immunoglobulins (Banerji et al (1983) Cell 33:729-740; Queen and Baltimore (1983) Cell 33:741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477), pancreas-specific promoters (Edlund et al. (1985) Science 230:912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Patent No. 4,873,316 and European Application Publication No. 264,166). Developmentally-regulated promoters are also encompassed, for example the murine hox promoters (Kessel and Gruss (1990) Science 249:374-379) and the α-fεtoprotein promoter (Campes and Tilghman (1989) Genes Dev. 3:537-546).

The invention further provides a recombinant expression vector comprising a DNA molecule of the invention cloned into the expression vector in an antisense orientation. That is, the DNA molecule is operatively linked to a regulatory sequence in a manner which allows for expression (by transcription of the DNA molecule) of an RNA molecule which is antisense to the transactivator fusion protein mRNA. Regulatory sequences operatively linked to a nucleic acid molecule cloned in the antisense orientation can be chosen which direct the continuous expression of the antisense RNA molecule in a variety of cell types, for instance viral promoters and/or enhancers, or regulatory sequences can be chosen which direct constitutive, tissue specific or cell type specific expression of antisense RNA. The antisense expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which antisense nucleic acid molecules are produced under the control of a high efficiency regulatory region, the activity of which can be determined by the cell type into which the vector is introduced. For a discussion of the regulation of gene expression using antisense genes see Weinfraub, H. et al, Antisense RNA as a molecular tool for genetic analysis, Reviews - Trends in Genetics, Vol. 1(1) 1986.

Another aspect of the invention pertains to host cells into which an inducer specific TetR nucleic acid molecule of the invention is introduced, e.g., an inducer specific transactivator fusion protein nucleic acid molecule within a recombinant expression vector or an inducer specific transactivator fusion protein nucleic acid molecule containing sequences which allow it to homologously recombine into a specific site of the host cell's genome.

The TetR mutants of the invention allow independent expression control of more than one gene by the Tet system in the same cell. For example, using the modified inducer specific TetR of the invention, franscription of a tetO linked gene of interest could be controlled in a single cell using the 4-ddma-atc inducer specific TetR of the invention, while a second tetO linked gene of interest may be controlled using a wild type TetR which binds tc and tc analogs. Alternatively, transcription of at least two tetO linked genes of interest may be controlled using two unique inducer specific modified TetR molecules, wherein expression of each gene is dependent on the specific type of tc analog or tc which is contacted with a single host cell.

Nucleic acid molecules encoding the fusion protein can be introduced into a host cell by standard techniques for transfεcting eukaryotic cells. The term "transfecting" or "transfection" is intended to encompass all conventional techniques for introducing nucleic acid molecules into host cells, including calcixim phosphate co-precipitation, DEAE- dextran-mediated transfection, lipofection, electroporation and microinjection. Suitable methods for transfecting host cells can be found in Sambrook et al. (Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory press (1989)), and other laboratory textbooks. Nucleic acid molecules can also be transferred into cells in vivo, for example by application of a delivery mechanism suitable for introduction of nucleic acid molecules into cells in vivo, such as retroviral vectors (see e.g., Ferry, N et al. (1991) Proc. Natl. Acad. Sci. USA 88:8377-8381; and Kay, M.A. et al. (1992) Human Gene Therapy 3:641-647), adenoviral vectors (see e.g., Rosenfeld, M.A. (1992) Cell 68:143-155; and Herz, J. and Gerard, R.D. (1993) Proc. Natl. Acad. Sci. USA 90_ι2812-2816), receptor- mediated DNA uptake (see e.g., Wu, G. and Wu, CH. (1988) J. Biol. Chem. 263:14621; Wilson et al. (1992) J. Biol. Chem. 267:963-967; and U.S. Patent No. 5,166,320), direct injection of DNA (see e.g., Acsadi et al. (1991) Nature 332l 815-818; and Wolff et al. (1990) Science 2A1 465- 1468) or particle bombardment (see e.g., Cheng, L. et al. (1993) Proc. Natl. Acad. Sci. USA 90:4455-4459; and Zelenin, AN. et al. (1993) FEBS Letters 315:29-32). Thus, for gene therapy puφoses, cells can be modified in vitro and administered to a subject or, alternatively, cells can be directly modified in vivo.

The number of host cells transformed with a nucleic acid molecule of the invention will depend, at least in part, upon the type of recombinant expression vector used and the type of transfection technique used. Nucleic acid molecules can be introduced into a host cell transiently, or more typically, for long term regulation of gene expression, the nucleic acid molecule is stably integrated into the genome of the host cell or remains as a stable episome in the host cell. Plasmid vectors introduced into mammalian cells are typically integrated into host cell DNA at only a low frequency. In order to identify these integrants, a gene that contains a selectable marker (e.g., drug resistance) is generally introduced into the host cells along with the nucleic acid molecule of interest. Preferred selectable markers include those which confer resistance to certain drugs, such as G418 and hygromycin. Selectable markers can be introduced on a separate plasmid from the nucleic acid molecule of interest or, are introduced on the same plasmid. Host cells transfected with a nucleic acid molecule of the invention (e.g., a recombinant expression vector) and a gene for a selectable marker can be identified by selecting for cells using the selectable marker. For example, if the selectable marker encodes a gene conferring neomycin resistance, host cells which have taken up nucleic acid molecule can be selected with G418. Cells that have incoφorated the selectable marker gene will survive, while the other cells die.

A host cell transfected with a nucleic acid molecule encoding a fusion protein of the invention can be further transfected with one or more nucleic acid molecules which serve as the target for the fusion protein. The target nucleic acid comprises a nucleotide sequence to be transcribed operatively linked to at least one tet operator sequence A host cell of the invention, such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i.e., express) a transactivator fusion protein. Accordingly, the invention further provides methods for producing a transactivator fusion protein using the host cells of the invention. In one embodiment, the method comprises culturing the host cell of the invention (into which a recombinant expression vector encoding a transactivator fusion protein has been introduced) in a suitable medium such that a transactivator fusion protein is produced.

A fusion protein of the invention is expressed in a exikaryotic cell by introducing a nucleic acid molecule encoding the fusion protein into a host cell, wherein the nucleic acid molecule is in a form suitable for expression of the fusion protein in the host cell. For example, a recombinant expression vector of the invention, encoding the fusion protein, is introduced into a host cell. Alternatively, nucleic acid molecules encoding the fusion protein which is operatively linked to regulatory sequences (e.g., promoter sequences) but without additional vector sequences can be introduced into a host cell.

In addition to cell lines, the invention is applicable to normal (e.g., primary) cells, such as cells to be modified for gene therapy pxiφoses or embryonic cells modified to create a transgenic or homologous recombinant animal. Examples of cell types of particular interest for gene therapy pxuposes include hematopoietic stem cells, myoblasts, beta cells of the pancreas, hepatocytes, lymphocytes, neuronal cells and skin epithelium and airway epithelium. Primary cells of interest also include cell lines in which genes involved in cell cycle confrol are placed xαnder rtTA regulation. Such novel cell lines would be conditionally proliferating and can recover their quiescent, differentiated state upon growth arrest via addition or withdrawal of tetracyclines, and will be of use in pharmacology and gene therapy. Additionally, for transgenic or homologous recombinant animals, embryonic stem cells and fertilized oocytes can be modified to contain nucleic acid molecules encoding a transactivator fusion protein. Moreover, plant cells can be modified to create transgenic plants.

A polynucleotide encoding an inducer specific TetR fusion protein (i.e. a transgene) can be transferred into a fertilized oocyte of a non-human animal to create a transgenic animal which expresses the fusion protein of the invention in one or more cell types. A transgenic animal is an animal having cells that contain a transgene, wherein the transgene was introduced into the animal or an ancestor of the animal at a prenatal, e.g., an embryonic, stage. A transgene is a DNA which is integrated into the genome of a cell from which a transgenic animal develops and which remains in the genome of the mature animal, thereby directing the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal. In one embodiment, the non-human animal is a mouse, although the invention is not limited thereto. In another embodiment, the transgenic animal is a rat. In other embodiments, the transgenic animal is a goat, sheep, pig, cow or other domestic farm animal. Such fransgenic ammals are useful for large scale production of proteins (so called "gene pharming").

A fransgenic animal can be created, for example, by introducing a nucleic acid molecule encoding the fusion protein (typically linked to appropriate regulatory elements, such as a constitutive or tissue-specific enhancer) into the male pronuclei of a fertilized oocyte, e.g., by microinjection, and allowing the oocyte to develop in a pseudopregnant female foster animal. Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene. Methods for generating fransgenic animals, particularly animals such as mice, have become conventional in the art and are described, for example, in U.S. Patent Nos. 4,736,866 and 4,870,009 and Hogan,

B. et al, (1986) A Laboratory Manual, Cold Spring Harbor, New York, Cold Spring

Harbor Laboratory. A transgenic founder animal can be used to breed additional animals carrying the transgene. Transgenic animals carrying a transgene encoding the fusion protein of the invention can further be bred to other transgenic animals carrying other fransgenes, e.g., to a transgenic animal which contains a gene operatively linked to a tet operator sequence (discussed in more detail herein).

It will be appreciated that, in addition to fransgenic animals, the regulatory system described herein can be applied to other transgenic organisms, such as transgenic plants. Transgenic plants can be made by conventional techniques known in the art. Accordingly, the invention encompasses non-human fransgenic organisms, including animals and plants, that contains cells which express the transactivator fusion protein of the invention (i.e., a nucleic acid molecules encoding the transactivator is incoφorated into one or more chromosomes in cells of the transgenic organism).

The invention also provides a homologous recombinant non-human organism expressing a fusion protein of the invention. In one embodiment, the non-human animal is a mouse, although the invention is not limited thereto. An animal can be created in which nucleic acid molecules encoding the fusion protein has been introduced into a specific site of the genome, i.e., the nucleic acid molecule has homologously recombined with an endogenous gene.

To create such a homologous recombinant animal, a vector is prepared which contains DNA encoding the fusion protein flanked at its 5' and 3' ends by additional nucleic acids of a eukaryotic gene at which homologous recombination is to occur. The additional nucleic acid flanking that encoding the fusion protein is of sufficient length for successful homologous recombination with the eukaryotic gene. Typically, several kilobases of flanking DNA (both at the 5' and 3' ends) are included in the vector (see e.g., Thomas, K.R. and Capecchi, M. R. (1987) Cell 51_:503 for a description of homologous recombination vectors). The vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected (see e.g., Li, E. et al. (1992) Cell 69:915). The selected cells are then injected into a blastocyst of an animal (e.g., a mouse) to form aggregation chimeras (see e.g., Bradley, A. in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E.J. Robertson, ed. (ERL, Oxford, 1987) pp. 113-152). A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term. Progeny harboring the homologously recombined DNA in their germ cells can be used to breed animals in which all cells of the animal contain the homologously recombined DNA. These "germline transmission" animals can further be mated to animals carrying a gene operatively linked to at least one tet operator sequence (discussed in more detail in below).

In addition to the homologous recombination approaches described above, enzyme-assisted site-specific integration systems are known in the art and can be applied to the components of the regulatory system of the invention to integrate a DNA molecule at a predetermined location in a second target DNA molecule. Examples of such enzyme-assisted integration systems include the Cre recombinase-lox target system (e.g., as described in Baubonis, W. and Sauer, B. (1993) Nucl. Acids Res. 21:2025-2029; and Fukushige, S. and Sauer, B. (1992) Proc. Natl. Acad. Sci. USA 89:7905-7909) and the FLP recombinase-FRT target system (e.g., as described in Dang, D.T. and Perrimon, N. (1992) Dev. Genet. 13:367-375; and Fiering, S. et al (1993) Proc. Natl Acad. Sci. USA 90:8469-8473).

In a preferred embodiment, said homologous recombinant transgenic organism is a mouse. Expression of a tet operator-linked nucleotide sequences is regulated by a inducer specific modified TetR protein of the invention. Thus, the inducer specific modified TetR protein and the target nucleic acid molecule are both present in a host cell or organism. The presence of both the inducer specific modified TetR protein and the target transcription unit in the same host cell or organism can be achieved in a number of different ways. For example, a host cell can be transfected with one nucleic acid molecule of the expression system (e.g., encoding the transactivator fusion protein), stably transfected cells can be selected and then the transfected cells can be re-transfected (also referred to as "supertransfected") with nucleic acid molecule corresponding to the other nucleic acid molecules of the expression system (e.g., the target nucleic acid molecule to be transcribed). Two distinct selectable markers can be used for selection, e.g., uptake of the first nucleic acid molecule can be selected with G418 and uptake of the second nucleic acid molecule can be selected with hygromycin. Alternatively, a single population of cells can be transfected with nucleic acid molecules corresponding to both components of the system.

The host cell may be a cell cultured in vitro or a cell present in vivo (e.g., a cell targeted for gene therapy). The host cell can further be a fertilized ooctye, embryonic stem cell or any other embryonic cell used in the creation of non-human transgenic or homologous recombinant animals. Transgenic or homologous recombinant animals which comprise both nucleic acid components of the expression system can be created by introducing both nucleic acid molecules into the same cells at an embryonic stage, or more preferably, an animal which carries one nucleic acid component of the system in its genome is mated to an animal which carries the other nucleic acid component of the system in its genome. Offspring which have inherited both nucleic acid components can then be identified by standard techniques.

In a host cell which carries nucleic acid molecules encoding a transactivator fusion protein of the invention and a nucleotide sequence operatively linked to the tet operator sequence (i.e., gene of interest to be transcribed), transcription of the nucleotide sequence operatively linked to the tet operator sequence(s) can be regulated by tetracycline, or analogs thereof. Accordingly, another aspect of the invention pertains to methods for stimulating transcription of a nucleotide sequence operatively linked to a tet operator sequence in a host cell or animal which expresses a transactivator fusion protein of the invention. The methods involve contacting the cell with tetracycline or a tetracycline analogue or administering tefracycline or a tefracycline analogue to a subject containing the cell.

To induce gene expression in a cell in vitro, the cell is contacted with Tc or an analog thereof by culturing the cell in a medium containing the compound. To induce gene expression in vivo, cells within in a subject are contacted with Tc or an analog thereof by administering the compoxind to the subject. The term "subject" is intended to include humans and other non-human mammals including monkeys, cows, goats, sheep, dogs, cats, rabbits, rats, mice, and transgenic and homologous recombinant species thereof. Fx rthermore, the term "subject" is intended to include plants, such as transgenic plants. Tc or a Tc analog can be administered to a subject by any means effective for achieving an in vivo concentration sufficient for gene induction. Examples of suitable modes of administration include oral administration (e.g., dissolving the inducing agent in the drinking water), slow release pellets and implantation of a diffusion pump. To administer Tc or a Tc analog to a transgenic plant, the inducing agent can be dissolved in water administered to the plant.

The ability to use different Tc analogues as inducing agents in this system allows for modulate the level of expression of a tet operator-linked nucleotide sequence. Thus, an appropriate tefracycline analog is chosen as an inducing agent based upon the desired level of induction of gene expression. It is also possible to change the level of gene expression in a host cell or animal over time by changing the Tc analogue used as the inducing agent. For example, there may be situations where it is desirable to have a strong burst of gene expression initially and then have a sustained lower level of gene expression. Accordingly, an analog which stimulates a high levels of transcription can be used initially as the inducing agent and then the inducing agent can be switched to an analogue which stimulates a lower level of transcription. Moreover, when regulating the expression of multiple nucleotide sequences (e.g. , when one sequence is regulated by a one of class tet operator sequence(s) and the other is regulated by another class of tet operator sequence(s)), it may be possible to independently vary the level of expression of each sequence depending upon which transactivator fusion protein is used to regulate transcription and which Tc analogue(s) is used as the inducing agent. Different transactivator fusion proteins are likely to exhibit different levels of responsiveness to Tc analogues. The level of induction of gene expression by a particular combination of transactivator fusion protein and inducing agent (Tc or Tc analogue) can be determined by techniques described herein. Additionally, the level of gene expression can be modulated by varying the concentration of the inducing agent. Thus, the expression system of the invention provides a mechanism not only for turning gene expression on or off, but also for "fine tuning" the level of gene expression at intermediate levels depending upon the type and concentration of inducing agent used.

The present invention is widely applicable to a variety of situations where it is desirable to be able to turn gene expression on and off, or regulate the level of gene expression, in a rapid, efficient and controlled manner without causing pleio ropic effects or cytotoxicity. For example, the nucleic acid molecules and proteins of the invention have use in the study of cellular development and differentiation in eukaryotic cells, plants and animals. The expression of oncogenes can be regulated in a controlled manner in cells to study their function. Additionally, the system can be used to regulate the expression of site-specific recombinases, such as CRE or FLP, to allow for irreversible modification of the genotype of a transgenic organism under controlled conditions at a particular stage of development. For example, drug resistance markers inserted into the genome of transgenic plants that allow for selection of a particular fransgenic plant could be irreversibly removed via a Tc- regulated site specific recombinase. Other applications of the regulatory system of the invention include:

The invention may be particularly useful for gene therapy puφoses, in treatments for either genetic or acquired diseases. The general approach of gene therapy involves the introduction of nucleic acid molecules into cells such that one or more gene products encoded by the introduced genetic material are produced in the cells to restore or enhance a functional activity. For reviews on gene therapy approaches see Anderson, W.F. (1992) Science 256:808-813; Miller, A.D. (1992) Nature 357:455-460; Friedmann, T. (1989) Science 244:1275-1281; and Cournoyer, D., et al. (1990) Curr. Opin. Biotech. 1 :196-208. However, current gene therapy vectors typically utilize constitutive regulatory elements which are responsive to endogenous transcriptions factors. These vector systems do not allow for the ability to modulate the level of gene expression in a subject. In contrast, the proteins, modulator compounds and gene regulatory sequences identified by the methods of the invention provides the ability to modulate gene expression in a cell in vitro or in vivo.

To use the system of the invention for gene therapy pxuposes, in one embodiment, cells of a subject in need of gene therapy are modified to contain 1) a nucleic acid molecule encoding a transactivator fusion protein of the invention in a form suitable for expression of the transactivator in the host cells and 2) a gene of interest (e.g., for therapeutic puφoses) operatively linked to a tet operator sequence(s). The cells of the subject can be modified ex vivo and then introduced into the subject or the cells can be directly modified in vivo. Expression of the gene of interest in the cells of the subject is then stimulated by administering Tc or a Tc analogue to the patient. The level of gene expression can be varied depending upon which particular Tc analogue is used as the inducing agent. The level of gene expression can also be modulated by adjusting the dose of the tefracycline, or analogue thereof, administered to the patient to thereby adjust the concentration achieved in the circulation and the tissues of interest.

The nucleic acid molecules of the invention can be inserted into vectors and used as gene therapy vectors. Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (see U.S. Patent 5,328,470) or by stereotactic injection (see e.g., Chen et al. (1994) Proc. Natl. Acad. Sci. USA 91:3054-3057). The pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded. Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can include one or more cells which produce the gene delivery system. The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.

Conventional detection methods known in the art, such as an enzyme linked immunosorbent assay, can be used to monitor the expression of the regulated protein of interest in the host cells and the concentration of Tc or Tc analogue can be varied xmtil the desired level of expression of the protein of interest is achieved. Accordingly, expression of a protein of interest can be adjusted according to the medical needs of an individual, which may vary throughout the lifetime of the individual. To stop expression of the gene of interest in cells of the subject, administration of the inducing agent is stopped. Thus, the regulatory system of the invention offers the advantage over constitutive regulatory systems of allowing for modulation of the level of gene expression depending upon the requirements of the therapeutic situation.

Genes of particular interest to be expressed in cells of a subject for treatment of genetic or acquired diseases include those encoding adenosine deaminase, Factor VIII, Factor EX, dystrophin, β-globin, LDL receptor, CFTR, insulin, erythropoietin, anti-angiogenesis factors, growth hormone, glucocerebrosidase, β-glucouronidase, αl-antitrypsin, phenylalanine hydroxylase, tyrosine hydroxylase, ornithine transcarbamylase, arginosuccinate synthetase, UDP-glucuronysyl transferase, apoAl, TNF, soluble TNF receptor, interleukins (e.g., IL-2), interferons (e.g., α- or γ-IFN) and other cytokines and growth factors. Cells types which can be modified for gene therapy puφoses include hematopoietic stem cells, myoblasts, hepatocytes, lymphocytes, skin epithelixim and airway epithelixim. For further descriptions of cell types, genes and methods for gene therapy see e.g., Wilson, J.M et al. (1988) Proc. Natl Acad. Sci. USA 85:3014-3018; Armentano, D. et al. (1990) Proc. Natl Acad. Sci. USA 87:6141-6145; Wolff, J.A. et al. (1990) Science 247:1465-1468; Chowdhury, J.R. et al. (1991) Science 254:1802-1805; Ferry, N. et al (1991) Proc. Natl Acad. Sci. USA 88:8377-8381; Wilson, J.M. et al. (1992) J. Biol Chem. 267:963-967; Quantin, B. et al (1992) Proc. Natl. Acad. Sci. USA 89:2581- 2584; Dai, Y. et al. (1992) Proc. Natl Acad. Sci. USA 89:10892-10895; van Beusechem, V.W. et al. (1992) Proc. Natl. Acad. Sci. USA 89:7640-7644; Rosenfeld, M.A. et al. (1992) Cell 68:143-155; Kay, M.A. et al. (1992) Human Gene Therapy 3:641-647; Cristiano, R.J. et al. (1993) Proc. Natl. Acad. Sci. USA 90:2122-2126; Hwu, P. et al. (1993) J. Immunol. 150:4104-4115; and Herz, J. and Gerard, R.D. (1993) Proc. Natl. Acad. Sci. USA 90:2812- 2816.

Gene therapy applications of particular interest in cancer freatment include overexpression of a cytokine gene (e.g., TNF-α) in tumor infiltrating lymphocytes or ectopic expression of cytokines in tumor cells to induce an anti-tumor immune response at the tumor site, expression of an enzyme in tumor cells which can convert a non-toxic agent into a toxic agent, expression of tumor specific antigens to induce an anti-tumor immune response, expression of tumor suppressor genes (e.g., p53 or Rb) in tumor cells, expression of a multidrug resistance gene (e.g., MDR1 and/or MRP) in bone marrow cells to protect them from the toxicity of chemotherapy.

Gene therapy applications of particular interest in treatment of viral diseases include expression of frans-dominant negative viral transactivation proteins, such as trans- dominant negative tat and rev mutants for HEV or trans-dominant ICp4 mutants for HSV (see e.g., Balboni, P.G. et al. (1993) J. Med. Virol. 41:289-295; Liem, S.E. et al (1993) Hum. Gene Ther. 4:625-634; Malim, M.H. et al. (1992) J. Exp. Med. 176:1197-1201; Daly, TJ. et al (1993) Biochemistry 32:8945-8954; and Smith, CA. et al. (1992) Virology 191:581-588), expression of frans-dominant negative envelope proteins, such as env mutants for HEV (see e.g., Steffy, K.R. et al. (1993) J. Virol 67:1854-1859), intracellular expression of antibodies, or fragments thereof, directed to viral products ("internal immunization", see e.g., Marasco, W.A. et al (1993) Proc. Natl Acad. Sci. USA 90:7889- 7893) and expression of soluble viral receptors, such as soluble CD4. Additionally, the system of the invention can be used to conditionally express a suicide gene in cells, thereby allowing for elimination of the cells after they have served an intended function. For example, cells used for vaccination can be eliminated in a subject after an immxine response has been generated the subject by inducing expression of a suicide gene in the cells by adrninistering Tc or a Tc analogue to the subject.

The inducer specific Tc-controlled regulatory system of the invention has numerous advantages properties that make it particularly suitable for application to gene therapy. For example, the system provides an "on"/"off" switch for gene expression that allows for regulated dosing of a gene product in a subject. There are several situations in which it may be desirable to be able to provide a gene product at specific levels and/or times in a regulated manner, rather than simply expressing the gene product constitutively at a set level. For example, a gene of interest can be switched "on" at fixed intervals (e.g., daily, alternate days, weekly, etc.) to provide the most effective level of a gene product of interest at the most effective time. The level of gene product produced in a subject can be monitored by standard methods (e.g., direct monitoring using an immunological assay such as ELISA or RIA or indirectly by monitoring of a laboratory parameter dependent upon the function of the gene product of interest, e.g., blood glucose levels and the like). This ability to turn "on" expression of a gene at discrete time intervals in a subject while also allowing for the gene to be kept "off' at other times avoids the need for continued administration of a gene product of interest at intermittent intervals. This approach avoids the need for repeated injections of a gene product, which may be painful and/or cause side effects and would likely require continuous visits to a physician. In contrast, the system of the invention avoids these drawbacks. Moreover, the ability to turn "on" expression of a gene at discrete time intervals in a subject allows for focused freatment of diseases which involve "flare ups" of activity (e.g., many autoimmune diseases) only at times when treatment is necessary during the acute phase when pain and symptoms are evident. At times when such diseases are in remission, the expression system can be kept in the "off' state.

Gene therapy applications that may particularly benefit from this ability to modulate gene expression during discrete time intervals include the following non-limiting examples: Rheumatoid arthritis - genes which encode gene products that inhibit the production of inflammatory cytokines (e.g., TNF, IL-1 and IL-12). can be expressed in subjects. Examples of such inhibitors include soluble forms of a receptor for the cytokine. Additionally or alternatively, the cytokines IL-10 and/or IL-4 (which stimulate a protective Th2-type response) can be expressed. Moreover, a glucocorticomimetic receptor (GCMR) can be expressed.

Hypopituitarism - the gene for human growth hormone can be expressed in such subjects only in early childhood, when gene expression is necessary, until normal stature is achieved, at which time gene expression can be downregulated.

Wound healing/Tissue regeneration - Factors (e.g., growth factors, angiogenic factors, etc.) necessary for the healing process can be expressed only when needed and then downregulated.

Anti-Cancer Treatments - Expression of gene products useful in anti-cancer freatment can be limited to a therapeutic phase until retardation of tumor growth is achieved, at which time expression of the gene product can be downregulated. Possible systemic anti-cancer treatments include use of tumor infiltrating lymphocytes which express immimostimxilatory molecules (e.g., IL-2, IL-12 and the like), angiogenesis inhibitors (PF4, IL-12, etc.), Her-regulin, Leukoregulin (see PCT Publication No. WO 85/04662), and growth factors for bone marrow support therapy, such as G-CSF, GM-CSF and M- CSF. Regarding the latter, use of the regulatory system of the invention to express factors for bone marrow support therapy allows for simplified therapeutic switching at regular intervals from chemotherapy to bone marrow support therapy (similarly, such an approach can also be applied to AIDS treatment, e.g., simplified switching from anti -viral treatments to bone marrow support freatment). Furthermore, controlled local targeting of anti-cancer treatments are also possible. For example, expression of a suicide gene by a regulator of the invention, wherein the regulator itself is controlled by, for example, a tumor-specific promoter or a radiation-induced promoter.

In another embodiment, the regulatory proteins of the invention are used to express angiogenesis inhibitors) from within a tumor via a transgene regulated by the system of the invention. Expression of angiogenesis inhibitors in this manner may be more efficient than systemic administration of the inhibitor and would avoid any deleterious side effects that might accompany systemic adminisfration. In particular, restricting angiogenesis inhibitor expression to within tumors could be particularly useful in treating cancer in children still xindergoing angiogenesis associated with normal cell growth.

In another embodiment, high level regulated expression of cytokines may represent a method for focusing a patients own immxme response on tumor cells. Tumor cells can be transduced to express chemoattractant and growth promoting cytokines important in increasing an individual's natural immune response. Because the highest concentrations of cytokines will be in the proximity of the tumor, the likelihood of eliciting an immunological response to tumor antigens is increased. A potential problem with this type of therapy is that those tumor cells producing the cytokines will also be targets of the immune response and therefore the source of the cytokines will be eliminated before eradication of all tumor cells can be certain. To combat this, expression of viral proteins known to mask infected cells from the immune system can be placed under regulation, along with the cytokine gene(s), in the same cells. One such protein is the El 9 protein from adenovirus (see e.g., Cox, Science 247:715). This protein prevents transport of class I HLA antigens to the surface of the cell and hence prevents recognition and lysis of the cell by the host's cytotoxic T cells. Accordingly, regulated expression of El 9 in tumor cells could shield cytokine producer cells from cytotoxic T cells during the onset of an immxme response provoked by cytokine expression. After a sufficient period of time has elapsed to eradicate all tumor cells but those expressing El 9, El 9 expression can be turned off, causing these cells then to fall victim to the provoked anti-rumor immune response.

Benign prostatic hypertrophy - Similar to the above, a suicide gene can be regulated by a regulator of the invention, wherein the regulator itself is controlled by, for example, a prostate-specific promoter.

The ability to express a suicide gene (e.g., an apoptosis gene, TK gene, etc) in a controlled manner using the regulatory system of the invention adds to the general safety and usefulness of the system. For example, at the end of a desired therapy, expression of a suicide gene can be triggered to eliminate cells carrying the gene therapy vector, such as cells in a bioinert implant, cells that have disseminated beyond the intended original location, etc. Moreover, if a transplant becomes tumorigenic or has side effects, the cells can be rapidly eliminated by induction of the suicide gene. The use of more than one Tc- controlled "on'V'off ' switch in one cell allows for completely independent regulation of a suicide gene compared to regulation of a gene of therapeutic interest (as described in detail herein). The regulatory proteins of the invention further offer the ability to establish a therapeutically relevant expression level for a gene product of interest in a subject, in contrast to unregulated constitutive expression which offers no flexibility in the level of gene product expression that can be achieved. A physiologically relevant level of gene product expression can be established based on the particular medical need of the subject, e.g., based on laboratory tests that monitor relevant gene product levels (using methods as described above). In addition to the clinical examples and gene products already discussed above with gene to dosing of the gene product, other therapeutically relevant gene products which can be expressed at a desired level at a desired time include: Factor XIII and EX in hemophiliacs (e.g., expression can be elevated during times of risk of injury, such as during sports); insulin or amylin in diabetics (as needed, depending on the state of disease in the subject, diet, etc.); erythropoietin to treat erythrocytopenia (as needed, e.g., at end- stage renal failure); low-density lipoprotein receptor (LDLr) or very low-density lipoprotein receptor (VLDLr) for artherosclerosis or gene therapy in liver (e.g., using ex vivo implants). Applications to treatment of central nervous system disorders are also encompassed. For example, in Alzheimer's disease, "fine tuned" expression of choline acetyl transferase (ChAT) to restore acetylcholine levels, neurotrophic factors (e.g., NGF, BDNGF and the like) and/or complement inhibitors (e.g., sCRl, sMCP, sDAF, sCD59 etc.) can be accomplished. Such gene products can be provided, for example, by transplanted cells expressing the gene products in a regulated manner using the system of the invention. Moreover, Parkinson's disease can be freated by "fine tuned" expression of tyrosine hydroxylase (TH) to increase levodopa and dopamine levels.

In addition to the proteinaceous gene products discussed above, gene products that are functional RNA molecules (such as anti-sense RNAs and ribozymes) can be expressed in a controlled manner in a subject for therapeutic pxuposes. For example, a ribozyme can be designed which discriminates between a mutated form of a gene and a wild-type gene. Accordingly, a "correct" gene (e.g., a wild-type p53 gene) can be introduced into a cell in parallel with introduction of a regulated ribozyme specific for the mutated form of the gene (e.g., a mutated endogenous p53 gene) to remove the defective mRNA expressed from the endogenous gene. This approach is particularly advantageous in situations in which a gene product from the defective gene would interfere with the action of the exogenous wild-type gene. Expression of a gene product in a subject using the regxilatory proteins of the invention is modulated using tetracycline or analogues thereof. Such drugs can be administered by any route appropriate for delivery of the drug to its desired site of action (e.g., delivery to cells containing a gene whose expression is to be regulated). Depending on the particular cell types involved, preferred routes of a ninistration may include oral administration, intravenous administration and topical administration (e.g., using a transdermal patch to reach cells of a localized transplant under the skin, such as keratinocytes, while avoiding any possible side effects from systemic treatment).

In certain gene therapy situations, it may be necessary or desirable to take steps to avoid or inhibit unwanted immune reactions in a subject receiving treatment. To avoid a reaction against the cells expressing the therapeutic gene product, a subject's own cells are generally used, when possible, to express the therapeutic gene product, either by in vivo modification of the subject's cells or by obtaining cells from the subject, modifying them ex vivo and returning them to the subject. In situations where allogeneic or xenogeneic cells are used to express a gene product of interest, the regulatory system of the invention, in addition to regulating a therapeutic gene, can also be used to regulate one or more genes involved in the immune recognition of the cells to inhibit an immune reaction against the foreign cells. For example, cell-surface molecules involved in recognition of a foreign cell by T lymphocytes can be downmodulated on the surface of a foreign cell used for delivery of a therapeutic gene product, such as by regulated expression in the foreign cell of a ribozyme which cleaves the mRNA encoding the cell-sxirface molecule. Particularly preferred cell surface molecules which can be downmodulated in this manner to inhibit an unwanted immune response include class I and/or class II major histocompatibility complex (MHC) molecules, costimulatory molecules (e.g., B7-1 and/or B7-2), CD40, and various "adhesion" molecules, such as ICAM-1 or ICAM-2. Using approaches described herein for independent but coordinate regulation of multiple genes in the same cell, the down- regulation of expression of a cell-surface molecule(s) in a host cell can be coordinated with the up-regulation of expression of a therapeutic gene. Accordingly, after therapy is completed and expression of the therapeutic gene is halted, expression of the endogenous cell surface molecule(s) can be restored to normal.

Furthermore, as described above regarding anti-cancer treatments, a viral protein (e.g., adenovirus El 9 protein) that downmodulates expression of MHC antigens can be regulated in host cells using the system of the invention as a means of avoiding unwanted immunological reactions. In addition to avoiding or inhibiting an immune response against a foreign cell delivering a therapeutic gene product, it may also be necessary, in certain situations, to avoid or inhibit an immune response against certain components of the regulatory system of the invention (e.g., the regulator fusion proteins described herein) that are expressed in a subject, since these fusion proteins contain non-mammalian polypeptides that may stimulate an unwanted immxme reaction. In this regard, regulator fusion proteins can be designed and/or selected for a decreased ability to stimulate an immune response in a host. For example, a transcriptional activator domain for use in the regulator fusion protein can be chosen which has minimal immxmogenicity. In this regard, a wild-type transcriptional activation domain of the heφes simplex virus protein VP16 may not be a preferred transcriptional activation domain for use in vivo, since it may stimulate an immune response in mammals. Alternative franscriptional activation domains can be used, as described herein, based on their reduced immunogenicity in a subject. For example, a franscriptional activation domain of a protein of the same species as the host may be preferred (e.g. , a transcriptional activation domain from a human protein for use of a regulatory fusion protein in humans). Alternatively, a regulatory fusion protein of the invention can be modified to reduce its immunogenicity in subjects, e.g., by identifying and modifying one or more dominant T cell epitopes within a polypeptide of the fusion protein (e.g., either the Tet repressor moiety or the transcriptional modulator moiety, such as a VP16 polypeptide). Such T cell epitopes can be identified by standard methods and altered by mutagenesis, again by standard methods. A modified form of a regulator fusion protein can then be selected which retains its original transcriptional regulatory ability yet which exhibits reduced immunogenicity in a subject as compared to an unmodified fusion protein.

In addition to the foregoing, all conventional methods for generally or specifically downmodulating immxme responses in subjects can be combined with the use of the regulatory system of the invention in situations where inhibition of immxme responses is desired. General immunosuppressive agents, such as cyclosporin A and/or FK506, can be administered to the subject. Alternatively, immunomodulatory agents which may allow for more specific immunosuppression can be used. Such agents may include inhibitors of costimulatory molecules (e.g., a CTLA4Ig fusion protein, soluble CD4, anti-CD4 antibodies, anti-B7-l and/or anti-B7-2 antibodies or anti-gp39 antibodies).

Finally, in certain situations, a delivery vehicle for cells expressing a therapeutic gene can be chosen which minimizes exposure of transplanted cells to the immune system. For example, cells can be implanted into bioinert capsules/biocompatible membranes with pores which allow for diffusion of proteins (e.g., a therapeutic gene product of interest) out of the implant and diffusion of nutrients and oxygen into the implant but which prevent entry of immune cells, thereby avoiding exposure of the transplanted cells to the immxme system (as has been applied to islet cell transplantation).

The inducer specific modified TetR nucleic acid molecules, fragments of inducer specific TetR proteins, and anti-transactivator inducer specific fusion protein antibodies (also referred to herein as "active compounds") of the invention can be incoφorated into pharmaceutical compositions suitable for administration. Such compositions typically comprise the nucleic acid molecule, protein, or antibody and a pharmaceutically acceptable carrier. As used herein the language "pharmaceutically acceptable carrier" is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absoφtion delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incoφorated into the compositions. A pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration.

Large scale production of a protein of interest can be accomplished using cultured cells in vitro which have been modified to contain: 1) a nucleic acid molecule encoding a reverse transactivator fusion protein of the invention in a form suitable for expression of the transactivator in the cells; and 2) a gene encoding the protein of interest operatively linked to a tet operator sequence(s). For example, mammalian, yeast or fungal cells can be modified to contain these nucleic acid molecules components as described herein. The modified mammalian, yeast or fungal cells can then be cultured by standard fermentation techniques in the presence of Tc or an analogue thereof to induce expression of the gene and produce the protein of interest. Accordingly, the invention provides a production process for isolating a protein of interest. In the process, a host cell (e.g., a yeast or fungus), into which has been introduced both a nucleic acid molecule encoding a transactivator fusion protein of the invention and a nucleic acid molecule encoding the protein of the interest operatively linked to at least one tet operator sequence, is grown at production scale in a culture medium in the presence of tefracycline or a tefracycline analogue to stimulate transcription of the nucleotides sequence encoding the protein of interest (i.e., the nucleotide sequence operatively linked to the tet operator sequence(s)) and the protein of interest is isolated from harvested host cells or from the culture medium. Standard protein purification techniques can be used to isolate the protein of interest from the medium or from the harvested cells.

The invention also provides for large scale production of a protein of interest in animals, such as in transgenic farm animals. Advances in transgenic technology have made it possible to produce transgenic livestock, such as cattle, goats, pigs and sheep (reviewed in Wall, R.J. et al. (1992) J. Cell. Biochem. 49:113-120; and Clark, A.J. et al. (1987) Trends in Biotechnology 5:20-24). Accordingly, transgenic livestock carrying in their genome the components of the inducible regulatory system of the invention can be constructed, wherein a gene encoding a protein of interest is operatively linked to at least one tet operator sequence. Gene expression, and thus protein production, is induced by administering certain Tc (or analogue thereof) to the transgenic animal. Protein production can be targeted to a particular tissue by linking the nucleic acid molecule encoding the transactivator fusion protein to an appropriate tissue-specific regulatory elements) which limits expression of the transactivator to certain cells. For example, a mammary gland- specific regulatory element, such as the milk whey promoter (U.S. Patent No. 4,873,316 and European Application Publication No. 264,166), can be linked to the transactivator transgene to limit expression of the transactivator to mammary tissue. Thus, in the presence of Tc (or analogue), the protein of interest will be produced in the mammary tissue of the transgenic animal. The protein can be designed to be secreted into the milk of the transgenic animal, and if desired, the protein can then be isolated from the milk.

Inducer specific modified TetR proteins of the invention can be used alone or in combination to stimulate expression of specific genes in animals to mimic the pathophysiology of human disease to thereby create animal models of human disease. For example, in a host animal, a gene of interest thought to be involved in a disease can be placed under the transcriptional control of one or more tet operator sequences (e.g., by homologous recombination, as described herein). Such an animal can be mated to a second animal carrying one or more transgenes for a transactivator fusion protein and/or an inhibitor fusion protein to create progeny that carry both a tetracycline-regulated fusion protein(s) gene and a tet-regulated target sequence. Expression of the gene of interest in these progeny can be modulated using tetracycline (or analogue). For example, expression of the gene of interest can be downmodulated using a transcriptional inhibitor fusion protein to examine the relationship between gene expression and the disease. Such an approach may be advantageous over gene "knock out" by homologous recombination to create animal models of disease, since the tet-regulated system described herein allows for control over both the levels of expression of the gene of interest and the timing of when gene expression is down- or up-regulated.

Inducer specific modified TetR proteins described herein can be used to regulate gene expression, and thereby allow production of stable cell lines that otherwise may not be produced. For example, stable cell lines carrying genes that are cytotoxic to the cells can be difficult or impossible to create due to "leakiness" in the expression of the toxic genes. By tightly regulating gene expression of such toxic genes using the transcriptional activator fusion proteins of the invention, stable cell lines carrying toxic genes may be created. Such stable cell lines can then be used to clone such toxic genes (e.g., inducing the expression of the toxic genes under controlled conditions using Tc or analog). General methods for expression cloning of genes, to which the franscriptional inhibitor system of the invention can be applied, are known in the art (see e.g., Edwards, C P. and Aruffo, A. (1993) Curr. Opin. Biotech. 4:558-563) Moreover, the reverse franscriptional regulatory proteins can be applied to modulate the expression of genes in other cells to create stable cell lines, such as in embryonic stem (ES) cells. Residual expression of certain genes introduced into ES cells may result in an inability to isolate stably transfected clones. Regulation of transcription of such genes using the reverse transcriptional activator proteins described herein may be useful in overcoming this problem.

In a further embodiment, expression of one or more target genes in a cell is modulated via tet-regulated expression of an antisense RNA molecule that inhibits translation of mRNA transcribed from the target gene(s). In this embodiment, a coding region encoding a target- gene-specific antisense RNA is operatively associated with a promoter and a tefracycline operator sequence in such a manner that binding of a tetracycline repressor to that operator prevents synthesis of the antisense RNA molecule in the host cell. In various aspects of this embodiment, the level of expression of an antisense RNA molecule, and translation of a target gene mRNA inhibited by the antisense RNA molecule, may be modulated by the concentration of tetracyline or its analog, the level of expression of the inducer specific TetR protein, and/or the temperature. For example, in the presence of 4-ddma-atc, the expression of a target gene is inhibited in a host cell carrying a tet-regulated antisense RNA coding sequence which is specific for the target gene, and at least one inducer specific TetR-encoding gene, since the expression of antisense RNA is permitted. However, in the absence of 4-ddma-atc, the expression of a target gene is uninhibited in a prokaryotic host cell carrying a tet-regulated antisense RNA coding sequence which is specific for the target gene, and at least one inducer specific TetR-encoding gene, since the expression of the antisense RNA is inhibited. In a particular aspect of this embodiment, the target gene corresponds to one copy of a duplicated gene in a prokaryotic organism, thereby allowing the construction of a host cell that can be functionally haploid for that gene product. Such organisms are particularly useful for the detection of anti-microbial agents active against the encoded target gene product.

The present invention is further directed toward kits comprising components of the tetracycline-regulated expression systems disclosed herein, and instructions for use thereof. Such kits include a recombinant expression vector that encodes at least one inducer specific TetR protein operably associated with a promoter active in the host into which the present tet-regulatory system is to be introduced. In another embodiment, the expression vector comprises a structural gene encoding a inducer specific TetR protein of the present invention, and an upstream restriction site, generally as part of a polylinker sequence, into which the end user can insert any promoter of interest to that user.

The inducer specific Tet gene expression system of the invention may also be used in ribonucleic acid molecule interference (RNAi) to control expression of small interfering RNAs (siRNAs) which are used to inhibit expression of a gene of interest.

As used herein, the term "RNA interference" or "RNAi" refers to selective intracellular degradation of RNA used to silence expression of a selected target gene. RNAi is a process of sequence-specific, post-franscriptional gene silencing in organisms initiated by double- stranded RNA (dsRNA) that is homologous in sequence to the gene to be silenced. The RNAi technique involves small interfering RNAs (siRNAs) that are complementary to target RNAs (encoding a gene of interest) and specifically destroy the known mRNA, thereby diminishing or abolishing gene expression. RNAi is generally used to silence expression of a gene of interest by targeting mRNA, however, any type of RNA is encompassed by the RNAi methods of the invention. Briefly, the process of RNAi in the cell is initiated by long double stranded RNAs (dsRNAs) being cleaved by a ribonuclease, thus producing siRNA duplexes. The siRNA binds to another intracellular enzyme complex which is thereby activated to target whatever mRNA molecules are homologous (or complementary) to the siRNA sequence. The function of the complex is to target the homologous mRNA molecule through base pairing interactions between one of the siRNA strands and the target mRNA. The mRNA is then cleaved approximately 12 nucleotides from the 3' terminus of the siRNA and degraded. In this manner, specific mRNAs can be targeted and degraded, thereby resulting in a loss of protein expression from the targeted mRNA.

As used herein, the term "complementary nucleotide sequence" refers to the region on the RNA strand that is complementary to an RNA transcript of a portion of the gene of interest.

The term "dsRNA" refers to RNA having a duplex structure comprising two complementary and anti-parallel nucleic acid strands. Not all nucleotides of a dsRNA necessarily exhibit complete Watson-Crick base pairs; the two RNA strands may be substantially complementary. The RNA strands forming the dsRNA may have the same or a different nxαmber of nucleotides, with the maximum number of base pairs being the number of nucleotides in the shortest strand of the dsRNA. Preferably, the dsRNA is no more than 49, more preferably less than 25, and most preferably between 19 and 23, nucleotides in length. dsRNAs of this length are particularly efficient in inhibiting the expression of the target gene using RNAi techniques. dsRNAs are subsequently degraded by a ribonuclease enzyme into short interfering RNAs (siRNAs).

RNAi is mediated by small interfering RNAs (siRNAs). The term "small interfering RNA" or "siRNA" refers to a nucleic acid molecule which is a double stranded RNA agent that is complementary to i.e., able to base-pair with, a portion of a target RNA (generally mRNA). siRNA acts to specifically guide enzymes in the host cell to cleave the target RNA. By virtue of the specificity of the siRNA sequence and its homology to the RNA target, siRNA is able to cause cleavage of the target RNA sfrand, thereby inactivating the target RNA molecule. Preferably, the siRNA which is sufficient to mediate RNAi comprises a nucleic acid sequence comprising an inverted repeat fragment of the target gene and the coding region of the gene of interest (or portion thereof) Also preferably, a nucleic acid sequence encoding a siRNA comprising a sequence sufficiently complementary to a target gene is operatively linked to a tet operator sequence. Thus, the mediation of RNAi to inhibit expression of the target gene can be modulated by the presence or absence of tetracycline (or an analogue thereof) and the subsequent binding of a Tet transactivator or inhibitor.

The complementary regions of the siRNA allow sufficient hybridization of the siRNA to the target RNA and thus mediate RNAi. In mammalian cells, siRNAs are approximately 21-25 nucleotides in length (see Tuschl et al. 1999 and Elbashir et al. 2001). The siRNA sequence needs to be of sufficient length to bring the siRNA and target RNA together through complementary base-pairing interactions. The siRNA used with the Tet expression system of the invention may be of varying lengths. The length of the siRNA is preferably greater than or equal to ten nucleotides and of sufficient length to stably interact with the target RNA; specifically 15-30 nucleotides; more specifically any integer between 15 and 30 nucleotides, such as 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and 30. By "sufficient length" is meant an oligonucleotide of greater than or equal to 15 nucleotides that is of a length great enough to provide the intended function under the expected condition. By "stably interact" is meant interaction of the small interfering RNA with target nucleic acid (e.g., by forming hydrogen bonds with complementary nucleotides in the target xinder physiological conditions).

Generally, such complementarity is 100% between the siRNA and the RNA target, but can be less if desired, such as 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%. For example, 19 bases out of 21 bases may be base-paired. In some instances, where selection between various allelic variants is desired, 100% complementary to the target gene is required in order to effectively discern the target sequence from the other allelic sequence. When selecting between allelic targets, choice of length is also an important factor because it is the other factor involved in the percent complementary and the ability to differentiate between allelic differences.

Methods relating to the use of RNAi to silence genes in organisms, including C elegans, Drosophila, plants, and mammals, are known in the art (see, for example, Fire et al., Nature (1998) 391 :806-811; Fire, Trends Genet. 15, 358-363 (1999); Shaφ, RNA interference 2001. Genes Dev. 15,485-490 (2001); Hammond et al. Nature Rev. Genet. 2, 1110-1119 (2001); Tuschl, Chem. Biochem. 2, 239-245 (2001); Hamilton et al., Science 286, 950-952 (1999); Hammond et al., Nature 404, 293-296 (2000); Zamore et al., Cell 101, 25-33 (2000); Bernstein et al., Nature 409, 363-366 (2001); Elbashir et al., Genes Dev. 15, 188- 200 (2001); WO 0129058; WO 09932619; and Elbashir et al., 2001 Nature 411: 494-498)

The inducer specific Tet expression system of the invention may be used to control expression of an siRNA resulting in the ability to control RNAi. In one embodiment, the invention features a vector comprising an siRNA operatively linked to a tet operator. The siRNA comprises a nucleic acid molecule comprising the inverted repeat fragment and the coding region of the gene of interest (or portion thereof) are operably linked to the tet operator. The Tet fransactivator or inhibitor of the invention may be used to activate or inhibit expression of the siRNA, i.e., inverted repeat fragment and the coding region of the gene of interest (or portion thereof). Using the Tet transactivator or inhibitor of the invention allows for control of the activation or inhibition of RNAi mediation through an inducer molecule, e.g., tetracycline. Expression of the siRNA results in RNAi mediation and silencing of endogenous gene expression at the RNA level.

The inducer specific Tet expression system of the invention in combination with RNAi techniques provides the ability to specifically inhibit expression of a target gene of interest. RNAi may be used to study gene function, whereby placing expression of an siRNA under confrol of the tetO provides the ability to confrol expression of the siRNA and thus RNAi using a Tet transactivator or inhibitor. In addition, the inducer specific Tet expression system of the invention provides a means for controlling RNAi for freatment of disease, wherein the expressed siRNA is used to inhibit the expression of deleterious genes in vivo and, therefore, alleviate symptoms of, or cxire, disease. siRNA delivery using the inducer specific Tet expression system of the invention may also aid in drug discovery and target validation in pharmaceutical research.

RNAi targets a gene of interest or target gene whose expression is to be selectively inhibited or silenced through RNAi mediation. Preferably, RNAi targets a gene of interest including any cellular gene or gene fragment whose expression or activity is associated with a disease or disorder (e.g., an oncogene), as well as any foreign or exogenous gene or gene fragment whose expression or activity is associated with a disease, such as a gene from a pathogenic organism (e.g., a viral or pro-viral gene, viroid, or plasmodixim).

In another embodiment, the kit further comprises a second recombinant expression vector, comprising at least one TetO sequence bracketed by at least two restriction sites positioned on opposite sides of the operator sequence. The end user can insert a promoter into one of these sites and a structural gene encoding a protein (or an antisense RNA molecule) to be placed under tetracycline regulation into the second site. In other embodiments, the second expression vector may comprise a promoter already operably associated with the operator sequence. In still another embodiment, the operator sequence is not a TetO sequence but, rather, corresponds to a binding site for a non-TetR DNA-binding protein which is bound by the DNA binding domain of a chimeric revTetR protein as disclosed herein.

In a further embodiment, the kit may also comprise at least one tetracycline or tetracycline analogue, such as, but not limited to 4-ddma-atc.

In yet another embodiment of the present invention, the modified inducer specific TetR repressors may be used in methods for identifying non-antibiotic compounds that specifically interact with the inducer specific TetR, but not wild type repressors. In one embodiment, a method for identifying non-antibiotic compoxmds that specifically interact with inducer specific TetR in a eukaryotic organism is provided, said method comprising introducing into a cell first nucleic acid molecules comprising a reporter gene operatively linked to a promoter regulated by tefracycline or tetracycline analog, introducing an expression vector comprising a nucleotide sequence encoding a modified tetracycline repressor into the eukaryotic organism, expressing the modified tetracycline repressor, contacting the cell with a plurality of candidate compounds, and identifying those compoxmds that repress expression of the reporter gene product.

The candidate compoxmds can be obtained from a nximber of commercially available sources and include, for example, combinatorial libraries, natural product libraries, peptides, antibodies (including, but not limited to polyclonal, monoclonal, human, humanized, anti-idiotypic, chimeric or single chain antibodies, and FAb, F(ab')₂ and FAb expression library fragments, and epitope-binding fragments thereof), and small organic or inorganic molecules.

All patents, published patent applications, sequences, figures, accession numbers and other references disclosed herein are hereby expressly incoφorated herein in their entireties by reference.

The figures show: Figure la: Figure 1 depicts chemical structures of tetracycline derivatives described in the invention, including tetracycline (tc), anhydrotefracycline (ate), doxycycline (dox), 4- dedimethylaminoanhydrotetracycline (4-ddma-atc), and 4-dedimethylamino-6-dernethyl-6- deoxytetracyline (cmt 3). Figure lb: Figure lb provides an overview of all tc contacting residues. Tc is shown as a yellow stick model, Mg as a yellow ball and the three coordinating water molecules as red balls. The TetR residues from one monomer are colored blue and those from the other monomer are green. Hydrophobic interactions are symbolized by dashed lines, H-bonds by broken lines. Figure 2a: Figure 2a provides a stereo view of the N82 and S138 residues in proximity to the 4-dma moiety. Tc is shown as yellow stick model and the side chains of N82 and SI 38 are shown in red attached to the blue colored backbones of helices α5 and α8, respectively. The distances between the nearest atoms are indicated by green broken lines. The C¹³ atom of Serl38 is 3.46 A from the CH₃ of tc and O^δl of Asn82 is 3.26 A from the nifrogen of the 4-dma function.

Figure 2b: Figure 2b provides a stereo view of the location of SI 38 in the TetR four-helix bundle. The α-helices forming the foxir-helix-bxindle are indicated as blue and green ribbons from each monomer, respectively. SI 38 is located in helix α8 and the side chain (red) is oriented towards the 4-dma-moiety of tetracycline (yellow stick model). Mutation of S 138 may influence the dimerization of TetR.

Figure 2c: Figure 2c provides a diagram of the location of the residues F86, 1134 and L142 in proximity to S138. Serl38 is shown as red stick model and the side chains of F86,1134 and L142 are shown in light blue. The broken green lines indicate the nearest atoms of S138 and F86 relative to tc and of S138 relative to F86,1134 and L142. The distance between these residues is less than 5.3 A. The 6-methyl group of tc is in hydrophobic contact to He 134, and F86 accepts a hydrogen bond from the 12a hydroxide of tc (4). All three residues may be reoriented as a result of a mutation of the proximal residue at position 138, thereby influencing induction. Figure 3: An activity profile of cTA2^D-5 is shown. HeLa cells were transfected with a reporter plasmid (lOOng pUHC13-3) and either a regulator expressing plasmid [Ing pWHE120(BD)-i2.1; "cTA2D-5"] or pWHE121 (Ing; "none") which does not express a transactivator. The response of gene expression to effector tetracyclines was monitored by adding doxycycline ("dox") or 4-de(dimethylamino)-anhydrotefracycline ("4DATc") to the culture medium to final concentrations of 100 ng ml or 1 μg/ml, respectively. Firefly luciferase activity was determined as described after further incubation for 24 h. Figure 4: The dose response of cTA2^D-5 to cmt3 and 4DATc is shown. HeLa cells were cotransfected transiently with 100 ng of plasmid pUHC13-3 carrying the firefly luciferase gene under P_tet-ι control and 1 ng of plasmid encoding cTA2^D-5. Cells were grown at various concentrations of effector ranging from 0 to 0.6 μg/ l cmt3 and 4DATc. Luciferase activity was determined as described (Krueger et al., 2004). The luciferase activity detected without effector was set to 1000 standardized (stand.) ALU/μg protein. Figure 5. An activity profile of cTA2^D ₄c-5 is shown. HeLa cells were transfected with a reporter plasmid (lOOng pUHC13-8) and either a regulator expressing plasmid [Ing pWHE120(BD)-i2.1; "cTA2D4C-5"] or pWHE121 (Ing; "none") which does not express a transactivator. The response of gene expression to effector tetracyclines was monitored by adding doxycycline ("dox"), or 4-de(dimethylamino)-6-deoxy-6-demethyl-tetracycline ("cmt3") to the culture medium to final concentrations of 100 ng/ml or 200 ng/ml respectively. Firefly luciferase activity was determined as described after 24 h further incubation.

The following examples are provided to further illustrate various aspects of the present invention. They are not to be construed as limiting the invention.

Example 1: TetR Mutants With Distinct Tetracycline (Tc) Analog Affinity

Effects of mutations at Asn82 and Serl38 on 4-ddma-atc specificity

A TetR H64K S135L mutant has been described, wherein inducer specificity was modified such that TetR was induced by cmt3, a sancycline derivative lacking the 4-dma grouping (see Figure 1 for chemical structures), instead of tc (7). However, in the TetR H64K S135L mutant, TetR also responded to high affinity inducers ate and dox classifying it a relaxed specificity mutant (7).

In order to obtain a TetR variant with a truly new specificity, residues located in proximity of the 4-dma moiety in the TetR-[tc-Mg]⁺2 complex were changed. The following describes TetR mutants with affinity distinction between tc analogs, i.e., with and without the 4-dma grouping. The TetR-[tc-Mg]⁺2 crystal structure (3, 4) was used to identify amino acids to be mutated within the 4-dma moiety. The two most proximal residues Asn82 and Serl38 (see Figure 3) were chosen for randomization. The distance between the C^β atom of Serl38 and CH₃ of tc and between O^δl of Asn82 and the nifrogen of the 4-dma grouping is less than 3.5 .

Randomization of codons 82 and 138 was accomplished by PCR mutagenesis of teti? H64K S135L using oligonucleotides with the respective degenerated codons. The resulting PCR fragments were inserted into pWH1925 or in pWH1411, respectively, from which they are constitutively expressed. E. coli WH207/λtet50 was then transformed with the mutant pool at position 82, and E. coli WH207/pWH414 with that for position 138. E. coli WH207/λtet50and pWH414 provide tet-confrollable lacZ expression. The fransformants were screened for induction on MacConkey-agar plates or on X-Gal containing M9 minimal media plates, respectively, each containing 0.4 μM 4-ddma-atc. Candidates that were inducible by 4-ddma-atc were rescreened for repression in the presence of 0.4 μM ate and without inducer. This approach yielded SI 38 substitutions by He and Leu as well as Asn82 substitutions by Val and Tφ. In addition, random clones were sequenced, and 9 different residues were found at position 82 and 11 at position 138 (see Tables 1 and 2, respectively). The induction specificities of these mutants were analyzed in broth cultures by determining repression of β-galactosidase encoded by a chromosomally located tetO- lacZ fusion in E. coli WH207/λtet50 in the presence and absence of 0.4 μM of 4-ddma-atc, tc, or ate.

The results obtained with TetR H64K S135L with mutations at position 82 are shown below in Table 1. The host strain was E. coli WH207/λtet50. All tetR variants were on plasmids originating from pWH1925(BD). β-Galactosidase activities were determined at 37 °C in units according to Miller (15). They were given in percent of the value determined in a strain without tetR (not shown in the table). 100% corresponds to 5400+100 units for repression, 5300+90 units in the presence of 0.4 μM 4-ddma-atc, 5100+200 units in the presence of 0.4 μM ate and 5400+100 units in the presence of 0.4 μM tc.

Table 1 : In vivo repression and induction by different tc derivatives of TetR variants with mutations at : position Asn82. β -galactosidase activity [%] induction with

TetR variant repression 4-ddma-atc ate tc SEQ ID Nos. SEQ ID Nos. polynucleotides polypeptides

TetR(BD) 1.1 -0.1 1.1 ±O.l 82 ±5 65.8 ±03 1 2

H64KS135L 1.1±0.1 65 ±9 67 ±3 4.6 ±2 - -

H64KS135L-N82G 1.1 -0.1 28 ±2 39 ±1 1.1 ±0.1 7 8

H64KS135L-N82T 0.9±0.1 38 ±2 57 ±2 1.1 ±0.1 19 20

H64KS135L-N82S 0.9 ±0.1 4.6 ±0.6 14 ±1 2.0 ±0.9 17 18

H64KS135L-N82V l.O±O.l 8.4±0.4 1.6±0.1 1.1 ±0.1 21 22

H64KS135L-N82L 0.9±0.1 2.7 ±2 1.7 ±0.2 1.4 ±03 11 12

H64KS135L-N82I l.O±O.l 8.4 ±1.3 1.8 ±0.1 0.8 ±0.1 9 10

H64KS135L-N82M 0.9 ±0.1 6.8 ±0.6 0.9 ±0.1 0.8 ±0.1 13 14

H64KS135L-N82F 0.9 ±0.1 13 ±02 l.O±O.l 12 ±03 5 6

H64KS135L-N82W 03 ±0.1 4.4±02 0.7±0.1 0.6 ±0.5 23 24

H64KS135L-N82E 0.9 ±0.1 22±02 11±2 1.5 ±0.9 3 4

H64KS135L-N82Q 1.00 ±0.1 1.9±0.1 1.1 ±0.1 0.8 ±0.1 15 16

As shown in Table 1 , all Asn82 TetR mutants exhibited a reduction of inducibility. The N82G, N82E, N82S or N82T mutations in TetR H64K S135L showed reduced induction by ate and 4-ddma-atc and no induction by tc. The amino acid exchanges N82L with a hydrophobic side chain, N82F bearing an aromatic amino acid and N82Q yielded proteins with no response to all three inducers. The substitutions N82V, N82I, N82M and N82W resulted in proteins with strongly reduced inducibility but improved specificity for 4-ddma- atc, being a four- to six-fold better inducer than ate for these repressers. However, maximal induction was less than 15% of that obtained with TetR H64K S135L.

All N82 mutations lead to decreased affinities for tc and ate. An explanation for this result can be the contribution of N82 for tc binding. It undergoes two H-bonds to tc, one with the nitrogen of the 4-dma moiety and the other one with O-3 in the A-ring. Removal of these interactions in the TetR N82A mutant leads to almost complete loss of tc affinity, while the affinity for ate drops nearly four orders of magnitude (6). Since H-bonds are sterically sensitive they cannot be formed by other residues in most cases. Therefore any change of N82 weakens inducer binding and inducibility. This is true for all position 82 mutations shown here and found in previous studies (18, 19), including those with a 4-ddma-atc specificity increase. The latter mutants carry hydrophobic residues (V, I, M, W) at position 82. Thus, hydrophobicity at this position supports 4-ddma-atc more than ate binding, but these mutants were only poorly inducible.

The phenotypes of the S138 exchanges in TetR H64K S135L are shown below in Table 2. The host strain was E. coli WH207/λtet50. All tetR variants were on plasmids originating from pWH1411(BD). β-Galactosidase activities were determined at 37 °C in units according to Miller (15). They are given in percent of the value determined in a strain without tetR (not shown in the table). 100% corresponds to 6200+100 units for repression, 6600+200 units in the presence of 0.4 μM 4-ddma-atc, 4500+500 units in the presence of 0.4 μM tc and 65001100 units in the presence of 0.4 μM ate.

Table 2: In vivo repression and induction of TetR variants with mutations at Serl38. β-Galactosidase activity [%] induction with

TetR variant repression 4-ddma-atc ate tc Seq. A* Seq. B**

TetR 03D) 1.1 ±0.1 1.1 ±0.1 92±5 65. 8 ±0.5 1 2

H64K S135L 1.1 ±0.1 96 ± 2 90+1 8.0 ±0.7 - -

H64K S 135L- S138A 0.9 ±0.1 83 ± 3 80±2 2.4 ±0.1 25 26

H64K S 135L- S138G 3.3 ±0.6 92 ± 3 lOO±l 16 ±1.0 31 32

H64K S135L- S138T 0.8 ±0.1 84 ± 3 79±3 3.9±03 45 46

H64K S 135L- S138C 1.2 ±0.1 75 ± 3 54±4 8.7±0.4 27 28

H64K S 135L- S138V 2.2 ±0.2 86 ± 5 56±3 3.9±1.0 47 48

H64K S 135L- S138L 1.4 ±0.1 8.0 ±0.1 2±0.1 1.2+0.1 37 38

H64K S 135L- S138I 2.9 ±0.3 97 ± 2 7±0.1 2.5±1.4 35 36

H64K S 135L- S138P 62 ±1 67 ± 2 75±2 79 ±2 39 40

H64K S135L- S138W 0.2 ±0.1 5±0.5 0.9±0.1 O.ό±O.l 49 50

H64K S135L- S138D 1.5 ±0.8 88 ± 7 54±2 2.5±0.8 29 30

H64K S 135L- S138Q 1.1 ±0.1 81 ± 2 83±4 1.5±0.2 41 42

H64K S 135L- S138H 1.4 ±0.1 95 ± 3 96±3 10 ±2 33 34

H64K S 135L- S138R 5.1 ±03 4.9 ±0.4 6.5±0.2 5.7±0.2 43 44

* Seq. A = SEQ LO Nos. polynucleotides ** Seq. B = SEQ ID Nos. polypeptides Most SI 38 variants showed only weak effects on inducibility. In particular, S138G and SI38A with small residues and S138T and S138Q with polar residues and S138H were not or only marginally affected. Slightly reduced induction with ate and almost no change of 4- ddma-atc inducibility was seen with C, D and V at this position. P instead of S at position 138 lead to a mostly inactive protein with almost complete loss of repression. Reduced induction was seen with the S138R variant with all tc analogs. Hydrophobic residues at position 138 caused the strongest effects on induction. The SI 38V variant exhibited slightly lower induction by ate. S138L and S138W lead to the expected reduced induction by ate and dox, but also by 4-ddma-atc. The only mutant with reduced induction by ate and dox (3% and 7%, respectively) and full induction with 4-ddma-atc contained I at position 138. TetR H64K S135L S138I exhibited an indcuer specific phenotype.

In contrast, no contacts to the inducer were obvious for the SI38 residue in the crystal structure, and yet, this position was quite sensitive to changes. It is located in helix α8, which forms part of the dimerization interface (see Figure 4). The S138P exchange may alter the conformation of helix α8. Since Pro residues distort α-helices the repression deficient phenotype brought about by the S138P exchange may be due to lack of dimerization. Arg instead of Ser at position 138 caused reduced induction. This effect can be explained by the increased size and positive charge of Arg, which may be oriented towards the tc binding pocket clashing with the 10 hydroxide or 11 oxygen function of tefracycline. While the SI 381 exchange caused a complete shift to 4-ddma-atc specificity, the very similar S138L exchange leads to almost complete loss of induction. Both amino acids are of similar size and should clash with the 4-dma grouping. This assumption is corroborated by the affinity drop of all mutants containing He at position 138 for all tc derivatives with 4-dma as opposed to the rather small changes in affinity for tc derivatives lacking 4-dma, However, the different behaviour of He and Leu highlights the importance of the geometry of the side chain for 4-ddma-atc recognition. It may be explained by effects on the conformation of surrounding residues, which are involved in shaping the tc binding pocket. F86, 1134 and LI 42 are in close proximity to the 138 residue (see Figure 5). The methyl group at position 6 in ring C of tc forms hydrophobic contacts to He 134 (3). F86 accepts a hydrogen bond donated by the 12a hydroxide of tc and TetR F86L exhibits reduced inducibility (18). Though L142 is not directly involved in tc contacts, severely reduced induction was seen for TetR L142F and TetR L142R in previous work indicating the importance of this residue for induction. (18). Example 2: Characterization of S138I TetR mutant

Contribution of the SI 381 exchange to inducer specificity.

To determine the contributions of the SI 381 mutation to the phenotype of TetRH64K S135L SI381 all possible single and double exchange mutants were constructed and cloned into pWH1925. The host strain was E. coli WH207/λtet50. All tetR variants were on plasmids originating from pWH1925(BD). β-Galactosidase activities were determined at 37 °C in units according to Miller (15). They were given in percent of the value determined in a strain without tetR. 100% corresponds to 5400+100 units for repression, 5300+90 units in the presence of 0.4 μM 4-ddma-atc and 5100+200 units in the presence of 0.4 μM ate, 3400+100 units in the presence of 0.4 μM dox and 54001100 units in the presence of 0.4 μM tc. The steady-state protein levels of all mutants determined by Western Blot analysis were indistinguishable. Thus, the repression and induction properties as monitored by β- galactosidase expression reflect the activities of the various mutant proteins and not their stability.

The results are shown below in Table 3. Since pWH1925 leads to slightly different repression compared to the previously used pWH1411 (7) the induction properties of the TetR mutants H64K, S135L and H64K S135L for tc and dox were redetermined in addition to the ones with ate and 4-ddma-atc. TetR SI381 was not induced by 4-ddma-atc, while ate and dox induction decreased to 54% and 20%, respectively. Thus, SI 381 reduces tc, ate and dox induction. TetR H64K exhibited a five-fold increase in 4-ddma-atc induction and a strong reduction in tc, ate and dox response (below 10%) as compared to wild-type TetR. The double mutant TetR H64K SI381 showed largely reduced ate and dox induction, while the 4-ddma-atc response is the same as that of TetR H64K. The TetR S135L mutation does not interfere with ate, dox or tc induction, but 4-ddma-atc response is increased more than 30-fold as compared to the wild-type. TetR S135L S138I was fully induced by ate and dox while the response to 4-ddma-atc and tc was reduced. The double exchange mutant TetR H64K S135L was induced by 4-ddma-atc but not by tc, whereas it still responded to ate and dox. Thus, the triple mutant TetR H64K S135L S138I showed 4- ddma-atc specificity with respect to ate and dox. Table 3: In vivo repression and induction of the single and double mutants β-galactosidase activity [%] induction with

TetR variant repression 4-ddma-atc ate tc dox Seq. A* Seq. B*

TetR (BD) 0.9 ±0.1 1.1 ±0.1 82 ±5 44 ±1 93 ±3 - -

H64K 0.8 ±0.1 53±0.1 7.1 ±0.4 0.9 ±0.1 1.7±0.1 51 52

S135L 0.8 ±0.1 35 ±2 70 ±2 41±2 81+3 53 54

S138I 0.9 ±0.1 0.9 ±0.1 54 ±9 0.9 ±0.1 19+0.7 55 56

H64K S135L 1.1 ±0.1 65 ±9 67 ±3 4.6 ±2 59 ±1 57 58

H64K S138I 1.1 ±0.1 7.0 ±0.4 13±0.2 1.8 ±0.2 2.5 ±1.9 59 60

S135LS138I 1.1 ±0.1 2.8 ±0.2 77 ±5 5.6 ±2.7 69 ±2 61 62

H64K S135L S138I l.ό±O.l 57 ±4 3.1 ±0.4 2.2 ± 0.4 1.7 ±0.1 » _

* Seq. A = SEQ ID Nos. polynucleotides ** Seq. B = SEQ LO Nos. polypeptides

Example 3: Inducer binding constants of TetR mutants

To determine the binding constants of the TetR mutants to the [tc-Mg]⁺ complexes, the TetR mutants were overexpressed and purified to homogenity as previously described (16). The binding constants of the tc analogs to Mg and their Mg independent binding constants to the proteins are required for fitting the tifration curves for the Mg²⁺ dependent equilibrium binding constants. Therefore, the association constants of the tc analogs with Mg²⁺ (KM) were determined as described (6). Ate binds Mg²⁺ with K_M = 3.4 x 10³ M"¹, dox with a roughly two-fold and 4-ddma-atc with an about 5-fold increased constant.

Like ate (6), dox and 4-ddma-atc bind TetR also in the absence of Mg²⁺. These Mg²⁺-free binding constants (K_T) were determined by fluorescence tifration of wild-type and mutant TetR with the corresponding tc derivative in a Mg²⁺ free buffer (shown below in Table 4), wherein all constants were determined by fluorescence titrations as described previously (6).

The K_T values range between 10 and 10 10 x Myrπ"l . The highest affinity without Mg was seen for TetR S135L with ate and dox. The Mg ,2+ independent bindmg of ate was 50-fold, that of dox was 10-fold enhanced as compared to the wild-type protein. Table 4: Mg independent equilibrium binding constants of TetR variants

M * independent equilibrium binding constant ^b, K_τ [x 10⁷ M¹ ] TetR variant 4-ddma-atc ate dox

TetR(BD <0.01^a 6.5 5.3

S135L <0.01^a 338 51.6

S138I 1.7 ^c 0.8

H64K S135L 0.6 0.1 0.03

S135L S138I 16.1 11.6

H64K S135L S138I 0.4 <0.01^a <0.01^a

^a The affinity is less then 1 x 10⁵ M^"1, which is too low for quantification. ^b The standard deviations typically range from 10% to 40%. ^c The standard deviation is 50%.

The binding constants (K_A) of [tc-Mg]⁺ with the TetR variants using ate, dox and 4-ddma- atc were determined using K and K_T for fitting the tifration curves (6). The resulting K_A values are summarized below in Table 5. The binding constants for [tc-Mg]⁺ and [cmt3- Mg]⁺ to TetR H64K, S135L and H64K S135L were presented in previous work (7). The affinity of TetR for [4-ddma-atc-Mg]⁺ was about six orders of magnitude lower compared to the one for [atc-Mg]⁺ and five orders of magnitude lower than that for [dox-Mg]⁺. The binding constant of TetR H64K S135L S138I to [4-ddma-atc-Mg]⁺ was increased 440-fold compared to the wild-type protein. The [atc-Mg]⁺ affinity, on the other hand, was 7 x 10⁴- fold and the [dox-Mg]⁺ affinity 2 x 10⁴-fold lower for the mutant compared to the wild type. The increase in specificity conferred by the additional SI 381 exchange compared to TetR H64K S135L was resembled by almost unchanged affinity for [4-ddma-atc-Mg]⁺, whereas the drop in affinity was 150-fold for [atc-Mg]⁺ and 70-fold for [dox-Mg]⁺. This effect was also seen in the TetR SI 381 mutant showing 470-fold reduced [atc-Mg]⁺ binding compared to the wild-type. [dox-Mg]⁺ binding is 30-fold reduced. The H64K mutation led to decreased binding of [atc-Mg]⁺ and [dox-Mg]⁺, while [4-ddma-atc-Mg]⁺ affinity was enhanced 17-fold. TetR S135L exhibited 250-fold higher affinity for [4-ddma- atc-Mg]⁺ than the wild type, while [atc-Mg]⁺ binding was only slightly and [dox-Mg]⁺ binding was xmaffected. Combination of the mutations in TetR H64K S135L led to adding up the properties of the single mutants (7) for [tc-Mg]⁺, but not for [4-ddma-atc-Mg]⁺, [atc- Mg]⁺ or [dox-Mg]⁺ binding. The binding constant of [4-ddma-atc-Mg]⁺ is 770-fold increased and there was detectable [atc-Mg]⁺ and [dox-Mg]⁺ binding. The binding constants of the double mutant TetR H64K SI 381 resembled its in vivo properties. [4- ddma-atc-Mg]⁺ binding was slightly enhanced compared to the single exchange mutants, while [atc-Mg]⁺ and [dox-Mg]⁺ binding was reduced. The TetR S135L SI 381 protein shows increased [4-ddma-atc-Mg]⁺ affinity as compared to TetR SI381 but decreased binding with respect to TetR S135L. [dox-Mg]⁺ binding was only slightly reduced compared to S135L but strongly increased compared to TetR SI 381. Binding of [atc-Mg]⁺ was increased three-fold compared to SI 381 but 330-fold reduced regarding the S135L mutant, while the Mg independent binding constant of ate increased compared to the wild-type protein.

Comparison of the single mutants TetR H64K, TetR S135L and TetR SI 381 with the triple mutant shows, that S135L mediates recognition of 4-ddma-atc, H64K reduced binding of all tc analogs except 4-ddma-atc, and SI 381 reduced ate and dox binding but did not interfere with 4-ddma-atc recognition. The combination of all three mutations led to a 4- ddma-atc specific phenotype. The ratio of binding constants for the inducer pairs 4-ddma- atc and ate or 4-ddma-atc and dox served as measure for the specificity of the corresponding mutants. Comparing TetR and the H64K S135L S138I triple mutants, this ratio increases 3 x 10⁷-fold for ate and 8 x 10⁶-fold for dox. This exceeds the 20,000-fold specificity gain found in the previous TetR inducer specificity study (7).

Table 5: Tc derivative binding constants of TetR mutants

Mg²⁺ dependent equilibrium binding constant ^a,K_A [x l0⁷M'¹]

TetR variant 4-dd__a-atc ate dox

TetR(BD) 0.3 119600 16700

H64K 4.9 42.5 19

S135L 75 240200 14600

S138I 0.5 252 578

H64K S135L 224 260 64

H64K S138I 6.2 0.7 0.7

S135L S138I 1.6 980 14020

H64K S135L S138I 132 1.7 0.9

' The standard deviations typically range from 10% to 40% All constants have been determined by fluorescence titrations under limiting Mg ⁺ concentrations as described (17).

The amino acid alterations H64K, S135L or SI 381 contributed to different degrees of inducer affinity in the TetR mutants, depending on their combinations and the respective inducer. The effects of H64K and S138I on 4-ddma-atc binding determined in the single mutants add up in the corresponding double mutant, while all other combinations do not yield the sum of the effects seen for the respective single mutations. This results in a smaller affinity increase than predicted from the single exchange mutants. In contrast, an analogous consideration for ate shows that only the affinity changes resulting from the S135L and S138I mutations acted independently. The dox affinities of all combined mutations resembled approximately the values predicted from the addition of the single mutant effects. The tc variants may assume different positions in the tc binding pocket of TetR, as is the case for ate compared to tc, and even more pronounced for the tc variant lacking the 4-dma grouping.

Taken together, TetR H64K S135L S138I exhibited 4-ddma-atc specificity in distinction to ate and dox in in vivo and in vitro experiments.

Methods were carried out as described below. Reagents and Materials were purchased as indicated. Tc was obtained from Merck (Darmstadt, Germany), ate from Acros (Geel, Belgium), dox from Sigma (Munich, Germany) and 4-ddma-atc was synthesized by Prof. Gmeiner (Pharmazeutische Chemie, FAU Erlangen-Niirnberg). All other chemicals were from Merck (Darmstadt, Germany), Roth (Karlsruhe, Germany) or Sigma (Munich, Germany). Enzymes for DNA restriction and modification were from New England Biolabs (Frankfurt/Main, Germany), Roche (Mannheim, Germany) or Pharmacia (Freiburg, Germany). Isolation and manipulation was performed as described (8).

Chemical synthesis of4-dedimethylamino-anhydrotetracycline

Starting from tetracycline, 4-dedimethylamino-anhydrotefracycline (4-ddma-atc) was synthesized by 7V-methylation, reductive removal of trimethylamine and dehydration (see, refs (9, 10) when concentrated aqueous hydrochloric acid was used instead of hydrobromic acid. Analytical data: C₂oHi₇NO₇ (383.4). - ELMS: m/z = 383 (M*). - mp 257 °C ((11), 256 - 258 °C). - ER (KBr): o = 3460, 3385, 3345, 3210, 1635, 1570, 1560, 1375, 1230, 670 cm'¹. - Η NMR (360 MHz, pyridine-d₅): 8 = 2.35 (s, 3 H, CH₃), 2.82 (dd, J = 18.2, 6.2 Hz, 1 H, H-4a), 3.06 (dd, J = 15.9, 7.8 Hz, 1 H, H-5a), 3.08-3.15 (m, 1 H, H-4a), 3.38 (br d,J= 18.2 Hz, 1 H, H-4B), 3.50 (dd, .7= 15.9, 3.0 Hz, 1 H, H-5B), 7.08 (d, J= 7.8 Hz, 1 H, H-9), 7.39 (d, J= 8.2 Hz, 1 H, H-7), 7.59 (dd, J = 8.2, 7.8 Hz, 1 H, H-8), 9.82 (s, 1 H, NH), 10.15 (s, 1 H, OH-10). -¹³C NMR (90 MHz, pyridine-d₅): 5 = 14.32 (CH₃), 29.4 (C-5), 36.3 (C- 4), 37.1 (C-4a), 78.5 (C-12a), 100.5 (C-2), 109.5 (C-lla), 111.5 (C-9), 113.1 (C-7), 115.4 (C-lOa), 122.5 (C-6), 131.9 (C-5a), 133.1 (C-8), 139.8 (C-6a), 159.3 (C-10), 165.0 (C-ll), 174.7 (CONH₂), 193.4 (C-l), 196.3 (C-3), 201.9 (C-12).

Construction of the plasmid pools

E. coli DH5α was used for cloning. Mutations for the codons N82 and SI38 were introduced as follows. Randomization was done by PCR mutagenesis with the primers N82mut (5"-tea gcg gtc (agct) (agct) (gc) gca atg agt ttc-3') (SEQ ID NO: 63) and S138mut (5'-tta gcg gtc (agct) (agct) (gc) cat ttt act tta ggt gcc-3') (SEQ ED NO: 64) according to the three primer method (12) with teti? H64K S135L as template. The tetR fragments containing the randomized codons and the H64KS135L mutations were introduced in pWH1411(BD) (7) and pWH1925(BD) (1), respectively for constitutive expression. Isolation, manipulation and sequencing were performed as described (8). E. coli screening system

The mutant pools were tested for inducibility with 0.4 μM of 4-ddma-atc and repression with 0.4 μM ate or without inducer in a genetic screen. The E. coli strain WH207 containing pWH414 (13) was fransformed with the pWH1411 H64KS135L S138mut mutant pool. pWH414 contains a tetA-lacZ fusion expressing β-galactosidase under tetO control. pWH1411 constitutively expresses the tetR mutants. The cells were plated on M9 minimal media (8) containing 0.2% (w/v) glucose as carbon source and 0.004% (w/v) X- gal. We screened for blue colonies on plates with 0.4 (0.4 μM 4-ddma-atc and for white on that without inducer and with 0.4 μM ate, respectively.

E. coli Wm07/ λtet50 (13) (14) was transformed with the pWH1925 H64KS135LN82mut mutant pool. The E. coli strain contains a chromosomal tetA-lacZ fusion under teti? control. The cells were plated on MacConkey Agar Base (Becton Dickinson, USA) containing 14 g/1 lactose, 0.0042% (w/v) neutral red and 0.0014% (w/v) crystal violett. The colonies were screened for their ability to repress P-galactosidase in the absence and the presence of 0.4 μM ate and to be induced on plates containing 0.4 μM 4-ddma-atc.

0-Galactosidase assays

Repression and induction with different tc analogs was determined in E. coli WH207/λtet50. Cells were grown in LB supplemented with 0.4 μM of tc, ate, dox or 4- ddma-atc at 28 °C. P-galactosidase activities were determined as described (15). Three independent cultures were assayed for each mutant and measurements were repeated at least twice.

Protein purification

E. coli RB791 fransformed with pWH610 derivatives (16) was used for expression of the TetR mutants. Purification of the TetR mutants to homogeneity was done as described (16). Protein concentrations were determined by UV spectroscopy and by saturating tifration with ate or 4-ddma-atc observing the change of fluorescence. Determination ofMg + -tc analog equilibrium binding constants.

The binding constant from Mg to the tc derivatives were determined using UN tifration as described (6). The following Mg²⁺ binding constants were obtained: ate, 3.4xl0³ M"¹; dox, 7.2xl0³ NT¹; 4-ddma-atc, 17.5xl0³ NT¹.

Fluorescence measurements

All fluorescence measurements were performed in a Spex Fluorolog with two double monochromators. Ate fluorescence was excited at 455 nm and monitored at 545 nm. For dox, the excitation wavelength was set to 370 nm and detected at 515 nm. To observe 4- ddma-atc fluorescence we used 420 nm excitation and 540 nm for detection.

Mg²⁺ independent binding constants were determined using a buffer containing 100 mM Tris-Hcl, 100 M NaCl and 1 mM EDTA at pH 8. Tifration and calculation of the equilibrium binding constants was done as described (6). TetR-[tc-Mg]⁺2 binding constants were obtained from fluorescence titration at limiting Mg²⁺ concenfrations as described (17). We adjusted free Mg²⁺ concenfrations ranging from 10"¹⁰ to 10"³ M using a buffer containing 0.1 mM EDTA as metal chelator. In all cases a 10% molar excess of TetR over the tc derivative and total concentrations of 1.1 μM, 0.11 μM and 0.011 μM protein were used. Calculation was done as described previously (17) and repeated at least twice.

Example 4: A TetR Mutant With Distinct Tetracycline Analog Specificity Is Active As A Transactivator in HeLa Cells

The TetR mutant TetR(B/D) H64K S135L S138I was cloned into a pWHE120 background (Krueger et al., 2003) yielding a fusion of the tetR allele with sequences encoding three repeats of a minimal activation domain (Baron et al., 1997). This eukaryotic fransactivator was termed cTA2^D-5 (The corresponding nucleic acid sequence is shown in SEQ ED NO: 63, the encoded amino acid sequence in SEQ ID NO: 64) and is expressed by a human CMV immediate early promoter/enhancer (Gossen and Bujard, 1992). The plasmid expressing cTA2^D-5 was fransiently transfected with a reporter plasmid expressing firefly luciferase under control of P_tet-ι [pUHC13-3; (Gossen and Bujard, 1992)] into HeLa cells. Effector tetracyclines were added and luciferase activity was determined after 24 h (Krueger et al., 2004). The result is shown in Figure 3.

The transactivator cTA2^D-5 increases luciferase activity by a factor of about ten. Addition of dox does not affect gene expression, while the addition of 4-DATc reduces luciferase activity to basal levels in the absence of any transactivator.

Having established that the transactivator is functional, we determined its sensitivity towards the effectors 4-DATc (Henssler et al., 2004) and cmt3 [(Stephens et al., 1963); 4- de(d_methylamino)-6-deoxy-6-demethyl-tefracycline]. Both tefracycline analogs lack the dimethylamino group at position 4. HeLa cells were transiently transfected with plasmids expressing cTA2^D-5 and firefly luciferase under confrol of P_tet-ι and incubated for 24 h with effector concentrations ranging from 0 to 1 μg/ml 4DATc or cmt3. The results are shown in Figure 4. Activation was reduced to background levels at 0.6 μg/ml 4DATc and 0.2 μg/ml cmt3. The dose response curve is also less steep for 4DATc. Thus, cTA2^D-5 is more sensitive towards cmt3.

A Tet transactivator with altered tefracycline specificity would be of great advantage as it allows fully independent control over two different genes by a combination of any two Tet transregulators. For this, the Tet fransregulators would additionally need to recognize different tet operators. TetR mutants with altered DNA-binding specificity have been described (Helbl and Hillen, 1998; Helbl et al., 1998) and their functionality in eukaryotic transactivators has been demonstrated (Baron et al., 1999; Forster et al., 1999; Krueger et al., 2004). We therefore combined cTA2^D-5 with the mutations for specific recognition of the tetO-4C variant (Helbl and Hillen, 1998) and determined the regulatory properties of the resulting transactivator cTA2^D ₄c-5 in HeLa cells by transient co-fransfection with the reporter plasmid pUHC13-8 (Baron et al., 1999). The corresponding nucleic acid sequence for cTA2^D4c-5 is shown in SEQ ID NO: 65, the encoded amino acid sequence in SEQ ID NO: 66. Firefly luciferase activities were determined as described (Krueger et al., 2004) after 24 h incubation with the various effectors anfd the results are shown in Figure 5.

The transactivator cTA2^D-5 increases luciferase activity by about a thousand-fold. Addition of dox does not affect gene expression, while the addition of cmt3 reduces luciferase activity about sixty-fold, to a level about fifteen-fold higher than the basal activity in the absence of any transactivator. Taken together, eukaryotic transactivators carrying mutations leading to an altered tefracycline analog specificity are active. They do not respond to the commonly used effector doxycycline and they can be combined with mutations leading to an altered operator specificity.

Methods were carried out as described below. Cmt3 was purchased from Prof. Gmeiner (Pharmazeutische Chemie, FAU Erlangen-Nύrnberg.

Construction of the transactivators

pWHE120(B/D)-i2.1 (cTA2^D-5): The fragment from the tetR(BD) variant containing the mutations responsible for the effector specificity change were amplified by PCR from the pWHHHBD construct (Henssler et al., 2004) with the primers D-Apal and tetR(D)- Cterm-NgoMEV. The resulting PCR product was cut with Apal/NgoMEV and ligated into equally restricted pWHEl 20(B). pWHE120(B/D)4C-i2.1 (cTA2^D _4C-5): The tetO-4C specific DNA reading head was introduced by digesting pWH510EA37PQ39YM42 (Helbl and Hillen, 1998) with Xbal/Apal and cloning the fragment into likewise restricted pWHE120(B/D)-i2.1.

Transient transfection using PerFectin™

Transfections were performed at 60-80 % confluence in 6-well / 24-well plates using 1 / 0.2 μg of DNA and 2.5 / 1 μl PerFectin™ per well mixed to a total volume of 1 / 0.25 ml per well with OptiMEM medium according to the instructions of the producer. After 4 h incubation (PerFectin™) with the respective DNA mixes, medium supplemented with 20 % FBS and the respective effector was added. If not stated otherwise, cells were harvested after 24 h incubation in a humidified 37°C incubator under 7.5 % CO₂.

Harvesting for firefly luciferase assays and Western blot analyses

Cells were washed with PBS and incubated with 100 μl (6-well plates) or 50 μl (24-well plates) lysis buffer per well. After 10 min, crude cell lysates were transferred to 1.5 ml reaction tubes and stored at -20°C

Determination of protein concentrations Protein concentrations were determined specfrophotometrically. 2 μl of crude cell lysate were mixed with 60 μl Bio Rad solution and 240 μl MilHpore water in 96 well plates. After incubation for 10 min at RT the absorbance at 595 nm was determined using the TEC AN SpecfraFluor Plus. BSA-solution was used as a standard.

β-galactosidase assay

To determine β-galactosidase activity, 5 μl crude cell lysate were mixed with 120 μl Millipore water and 30 μl 5x LacZ buffer in 96 well plates at room temperature. The reaction was started by addition of 30 μl ONPG solution and all reactions were stopped at the same time with 100 μl 1 M Na₂CO₃ when samples turned yellow. Absorbance was measured at 420 nm using the TECAN SpecfraFluor Plus.

Luciferase assay

Luciferase activity was quantified either in a Berthold tube luminometer or a 96-well plate luminometer using the following conditions:

Tube luminometer: 5-10 μl of crude lysate were mixed with 100 μl measurement buffer in a detection tube. Measuring buffer containing 250 μM luciferin was injected and light emission was detected for 10 s. Values are designated as arbitrary light units (ALU).

96-well plate luminometer: 100 μl of measurement buffer containing 250 μM luciferin was injected into 10 μl of crude lysates. After 8 s, light emission was detected for 4 s and divided by four. Values are designated as arbitrary light units (ALU).

Normalisation of luciferase activity

ALU were corrected transfection efficiency (β-galactosidase activity) and protein concentration according to:

ALU mean (β - gal) μg protein (β - gal) References

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Claims

1. A polynucleotide comprising a nucleic acid molecule selected from the group consisting of: a) a nucleic acid molecule having a nucleic acid sequence as shown in 9, 13, 21, 23, 29, 35, 37, 47, 49, 63 or 65; b) a nucleic acid molecule encoding a polypeptide having an amino acid sequence as shown in 10, 14, 22, 24, 30, 36, 38, 48 50, 64 or 66; c) a nucleic acid molecule having a nucleic acid sequence which is at least 70 % identical to the nucleic acid sequence of a) or b), wherein the polypeptide encoded by said nucleic acid molecule is specifically induced by a tetracycline analog lacking a 4-dma grouping, d) a nucleic acid molecule encoding a polypeptide having an amino acid sequence which is at least 70 % identical to the amino acid sequence of a polypeptide which is encoded by the nucleic acid molecule of any one of a) to c), wherein the polypeptide encoded by said nucleic acid molecule is specifically induced by a tetracycline analog lacking a 4-dma grouping, and e) a nucleic acid molecule comprising a biologically active fragment comprising at least 100 contiguous nucleotides of the nucleic acid molecules of any one of a) to d), wherein said fragment encodes a polypeptide which is specifically induced by a tefracycline analog lacking a 4-dma grouping; f) a nucleic acid molecule comprising a biologically active fragment comprising at least 30 contiguous amino acids of the amino acid sequence encoded by the nucleic acid molecules of any one a) to d), wherein the polypeptide encoded by said nucleic acid molecule is specifically induced by a tetracycline analog lacking a 4-dma grouping.

2. The polynucleotide of claim 1, wherein said polynucleotide further encodes a polypeptide domain which directly or indirectly activates franscription in a eukaryotic cell.

3. The polynucleotide of claim 2, wherein said polypeptide domain which directly or indirectly activates transcription in a exikaryotic cell consists of at least one, at least two or at least three copies of the NP-16 minimal activator domain.

4. A vector containing the polynucleotide of any one of claims 1 to 3.

5. The vector of claim 4 which is selected from the group consisting of pCM190GFP+, pUHD15-l, pREP9, pUHD and baculovirus expression vectors.

6. A host cell comprising the polynucleotide of any one of claims 1 to 3 or the vector of claim 4 or 5.

7. The host cell of claim 6, wherein said cell is a plant cell, an insect cell, a fungal cell, a bacterial cell or a mammalian cell.

8. The host cell of claims 6 or 7, wherein said cell further comprises an expressible polynucleotide under the control of the tet operator (tetO).

9. A polypeptide encoded by the polynucleotide of any one of claims 1 to 3, the vector of claim 4 or 5 or which is obtainable by the host cell of any one of claims 6 to 8 and being encoded by the polynucleotide of any one of claims 1 to 3.

10. An antibody which specifically recognizes the polypeptide of claim 9.

11. The antibody of claim 10, wherein said antibody is polyclonal or monoclonal.

12. A non-human transgenic animal comprising the polynucleotide of any one of claims 1 to 3 or the vector of claim 4 or 5.

13. The non-human transgenic animal of claim 12, wherein the polynucleotide or vector is homologously recombined with an endogenous gene.

14. The non-human fransgenic animal of claim 12 or 13, wherein said animal is selected from the group consisting of monkey, cow, goat, sheep, dog, cat, rabbit, rat, mouse.

15. A pharmaceutical composition comprising the polynucleotide of any one of claims 1 to 3, the vector of claim 4 or 5, the host cell of any one of claims 6 to 8, the polypeptide of claim 9 or the antibody of claim 10 or 11.

16. Use of the polynucleotide of the polynucleotide of any one of claims 1 to 3, the vector of claim 4 or 5, the host cell of any one of claims 6 to 8, the polypeptide of claim 9 or the antibody of claim 10 or 11 for the preparation of a pharmaceutical composition to be applied in gene therapy.

17. A method for producing a polypeptide comprising a) culturing the host cell of any one of claims 6 to 8 further comprising a polynucleotide encoding the polypeptide to be produced operatively linked to a tet operator sequence; and b) isolating the polypeptide to be produced from said host cells or from the cell culture medium.

18. A method for regulating transcription of a tet operator-linked gene in a host cell comprising providing a host cell of any one of claims 6 to 8; and modulating the concentration of a tefracycline analog lacking a 4-dma grouping in contact with the host cell.

19. A method for producing a polynucleotide encoding a polypeptide which is specifically induced by a tefracycline analog lacking a 4-dma grouping comprising mutating the codons for amino acids 82 and 138 of the mutated Tet repressor H64K S135L.