KETOREDUCTASE GENE AND PROTEIN FROM YEAST

FIELD OF INVENTION

[0002] This invention relates to recombinant DNA technology. In particular the invention pertains to the generation and use of recombinant hosts harboring genetic mutations which provide for increased expression levels of a fungal ketoreductase polypeptide useful in bioenzymatic processes for the stereospecific reduction of ketones.

BACKGROUND OF THE INVENTION

[0003] 2,3 Benzodiazepine derivatives are potent antagonists of the AMPA (α-amino-3-hydroxy-5 methylisoxazole-4-propionic acid) class of receptors in the mammalian central nervous system (See I. Tarnawa et al. In Amino Acids: Chemistry, Biology and Medicine, Eds. Lubec and Rosenthal, Leiden, 1990). These derivative compounds have potentially widespread applications as neuroprotective agents, particularly as anti-convulsants. One series of 2,3 benzodiazepines is considered particularly advantageous for such use, and this series of compounds has the following general formula:

[0004] Wherein R is hydrogen or C1-C10 alkyl; and

[0005] X is hydrogen, C1-C10 alkyl, acyl, aryl, amido or carboxyl, or a substituted derivative thereof.

[0006] The clinical potential for these compounds has led to interest in developing more efficient synthetic methods. Biologically-based methods in which a ketoreductase enzyme provides a stereospecific reduction in a whole-cell process using fungal cells have been described in U.S. patent application Ser. No. 08/413,036. U.S. patent application Ser. No. 09/182,985 described the cloning of a ketoreductase gene from Z.rouxii, recombinant host cells that express the ketoreductase gene, and methods for stereospecifically reducing a ketone using either the recombinantly expressed ketoreductase or host cells expressing the cloned ketoreductase.

[0007] Maximizing expression levels of commercially important recombinantly expressed proteins is a common objective in the realm of biotechnology. Traditionally, protein properties have been modified by engineering changes in the DNA, mRNA, or polypeptide sequence based on a structural and/or functional understanding of that particular molecule, and testing for an improvement in the property which is being optimized. However, attempts to rationally alter one property of a recombinantly expressed polypeptide are often tedious, information intensive efforts. Additionally, these pursuits of a optimally expressed polypeptide often result in alterations which improve a targeted property at the expense of other important previously existing characteristics.

[0008] Recently, molecular “breeding” and directed evolution techniques have gained favor as methods of optimizing a particular protein's characteristics (Ness et al., (1999), DNA shuffling of subgenomic sequences of subtilisin, Nat. Biotechnol., 17 (9):893). Directed evolution procedures are typically used to make desired changes in the characteristics of a protein absent specific knowledge of the genetic sequence or protein structure which confers that characteristic to the molecule. Changes in enzyme specific activity, substrate specificity, thermal stability, chemical stability, and other properties have been successfully modified by this approach (see Ness, et al.). The procedure typically involves incorporating random mutations into a genetic sequence, and/or inducing random recombination between similar coding nucleotide sequences, and screening or selecting for altered but desirable phenotypes in hosts expressing the resulting mutations.

[0009] Subsequent to the selection of hosts exhibiting the desired or improved upon properties, sequence analysis often reveals that the mutated coding sequences contain a combination of missense and silent mutations. Backcrossing against the unmated wild type sequence is generally employed to remove mutations that do not contribute to the desired property of the protein and could potentially have detrimental effects on untargeted but desired properties of the original molecule. In at least one relevant example the expression level of an enzyme increased measurably as a result of mutations in the promoter region of a targeted gene (Stemmer et al., (1994), Rapid evolution of a protein in vitro by DNA shuffling, Nature 370:389-391). Back-crossing resulted in a protein having the same property as the best mutant after all four silent mutations had been reverted back to the wild type sequence. Likewise, Ness et. al. (J. E. Ness, et al., DNA shuffling of subgenomic sequences of subtilisin, Nature Biotechnology 17: 893-896, 1999) reported directed evolution experiments resulted in hosts having altered expression levels. Ness et al. suggested that this phenotype was likely attributable to recombination within the coding sequence which affected secretion or maturation of the expressed protein product.

[0010] The present invention provides a method of increasing the ability of a recombinant host cell to express an hetereologous polypeptide which is more efficient, and less labor and knowledge intensive than current methods. The present invention also provides for mutated ketoreductase encoding polynucleotides which are expressed in recombinant host cells at much greater levels than the wild-type polynucleotides.

BRIEF SUMMARY OF THE INVENTION

[0011] The present invention relates to increased expression of polypeptides. The present invention is based on the discovery that silent mutations within the coding region of a polynucleotide can have unexpected and profound effects upon the expression level of the polypeptide encoded thereby. Ketoreductase encoding polynucleotide sequences are disclosed which exhibit increased levels of expression of ketoreductase.

[0012] Accordingly, the present invention relates to an isolated DNA molecule encoding a ketoreductase enzyme from Z. rouxii, said DNA molecule comprising a nucleotide sequence identified as SEQ ID NO:1.

[0013] In particularly preferred embodiments the invention is directed to isolated DNA molecules encoding a ketoreductase protein, wherein said DNA molecules comprise any one of the polynucleotide sequences identified in SEQ ID NO:16.

[0014] Having the cloned ketoreductase encoding nucleic acid molecules enables the production of recombinant ketoreductase proteins, and the production of recombinant host cells expressing said proteins, wherein said recombinant cells can be used in a stereospecific reduction of ketones.

[0015] The invention also provides the protein products of said nucleic acids, in substantially purified form. Also provided are methods for the formation of chiral alcohols using a purified ketoreductase enzyme, or recombinant host cells that express said nucleic acid molecules.

[0016] In another embodiment the present invention relates to a substantially purified ketoreductase protein molecule from Z. rouxii.

[0017] In another embodiment the present invention relates to a ketoreductase protein molecule from Z. rouxii, wherein said protein molecule comprises the sequence identified as SEQ ID NO:2.

[0018] In particularly preferred embodiments the invention is directed to a ketoreductase protein molecule wherein said protein molecule comprises any one of the sequences identified in SEQ ID NO:17.

[0019] In a further embodiment the present invention relates to a ribonucleic acid molecule encoding ketoreductase protein, said ribonucleic acid molecule comprising the sequence identified as SEQ ID NO:3.

[0020] In particularly preferred embodiments the invention is directed to a ribonucleic acid molecule encoding ketoreductase protein, said ribonucleic acid molecule arising from the transcription of any one of the polynucleotide sequences identified in SEQ ID NO:16.

[0021] In yet another embodiment, the present invention relates to a recombinant DNA vector that incorporates a ketoreductase encoding polynucleotide of the present invention in operable-linkage to gene expression sequences, enabling said polynucleotide to be transcribed and translated in a host cell.

[0022] In still another embodiment the present invention relates to host cells that have been transformed or transfected with a recombinant DNA vector of the present invention such that said ketoreductase gene is expressed in the host cell.

[0023] In a still further embodiment, the present invention relates to a method for producing chiral alcohols using recombinant host cells that express an exogenously introduced ketoreductase gene of the present invention.

[0024] In yet another embodiment, the present invention relates to a method for producing chiral alcohols using recombinant host cells that have been transformed or transfected with a ketoreductase gene of the present invention derived from Z. rouxii, or S. cerevisiae.

[0025] In yet another embodiment, the present invention relates to a method for producing chiral alcohols using a purified fungal ketoreductase.

DETAILED DESCRIPTION OF THE INVENTION

Definitions

[0026] SEQ ID NO:1-SEQ ID NO:3 comprises the DNA, protein, and RNA sequences of ketoreductase from Z. rouxii.

[0027] SEQ ID NO:4-SEQ ID NO:6 comprises the DNA, protein, and RNA sequences of gene YDR541c from S. cerevisiae.

[0028] SEQ ID NO:7-SEQ ID NO:9 comprises the DNA, protein, and RNA sequences of YOL151w from S. cerevisiae.

[0029] SEQ ID NO:10-SEQ ID NO:12 comprises the DNA, protein, and RNA sequences of YGL157w from S. cerevisiae.

[0030] SEQ ID NO:13-SEQ ID NO:15 comprises the DNA, protein, and RNA sequences of YGL039w from S. cerevisiae.

[0031] SEQ ID NO:16-SEQ ID NO:17 comprises DNA and protein sequences, respectively, generated by directed evolution experiments targeting wild-type Z. rouxii ketoreductase which result in ketoreductase encoding polynucleotides which are expressed at higher levels than wild-type polynucleotides as identified in SEQ ID NO:1.

[0032] The term “fusion protein” denotes a hybrid protein molecule not found in nature comprising a translational fusion or enzymatic fusion in which two or more different proteins or fragments thereof are covalently linked on a single polypeptide chain.

[0033] The term “plasmid” refers to an extrachromosomal genetic element. The starting plasmids herein are either commercially available, publicly available on an unrestricted basis, or can be constructed from available plasmids in accordance with published procedures. In addition, equivalent plasmids to those described are known in the art and will be apparent to the ordinarily skilled artisan.

[0034] “Recombinant DNA cloning vector” as used herein refers to any autonomously replicating agent, including, but not limited to, plasmids and phages, comprising a DNA molecule to which one or more additional DNA segments can or have been added.

[0035] The term “recombinant DNA expression vector” or “expression vector” as used herein refers to any recombinant DNA cloning vector, for example a plasmid or phage, in which a promoter and other regulatory elements are present thereby enabling transcription of an inserted DNA.

[0036] The term “vector” as used herein refers to a nucleic acid compound used for introducing exogenous DNA into host cells. A vector comprises a nucleotide sequence which may encode one or more protein molecules. Plasmids, cosmids, viruses, and bacteriophages, in the natural state or which have undergone recombinant engineering, are examples of commonly used vectors.

[0037] The terms “complementary” or “complementarity” as used herein refers to the capacity of purine and pyrimidine nucleotides to associate through hydrogen bonding in double stranded nucleic acid molecules. The following base pairs are complementary: guanine and cytosine; adenine and thymine; and adenine and uracil. As used herein “complementary” means that at least one of two hybridizing strands is fully base-paired with the other member of said hybridizing strands, and there are no mismatches. Moreover, at each nucleotide position of said one strand, an “A” is paired with a “T”, a “T” is paired with an “A”, a “G” is paired with a “C”, and a “C” is paired with a “G”.

[0038] The term “conservative” in reference to an amino acid change or substitution is intended to indicate an amino acid has been replaced with a similar amino acid. Similar amino acids are amino acids that, because of size, charge, polarity and conformation, are more readily substituted without significantly affecting the structure and/or function of the protein. Thus, one skilled in the art generally does not expect a “conservative” amino acid change or substitution to result in any measurable difference in any particular characteristic, property, and/or activity of a polypeptide having a particular conservative amino acid substitution. Specific examples of amino acid changes or substitutions considered to be conservative are known in the art. These examples include, but are not limited to, the non-polar amino acids Glycine, Alanine, Valine, Isoleucine, and Leucine; the non-polar aromatic amino acids Phenylalanine, Tryptophan, and Tyrosine; the neutral polar amino acids Serine, Threonine, Cysteine, Glutamine, Asparagine, and Methionine; the negatively charged amino acids Lysine, Arginine, and Histidine; the positively charged amino acids Aspartate and Glutamate, represent groups of conservative amino acids. Substitution of any one for another in the same group would generally be considered to be a “conservative” substitution by one skilled in the art (See generally, James D. Watson et al., Molecular Biology of the Gene (1987)).

[0039] “Host cell” refers to any eucaryotic, procaryotic, or fusion or other cell or pseudo cell or membrane-containing construct that is suitable for propagating and/or expressing an isolated nucleic acid that is introduced into a host cell by any suitable means known in the art (e.g., but not limited to, transformation or transfection, or the like), or induced to express an endogenous nucleic acid encoding a polypeptide according to the present invention. The cell can be part of a tissue or organism, isolated in culture or in any other suitable form.

[0040] “Isolated nucleic acid compound” refers to any RNA or DNA sequence, however constructed or synthesized, which is locationally distinct from its natural location.

[0041] A “primer” is a nucleic acid fragment which functions as an initiating substrate for enzymatic or synthetic elongation of, for example, a nucleic acid molecule.

[0042] The term “promoter” refers to a DNA sequence which directs transcription of DNA to RNA. An inducible promoter is one that is regulatable by environmental signals, such as carbon source, heat, metal ions, chemical inducers, etc.; a constitutive promoter generally is expressed at a constant level and is not regulatable.

[0043] A “probe” as used herein is a labeled nucleic acid compound which can hybridize wih another nucleic acid compound.

[0044] The term “hybridization” as used herein refers to a process in which a single-stranded nucleic acid molecule joins with a complementary strand through nucleotide base pairing. “Selective hybridization” refers to hybridization under conditions of high stringency. The degree of hybridization depends upon, for example, the degree of complementarity, the stringency of hybridization, and the length of hybridizing strands.

[0045] The terms “silent mutation” and “silent substitution” are used interchangeably throughout the present specification and are intended to denote a change in the nucleotide sequence of a polypeptide encoding polynucleotide which does not result in a change in the amino acid sequence of the polypeptide encoded thereby.

[0046] “Substantially identical” means a sequence having sufficient homology to hybridize under stringent conditions and/or be at least 90% identical to a sequence disclosed herein.

[0047] The term “stringency” relates to nucleic acid hybridization conditions. High stringency conditions disfavor non-homologous base pairing. Low stringency conditions have the opposite effect. Stringency may be altered, for example, by changes in temperature, denaturants, and salt concentration. Typical high stringency conditions comprise hybridizing at 50° C. to 65° C. in 5× SSPE and 50% formamide, and washing at 50° C. to 65° C. in 0.5× SSPE; typical low stringency conditions comprise hybridizing at 35° C. to 37° in 5× SSPE and 40% to 45% formamide and washing at 42° C. in 1×-2× SSPE.

[0048] “SSPE” denotes a hybridization and wash solution comprising sodium chloride, sodium phosphate, and EDTA, at pH 7.4. A 20× solution of SSPE is made by dissolving 174 g of NaCl, 27.6 g of NaH2PO4.H2O, and 7.4 g of EDTA in 800 ml of H2O. The pH is adjusted with NaOH and the volume brought to 1 liter.

[0049] “SSC” denotes a hybridization and wash solution comprising sodium chloride and sodium citrate at pH 7. A 20× solution of SSC is made by dissolving 175 g of NaCl and 88 g of sodium citrate in 800 ml of H2O. The volume is brought to 1 liter after adjusting the pH with 10 N NaOH.

[0050] The term “transformed” refers to any process for altering the DNA content of a host cell. This includes in vitro transformation procedures such as calcium phosphate or DEAE-dextran-mediated transfection, electroporation, nuclear injection, phage infection, or such other means for effecting controlled DNA uptake as are known in the art.

[0051] The ketoreductase gene encodes a novel enzyme that catalyzes an asymmetric reduction of selected ketone substrates (See Equation 1 and Table 1). The ketoreductase enzymes disclosed herein are members of the carbonyl reductase enzyme class. Carbonyl reductases are involved in the reduction of xenobiotic carbonyl compounds (Hara et. al, Arch. Biochem. Biophys., 244, 238-247, 1986) and have been classified into the short-chain dehydrogenase/reductase (SDR) enzyme superfamily (Jörnvall et. al, Biochemistry, 34, 6003-6013, 1995) and the single-domain reductase-epimerase-dehydrogenase (RED) enzyme superfamily (Labesse et. al, Biochem. J., 304, 95-99, 1994).

[0052] The ketoreductases of this invention are able to effectively reduce a variety of α-ketolactones, α-ketolactams, and diketones (Table 1).

1TABLE 1Substrate specificity of wild-type ketoreductase fromZ. rouxii (SEQ ID NO: 2).Concen-%Concen-%trationRelativetrationRelativeCompound(mM)ActivityCompound(mM)Activity

3100

3194

518

0.886

542

0.617

437

5100

0.6 4

532

0.6 0

[0053] The ketoreductase gene of Z. rouxii comprises a DNA sequence designated herein as SEQ ID NO:1. Those skilled in the art will recognize that owing to the degeneracy of the genetic code (i.e. 64 codons which encode 20 amino acids), numerous “silent” substitutions or “silent” mutations of nucleotide base pairs could be introduced into the sequence identified as SEQ ID NO:1 without altering the identity of the encoded amino acid(s) or protein product as shown in SEQ ID NO:2. Although “silent” substitutions or “silent” mutations of a given polynucleotide sequence are “silent” as far as the identity of the encoded amino acid or protein product is concerned, such substitutions or mutations can confer advantageous attributes to hosts expressing the altered sequences. Preferred “silent” mutations of the present invention are those which result in increased expression, volumetric potency, enzymatic activity, and/or production levels as compared to an unaltered polynucleotide upon expression in a particular host. Polynucleotides incorporating at least one “silent” mutation which results in increased expression, volumetric potency, enzymatic activity, and/or production levels of a particular polypeptide are intended to be within the scope of this invention. Preferred mutant ketoreductase polynucleotides include variants of the polynucleotide as shown in SEQ ID NO:1 which result in increased expression, volumetric potency, enzymatic activity, and/or production levels of the encoded ketoreductase enzyme. Most preferred mutant Z. rouxii ketoreductase polynucleotides include variants of the polynucleotide as shown in SEQ ID NO:1 which result in increased expression, volumetric potency, enzymatic activity, and/or production levels of the encoded ketoreductase enzyme wherein the polynucleotide of SEQ ID NO: 1 further comprises at least one silent mutation selected from the group consisting of 307T, 382T, 469C, 574C, 574A, 649C, 733C, 838A, 862C, 868C, 871C, 889G, 910G, 974C, 1004C, 1024G, 1036C, and 1138C.

[0054] It is also known in the art that “silent” mutations may result in the creation of codons which are known in the art to be preferred by a host harboring and expressing said polynucleotides. Targeted mutagenesis directed towards incorporating specific “silent” mutations which create codons, selected from among alternative codons specifying the same amino acid, on the basis of preferential expression in the host microorganism (e.g., E. Coli) projected to be transformed is a well-known means of increasing expression levels of a targeted polypeptide (see U.S. Pat. No. 5,082,767 which is incorporated herein by reference). Furthermore, targeted “silent” mutations are often incorporated into a polynucleotide in order to relieve known secondary structures which are thought to impede translational processes for the purpose of increasing expression levels of a targeted polypeptide. Similarly, targeted “silent” mutations are often incorporated into a polynucleotide in order to decrease the susceptibility of the encoded mRNA to degradation which subsequently may lead to improved expression levels of the encoded polypeptide.

[0055] The untargeted, randomly generated “silent” mutations disclosed herein do not result in codons known to be preferred in E. coli nor would one skilled in the art expect them to result in altered secondary structure which would influence expression levels. Therefore, another embodiment of the present invention includes a method for effecting increased expression levels of a heterologous polypeptide, as well as any functional fragments thereof, in a recombinant. host which comprises the generation of “silent” mutations within a polynucleotide encoding a polypeptide wherein the said mutations are not directed towards incorporating codons known to be preferred by a particular host nor altering secondary structures to increase mRNA stability and/or expression levels.

[0056] Gene Isolation Procedures

[0057] Those skilled in the art will recognize that the ketoreductase gene may be obtained by a plurality of applicable recombinant DNA techniques including, for example, polymerase chain reaction (PCR) amplification, hybridization to a genomic or cDNA library, or de novo DNA synthesis.(See e.g., J. Sambrook et al. Molecular Cloning, 2d Ed. Chap. 14 (1989)).

[0058] Methods for constructing cDNA libraries in a suitable vector such as a plasmid or phage for propagation in procaryotic or eucaryotic cells are well known to those skilled in the art. [See e.g. J. Sambrook et al. Supra]. Suitable cloning vectors are widely available.

[0059] Skilled artisans will recognize that the ketoreductase gene or fragment thereof could be isolated by PCR amplification from a human cDNA library prepared from a tissue in which said gene is expressed, using oligonucleotide primers targeted to any suitable region of SEQ ID NO:1. Methods for PCR amplification are widely known in the art. See e.g. PCR Protocols: A Guide to Method and Application, Ed. M. Innis et.al., Academic Press (1990). The amplification reaction comprises template DNA, suitable enzymes, primers, nucleoside triphosphates, and buffers, and is conveniently carried out in a DNA Thermal Cycler (Perkin Elmer Cetus, Norwalk, Conn.). A positive result is determined by detecting an appropriately-sized DNA fragment following gel electrophoresis.

[0060] Protein Production Methods

[0061] One embodiment of the present invention relates to the substantially purified ketoreductase enzyme (identified herein as SEQ ID NO:2) encoded by the Z. rouxii ketoreductase gene (identified herein as SEQ ID NO:1).

[0062] Skilled artisans will recognize that the proteins of the present invention can be synthesized by a number of different methods, such as chemical methods well known in the art, including solid phase peptide synthesis or recombinant methods. Both methods are described in U.S. Pat. No. 4,617,149, incorporated herein by reference. The proteins of the invention can also be purified by well known methods from a culture of cells that produce the protein, for example, Z. rouxii.

[0063] The principles of solid phase chemical synthesis of polypeptides are well known in the art and may be found in general texts in the area. See, e.g., H. Dugas and C. Penney, Bioorganic Chemistry (1981) Springer-Verlag, N.Y., 54-92. For example, peptides may be synthesized by solid-phase methodology utilizing an Applied Biosystems 430A peptide synthesizer (Applied Biosystems, Foster City, Calif.) and synthesis cycles supplied by Applied Biosystems.

[0064] The protein of the present invention can also be produced by recombinant DNA methods using a cloned ketoreductase gene. Recombinant methods are preferred if a high yield is desired. Expression of the cloned gene can be carried out in a variety of suitable host cells, well known to those skilled in the art. For this purpose, the ketoreductase gene is introduced into a host cell by any suitable means, well known to those skilled in the art. While chromosomal integration of the cloned gene is within the scope of the present invention, it is preferred that the gene be cloned into a suitable extra-chromosomally maintained expression vector so that the coding region of the ketoreductase gene is operably-linked to a constitutive or inducible promoter.

[0065] The basic steps in the recombinant production of the ketoreductase protein are:

[0066] a) constructing a natural, synthetic or semi-synthetic DNA encoding a ketoreductase protein;

[0067] b) integrating said DNA into an expression vector in a manner suitable for expressing the ketoreductase protein, either alone or as a fusion protein; or integrating said DNA into a host chromosome such that said DNA expresses ketoreductase;

[0068] c) transforming or otherwise introducing said vector into an appropriate eucaryotic or prokaryotic host cell forming a recombinant host cell,

[0069] d) culturing said recombinant host cell in a manner to express the ketoreductase protein; and

[0070] e) recovering and substantially purifying the ketoreductase protein by any suitable means, well known to those skilled in the art.

[0071] The wild-type ketoreductase protein of Z. rouxii comprises a polypeptide designated herein as SEQ ID NO:1. Those skilled in the art will recognize that amino acid substitutions can be incorporated into the polypeptides of the present invention without altering the enzymatic activity of the molecule. Using well known theories, one skilled in the art can reasonably predict protein variants which are likely retain biological activity and those which are not. Specifically, conserved amino acid substitutions can be readily incorporated into the polypeptides of the present invention with the expectation that result expression levels, volumetric potency, enzymatic activity, and/or production levels will not be affected.

[0072] Polynucleotides which incorporate at least one conservative amino acid substitution and which result in increased expression, volumetric potency, enzymatic activity, and/or production levels of the encoded polypeptide upon expression in a host are intended to be within the scope of this invention. Preferred ketoreductase polypeptides include variants of the polypeptide as shown in SEQ ID NO:2 wherein said variants comprise at least one conservative amino acid subsitutions as compared to the polypeptide shown in SEQ ID NO:2. More preferred ketoreductase polypeptide variants include any one of the polypeptides as identified in SEQ ID NO:17. Most preferred ketoreductase polypeptide variants include those encoded by any one of the polynucleotides as identified in SEQ ID NO:16.

[0073] Expressing Recombinant Ketoreductase Protein in Procaryotic and Eucaryotic Host Cells

[0074] Procaryotes may be employed in the production of the ketoreductase protein. For example, the Escherichia coli K12 strain 294 (ATCC No. 31446) or strain RV308 is particularly useful for the prokaryotic expression of foreign proteins. Other strains of E. coli, bacilli such as Bacillus subtilis, enterobacteriaceae such as Salmonella typhimuriuin or Serratia marcescans, various Pseudomonas species and other bacteria, such as Streptomyces, may also be employed as host cells in the cloning and expression of the recombinant proteins of this invention.

[0075] Promoter sequences suitable for driving the expression of genes in procaryotes include •••-lactamase [e.g. vector pGX2907, ATCC 39344, contains a replicon and ••-lactamase gene], lactose systems [Chang et al., Nature (London), 275:615 (1978); Goeddel et al., Nature (London), 281:544 (1979)], alkaline phosphatase, and the tryptophan (trp) promoter system [vector pATH1 (ATCC 37695) which is designed to facilitate expression of an open reading frame as a trpE fusion protein under the control of the trp promoter]. Hybrid promoters such as the tac promoter (isolatable from plasmid pDR540, ATCC-37282) are also suitable. Still other bacterial promoters, whose nucleotide sequences are generally known, enable one of skill in the art to ligate such promoter sequences to DNA encoding the proteins of the instant invention using linkers or adapters to supply any required restriction sites. Promoters for use in bacterial systems also will contain a Shine-Dalgarno sequence operably linked to the DNA encoding the desired polypeptides. These examples are illustrative rather than limiting.

[0076] The protein(s) of this invention may be synthesized either by direct expression or as a fusion protein comprising the protein of interest as a translational fusion with another protein or peptide which may be removable by enzymatic or chemical cleavage. It is often observed in the production of certain peptides in recombinant systems that expression as a fusion protein prolongs the lifespan, increases the yield of the desired peptide, or provides a convenient means of purifying the protein. A variety of peptidases (e.g. enterokinase and thrombin) which cleave a polypeptide at specific sites or digest the peptides from the amino or carboxy termini (e.g. diaminopeptidase) of the peptide chain are known. Furthermore, particular chemicals (e.g. cyanogen bromide) will cleave a polypeptide chain at specific sites. The skilled artisan will appreciate the modifications necessary to the amino acid sequence (and synthetic or semi-synthetic coding sequence if recombinant means are employed) to incorporate site-specific internal cleavage sites. See e.g., P. Carter, “Site Specific Proteolysis of Fusion Proteins”, Chapter 13, in Protein Purification: From Molecular Mechanisms to Large Scale Processes, American Chemical Society, Washington, D.C. (1990).

[0077] In addition to procaryotes, a variety of eucaryotic microorganisms including yeast are suitable host cells. The yeast Saccharomyces cerevisiae is the most commonly used eucaryotic microorganism. Other yeasts such as Kluyveromyces lactis, Schizosaccharomyces pombe, and Pichia pastoris are also suitable. For expression in Saccharomyces, the plasmid YRp7 (ATCC-40053), for example, may be used. See, e.g., L. Stinchcomb, et al., Nature, 282:39 (1979); J. Kingsman et al., Gene, 7:141 (1979); S. Tschemper et. al., Gene, 10:157 (1980). Plasmid YRp7 contains the TRP1 gene which provides a selectable marker for use in a trp1 auxotrophic mutant.

[0078] Purification of Recombinantly-Produced Ketoreductase Protein

[0079] An expression vector carrying a cloned ketoreductase gene is transformed or transfected into a suitable host cell using standard methods. Host cells may comprise procaryotes, such as E. coli, or simple eucaryotes, such as Z. rouxii, S. cerevisiae, S. pombe, P. pastoris, and K. Lactis. Cells which contain the vector are propagated under conditions suitable for expression of an encoded ketoreductase protein. If the recombinant gene has been placed under the control of an inducible promoter then suitable growth conditions would incorporate the appropriate inducer. The recombinantly-produced protein may be purified from cellular extracts of transformed cells by any suitable means.

[0080] In a preferred process for protein purification, the ketoreductase gene is modified at the 5′ end to incorporate several histidine residues at the amino terminus of the ketoreductase protein product. This “histidine tag” enables a single-step protein purification method referred to as “immobilized metal ion affinity chromatography” (IMAC), essentially as described in U.S. Pat. No. 4,569,794 which hereby is incorporated by reference. The IMAC method enables rapid isolation of substantially pure ketoreductase protein starting from a crude cellular extract.

[0081] Other embodiments of the present invention comprise isolated nucleic acid sequences which encode SEQ ID NO:2. As skilled artisans will recognize, the amino acid compounds of the invention can be encoded by a multitude of different nucleic acid sequences because most of the amino acids are encoded by more than one codon. Because these alternative nucleic acid sequences would encode the same amino acid sequences, the present invention further comprises these alternate nucleic acid sequences.

[0082] The ketoreductase genes disclosed herein, for example SEQ ID NO:1, may be produced using synthetic methodology. The synthesis of nucleic acids is well known in the art. See, e.g., E. L. Brown, R. Belagaje, M. J. Ryan, and H. G. Khorana, Methods in Enzymology, 68:109-151 (1979). A DNA segment corresponding to a ketoreductase gene could be generated using a conventional DNA synthesizing apparatus, such as the Applied Biosystems Model 380A or 380B DNA synthesizers (Applied Biosystems, Inc., 850 Lincoln Center Drive, Foster City, Calif. 94404) which employ phosphoramidite chemistry. Alternatively, phosphotriester chemistry may be employed to synthesize the nucleic acids of this invention. [See, e.g., M. J. Gait, ed., Oligonucleotide Synthesis, A Practical Approach, (1984).]

[0083] In an alternative methodology, namely PCR, a DNA sequence comprising a portion or all of SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:7, SEQ ID NO:10, or SEQ ID NO:13 can be generated from a suitable DNA source, for example Z. rouxii or S. cerevisiae genomic DNA or cDNA. For this purpose, suitable oligonucleotide primers targeting any of the polynucleotides identified in SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:7, SEQ ID NO:10, SEQ ID NO:13, SEQ ID NO: 16, or any region therein are prepared, as described in U.S. Pat. No. 4,889,818, which hereby is incorporated by reference. Protocols for performing the PCR are disclosed in, for example, PCR Protocols: A Guide to Method and Applications, Ed. Michael A. Innis et al., Academic Press, Inc. (1990).

[0084] Procedures for generating random mutations in a targeted DNA or cDNA molecule are known to one skilled in the art. These procedures may include, but are not limited to, techniques such as those described hereinafter which rely on PCR performed under conditions favorable for mutagenesis of the resulting polynucleotide product.

[0085] The ribonucleic acids of the present invention may be prepared using the polynucleotide synthetic methods discussed supra, or they may be prepared enzymatically using RNA polymerase to transcribe a ketoreductase DNA template. See e.g., J. Sambrook, et. al., supra, at 18.82-18.84.

[0086] This invention also provides nucleic acids, RNA or DNA, which are complementary to SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:15, or any of the polynucleotides identified in SEQ ID NO:16.

[0087] The present invention also provides probes and primers useful for a variety of molecular biology techniques including, for example, hybridization screens of genomic, subgenomic, or cDNA libraries. A nucleic acid compound comprising SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:15, any of the polynucleotides identified in SEQ ID NO:16, any complementary sequence thereof, or a fragment thereof, which is at least 18 base pairs in length, and which will selectively hybridize to DNA encoding a ketoreductase, is provided. Preferably, the 18 or more base pair compound is DNA. See e.g. B. Wallace and G. Miyada, “Oligonucleotide Probes for the Screening of Recombinant DNA Libraries,” In Methods in Enzymology, Vol. 152, 432-442, Academic Press (1987).

[0088] Probes and primers can be prepared by enzymatic methods well known to those skilled in the art (See e.g. Sambrook et al. supra). In a most preferred embodiment these probes and primers are synthesized using chemical means as described above.

[0089] Another aspect of the present invention relates to recombinant DNA cloning vectors and expression vectors comprising the nucleic acids of the present invention. The preferred nucleic acid vectors are those which comprise DNA. The most preferred recombinant DNA vectors comprise a isolated DNA sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:7, SEQ ID NO:10, SEQ ID NO:13, and any of the polynucleotides as shown in SEQ ID NO:16.

[0090] The skilled artisan understands that choosing the most appropriate cloning vector or expression vector depends upon a number of factors including the availability of restriction enzyme sites, the type of host cell into which the vector is to be transfected or transformed, the purpose of the transfection or transformation (e.g., stable transformation as an extrachromosomal element, or integration into the host chromosome), the presence or absence of readily assayable or selectable markers (e.g., antibiotic resistance and metabolic markers of one type and another), and the number of copies of the gene to be present in the host cell.

[0091] Vectors suitable to carry the nucleic acids of the present invention comprise RNA viruses, DNA viruses, lytic bacteriophages, lysogenic bacteriophages, stable bacteriophages, plasmids, viroids, and the like. The most preferred vectors are plasmids.

[0092] When preparing an expression vector the skilled artisan understands that there are many variables to be considered, for example, whether to use a constitutive or inducible promoter. Inducible promoters are preferred because they enable high level, regulatable expression of an operably-linked gene. Constitutive promoters are further suitable in instances for which secretion or extra-cellular export is desireable. The skilled artisan will recognize a number of inducible promoters which respond to a variety of inducers, for example, carbon source, metal ions, and heat. The practitioner also understands that the amount of nucleic acid or protein to be produced dictates, in part, the selection of the expression system. The addition of certain nucleotide sequences is useful for directing the localization of a recombinant protein. For example, a sequence encoding a signal peptide preceding the coding region of a gene, is useful for directing the extra-cellular export of a resulting polypeptide.

[0093] Host cells harboring the nucleic acids disclosed herein are also provided by the present invention. Suitable host cells include procaryotes, such as E. coli, or simple eucaryotes, such as fungal cells, which have been transfected or transformed with a vector which comprises a nucleic acid of the present invention.

[0094] The present invention also provides a method for constructing a recombinant host cell capable of expressing SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, SEQ ID NO:14, or any of the polypeptides as shown in SEQ ID NO:17 said method comprising transforming or otherwise introducing into a host cell a recombinant DNA vector that comprises an isolated DNA sequence which encodes SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, SEQ ID NO:14, or any of the polynucleotides as shown in SEQ ID NO:16. Preferred vectors for expression are those which comprise SEQ ID NO:1 or any of the polynucleotides as shown in SEQ ID NO:16. Transformed host cells may be cultured under conditions well known to skilled artisans such that SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, SEQ ID NO:14, or any one of the polypeptides as shown in SEQ ID NO:17 is expressed, thereby producing a ketoreductase protein in the recombinant host cell.

[0095] For the purpose of identifying or developing inhibitors or other modifiers of the enzymes disclosed herein, or for identifying suitable substrates for bioconversion, it would be desirable to identify compounds that bind and/or inhibit, or otherwise modify, the ketoreductase enzyme and its associated activity. A method for determining agents that will modify the ketoreductase activity comprises contacting the ketoreductase protein with a test compound and monitoring the alteration of enzyme activity by any suitable means.

[0096] The instant invention provides such a screening system useful for discovering compounds which bind the ketoreductase protein, said screening system comprising the steps of:

[0097] a) preparing ketoreductase protein;

[0098] b) exposing said ketoreductase protein to a test compound;

[0099] c) quantifying a modulation of activity by said compound.

[0100] Utilization of the screening system described above provides a means to determine compounds which may alter the activity of ketoreductase. This screening method may be adapted to automated procedures such as a PANDEX® (Baxter-Dade Diagnostics) system, allowing for efficient high-volume screening of potential modifying agents.

[0101] In such a screening protocol, ketoreductase is prepared as described herein, preferably using recombinant DNA technology. A test compound is introduced into a reaction vessel containing ketoreductase, followed by addition of enzyme substrate. For convenience the reaction can be coupled to the oxidation of NADPH, thereby enabling progress to be monitored spectrophotometrically by measuring the absorbance at 340 nm. Alternatively, substrate may be added simultaneously with a test compound. In one method radioactively or chemically-labeled compound may be used. The products of the enzymatic reaction are assayed for the chemical label or radioactivity by any suitable means. The absence or diminution of the chemical label or radioactivity indicates the degree to which the reaction is inhibited.

[0102] The following examples more fully describe the present invention. Those skilled in the art will recognize that the particular reagents, equipment, and procedures described are merely illustrative and are not intended to limit the present invention in any manner.

EXAMPLE 1

[0103] Construction of a DNA Vector for Expressing a Ketoreductase Gene in a Homologous or Heterologous Host

[0104] A plasmid comprising the Z. rouxii ketoreductase gene suitable for expressing said gene in a host cell, for example E. coli (DE3) strains, contains an origin of replication (Ori), an antibiotic resistance gene (i.e., Tet or Amp), useful for selecting cells which have incorporated the vector following a tranformation procedure, and further comprises the laci gene for repression of the lac operon, as well as the T7 promoter and T7 terminator sequences in operable linkage to the coding region of the ketoreductase gene. Parent plasmid pET11A (obtained from Novogen, Madison, Wis.) was linearized by digestion with endonucleases NdeI and BamHI. Linearized pET11A was ligated to a DNA fragment bearing NdeI and BamHI sticky ends and further comprising the coding region of the Z. rouxii ketoreductase gene.

[0105] The ketoreductase gene is isolated most conveniently by the PCR. Genomic DNA from Z. rouxii isolated by standard methods was used for amplification of the ketoreductase gene. Primers are synthesized corresponding to the 5′ and 3′ ends of the gene (SEQ ID NO:1) to enable amplification of the coding region.

[0106] The ketoreductase gene (nucleotides 164 through 1177 of SEQ ID NO:1) ligated into the vector may be modified at the 5′ end (amino terminus of encoded protein) in order to simplify purification of the encoded ketoreductase protein. For this purpose, an oligonucleotide encoding 8 histidine residues and a factor Xa cleavage site can be inserted after the ATG start codon at nucleotide positions 164 to 166 of SEQ ID NO:1. Placement of the histidine residues at the amino terminus of the encoded protein does not affect its activity and serves only to enable the IMAC one-step protein purification procedure.

[0107] For expression analysis in E. coli, recombinant plasmid DNA containing the complete Z. rouxii cDNA was digested with Nde I-Bam HI to release a 1.0-kb fragment. This fragment was then directly cloned into an expression vector (PHMM 176 (rop-)) downstream of the T7 promoter to produce pHRP2 that was transformed into E. coli RQ228 cells for protein production. Transformed RQ228 host cells were grown overnight at 37° C. in LB medium containing tetracycline (12.5 μg/mL), diluted, and induced at an OD600 of 0.6-0.8 in 50-mL LB medium plus 100 μM IPTG for 2-4 hrs. Extraction of ketoreductase enzyme from bacteria was performed using 3-mL B-PER reagent (Pierce, Rockland, Ill.) per bacterial pellet. The lysate was cleared by centrifugation at 15,000 rpm for 15 min.

EXAMPLE 2

[0108] Purification of Ketoreductase from Z. rouxii

[0109] Approximately 1 gram of Z. rouxii cell paste was resuspended in Lysing Buffer, comprising 50 mM Tris-Cl pH 7.5, 2 mM EDTA supplemented with pepstatin (1 μg/mL), leupeptin (1.25 μg/mL), aprotinin (2.5 μg/mL), and AEBSF (25 pg/mL). The cells were lysed using a DynoMill (GlenMills, Inc. Clifton, N.J.) equipped with 0.5-0.75 mm lead free beads under continuous flow conditions according to the manufacturer's recommended use. After four complete passes through the DynoMill, the material was centrifuged twice (25,000×g for 30 minutes at 4° C.). Solid ammonium sulfate (291 g/liter) was added slowly to the resulting clarified cell extract with stirring at 4° C. to achieve 50% saturation. After 1 hour, the mixture was centrifuged at 23,000×g for 30 minutes. The supernatant was then brought to 85% saturation by the addition of solid ammonium sulfate (159 g/liter) and stirred for 1 h at 4° C. before centrifugation (23,000×g for 30 min). The resultant 50-85% ammonium sulfate pellet was resuspended in 600 mL of Lysing Buffer and the residual ammonium sulfate was removed by dialysis against the same buffer at 4° C. The desalted material was centrifuged twice to remove particulate matter (23,000×g for 30 min) and 700-800 Units of the clarified material was loaded onto a Red-120 dye affinity column (32 mm×140 mm) equilibrated in 50 mM Tris-Cl pH 7.5, 1 mM MgCl2, pepstatin (1 μg/mL), leupeptin (1.25 μg/mL), and aprotinin (2.5 μg/mL). Reductase activity was eluted from the column at a flowrate of 8 mL/min under the following conditions: 1) a 10 minute linear gradient from 0-0.3 M NaCl; 2) 13 minutes at 0.3 M NaCl; 3) a 60 minute linear gradient from 0.3-1.5 M NaCl. The fractions containing reductase activity were pooled, and changed to 20 mM potassium phosphate buffer (pH 7.2), pepstatin (1 μg/mL), leupeptin (1.25 μg/mL), and aprotinin (2.5 μg/mL) by dialysis at 4° C. The sample was clarified by centrifugation (23,000×g for 30 min) and 400 Units was loaded onto a Bio-Scale CHT-I hydroxyapatite column (15 mm×113 mm, Bio-Rad, Inc.) equilibrated in the same buffer that had been made 5% in glycerol. Reductase activity was eluted from the column at a flowrate of 5.0 mL/min in a sodium chloride step gradient consisting of 5 minutes at 0 M NaCl, a gradient step to 0.7 M NaCl which was maintained for 10 minutes, and then a 20 minute linear gradient from 0.7-1.0 M NaCl. The fractions containing reductase activity were pooled and desalted with 20 mM potassium phosphate buffer (pH 7.2), pepstatin A (1 μg/mL), leupeptin (1.25 μug/mL), and aprotinin (2.5 μg/mL) by dialysis at 4° C. The sample (100-200 Units) was loaded onto a Bio-Scale CHT-I hydroxyapatite column (10 mm×64 mm) equilibrated in the same buffer which had been made 5% in glycerol. Reductase activity was eluted from the column at a flowrate of 2.0 mL/min in a 25 minute linear gradient from 0 to 50% 400 mM potassium phosphate (pH 6.8), 5% glycerol. Fractions containing reductase activity were pooled and changed into 10 mM Tris-Cl (pH 8.5) by dialysis at 4° C. The sample was then made 10% in glycerol, concentrated to 0.4 mg/mL by ultrafiltration (Amicon, YM-10), and stored at −70° C.

EXAMPLE 3

[0110] Reductase Activity Using the Ketoreductase from Z. rouxii

[0111] Reductase activity was measured using a suitable substrate and a partially purified or substantially purified ketoreductase from Z. rouxii. Activity was measured as a function of the absorbance change at 340 nm, resulting from the oxidation of NADPH. The 1 ml assay contained a mixture of 3.0 mM 3,4-methylenedioxyphenyl acetone, 162 μM NADPH, 50 mM MOPS buffer (pH 6.8), and 0.6 mU of ketoreductase and was carried out at 26° C. Reaction mixtures were first equilibrated at 26° C. for 10 min in the absence of NADPH, and then initiated by addition of NADPH. The absorbance was measured at 340 nm every 15 seconds over a 5 minute period; the change in absorbance was found to be linear over that time period. The kinetic parameters for 3,4-methylenedioxyphenyl acetone were determined at an NADPH concentration of 112 μM and a 3,4-methylenedioxyphenyl acetone concentration that varied from 1.7 mM -7.2 mM. The kinetic parameters for NADPH were determined by maintaining the 3,4-methylenedioxyphenyl acetone concentration at 3 mM and the NADPH concentration was varied from 20.5 μM-236.0 μM. An extinction coefficient of 6220 M−1 cm−1 for NADPH absorbance at 340 nm was used to calculate the specific activity of the enzyme. For assays using isatin, the change in absorbance with time was measured at 414 nm using an extinction coefficient of 849 M−1 cm−1 to calculate activity. One Unit of activity corresponds to 1 μmol of NADPH consumed per minute. For assays carried out at differing pH values, 10 mM Bis-Tris and 10 mM Tris were adjusted to the appropriate pH with HCl. Kinetic parameters were determined by non-linear regression using the JMP® statistics and graphics program.

[0112] The ketoreductase assay of recombinant E. coli expressed ketoreductase was performed as described above with only slight modifications. Specifically, 100 μl crude extracts of recombinant E. coli expressed ketoreductase in 1-mL volumes containing 3 mM of 1 and 50 mM MOPS (pH 6.8) were equilibrated at room temperature for 5 min. Reactions were then initiated by addition of 5 mg NADPH. Following a 1-hr incubation at 37° C., reaction mixtures were extracted against mobile phase before being analyzed by HPLC.

EXAMPLE 4

[0113] Whole Cell Method for Stereoselective Reduction of Ketone Using Recombinant Yeast Cell

[0114] A vector for expressing the cloned Z. rouxii ketoreductase gene (SEQ ID NO:1) in a procaryotic or fungal cell, such as S. cerevisiae, is constructed as follows. A 1014 base pair fragment of Z rouxii genomic DNA or cDNA, carrying the ketoreductase gene, is amplified by PCR using primers targeted to the ends of the coding region specified in SEQ ID NO:1. It is desireable that the primers also incorporate suitable cloning sites for cloning of said 1014 base pair fragment into an expression vector. The appropriate fragment encoding ketoreductase is amplified and purified using standard methods, for cloning into an expression vector.

[0115] A suitable vector for expression in E. coli and S. cerevisiae is pYX213 (available from Novagen, Inc., 597 Science Drive, Madison, Wis. 53711; Code MBV-029-10), a 7.5 Kb plasmid that carries the following genetic markers: ori, 2μ circle, AmpR, CEN, URA3, and the GAL promoter, for high level expression in yeast. Downstream of the GAL promoter, pYX213 carries a multiple cloning site (MCS), which will accommodate the ketoreductase gene amplified in the preceding step. A recombinant plasmid is created by digesting pYX213 and the amplified ketoreductase gene with a restriction enzyme, such as BamHI, and ligating the fragments together.

[0116] A recombinant fungal expression vector carrying the Z. rouxii ketoreductase gene is transformed into a suitable Ura− strain of S. cerevisiae, using well known methods. Ura+ transformants are selected on minimal medium lacking uracil.

[0117] Expression of the recombinant ketoreductase gene may be induced if desired by growing transformants in minimal medium that contains 2% galactose as the sole carbon source.

[0118] To carry out a whole cell stereospecific reduction, 3,4-methylenedioxyphenyl acetone is added to a culture of transformants to a concentration of about 10 grams per liter of culture. The culture is incubated with shaking at room temperature for 24 hours, and the presence of the chiral alcohol analyzed by HPLC.

EXAMPLE 5

[0119] Mutagenesis of wild-type Z. rouxii ketoreductase encoding cDNA sequence to generate recombinant E. Coli transformants exhibiting greater Z. rouxii ketoreductase volumetric potency activity

[0120] Primers RP001 and RP004 (having the nucleotide sequences ttaattaagcggccgccatatgacaaaagtcttcgtaacaggtgccaac and ttaattaagcggccgcggatcctattatttttttccatttttaacggac, respectively) were used to amplify under mutagenic PCR conditions a 1060 bp DNA fragment. PCR was performed under the following conditions: 5 ng template (plasmid DNA containing the wild-type Z. rouxii ketoreductase gene sequence prepared from a dam-positive E. Coli strain (DH5α), 10 mM Tris-HCl (pH 8.3 at 25° C.), 50 mM KCl, 7 mM MgCl2, 0.01% (w/v) gelatin, 0.15 mM MnCl2, 0.2 mM each of DATP and dGTP, 1.0 mM each of dCTP and dTTP, 0.3 μm of each primer, and 5 U Taq DNA polymerase (Promega) in a 100 μl final reaction volume. Cycling protocol: 94° C. for 2′, 13 cycles of 94° C. 1′, 50° C. 1′, 72° C. 1′, followed by 72° C. for 2′ and a 4° C. soak in a Perkin-Elmer 9600 Thermocycler (Perkin-Elmer, Foster City, Calif.). No template and no primer controls were included.

[0121] The StEP procedure was performed essentially as described by Zhao et al. (Zhao et al., Molecular evolution by staggered extension process (StEP) in vitro recombination. Nature Biotechnol. 16, 258-261 (1998)). Briefly, 5 μl of 1:10 diluted mutagenized template DNA, 10 mM Tris-HCl (pH 9.0 at 25° C.), 50 mM KCl, 1.5 mM MgCl2, 0.2 mM each dNTPs, 0.06 μM each of RP001 and RP004 primers, and 2.5 U Taq DNA polymerase (Promega) in a 50 μl final reaction volume. Cycling conditions: 94° C. for 2′, 90 cycles of 94° C. 30″, 55° C. 15″, followed by a 4° C. soak using a Perkin-Elmer 9600 Thermocycler. No template and no primer controls were included. Reaction products were electrophoresied in a 0.8% agarose gel. A discrete band of the correct size (approximately 1 kb) was band isolated from a smear of DNA fragments. DNA was purified away from agarose using GeneClean II (Bio 101, Vista, Calif.) and digested with Dpn I. In order to amplify the full-length product, standard PCR was then performed. Reaction conditions included: 1 μl (100 ng/μl) Dpn I digested StEP DNA, 10 mM Tris-HCl (pH 8.3 at 25° C.), 50 mM KCl, 1.5 mM MgCl2, 10% DMSO or 10% glycerol (included sometimes to enhance PCR), 0.2 mM each dNTPs, 0.5 each of RP001 and RP004 primers, and 2.5 U Taq DNA polymerase (Perkin-Elmer) in a 100 μl final reaction volume. Cycling conditions: 94° C. 2′, 30 cycles of 94° C. 30″, 55° C. 30″, 72° C. 1′, followed by 72° C. for 2′ and a 4° C. soak.

[0122] The PCR-amplified, reassembled product was purified using the QIAquick PCR purification kit (Qiagen, Chatsworth, Calif.), restriction-digested with Nde I and Bam HI, followed by gel electrophoresis in a 0.8% agarose gel. The DNA band of the correct size was isolated and purified using the QIAquick gel extraction kit (Qiagen). Purified digested DNA products were ligated with vector generated by Nde I-Bam HI digestion of the pHMM176 expression vector. The resultant gene library was amplified in E. coli DH5α and transferred into E. coli RQ228 competent cells. 1056 clones were picked and each was grown in 100 μl L-broth medium supplemented with 12.5 μg/μl tetracycline in twelve 96-well plates. Following overnight growth, the 96-well plate library was replicated to provide a working library. Glycerol to 17.5% was added t.o both libraries and the libraries were stored at −70° C.

[0123] To identify ketoreductase variants, a 96-well plate-screening assay was developed based on a scale down of the UV assay described in Example 3. Briefly, the working library described previously was replicated into 12 96-well plates containing 1 ml L-broth medium supplemented with 12.5 μg/μl tetracycline. From each well of the IPTG-induced/B-PER extracted 96-well plate, 10 μl of cellular extract was transferred to the corresponding wells of two new plates (library screened in duplicate, 24 plates total). To each well of the new plate was then added 60 μl of 50 mM MOPS (pH 6.8) plus 60 μl of 10 mM 3,4-methylene dioxyphenyl acetone (3 mM final concentration). Following a 10-min incubation at room temperature, the reaction was initiated by adding 70 μl of 571 μM NADPH (final concentration 200 μM). Ketoreductase activity was monitored in a 96-well plate reader (SPECTRAmax® Plus, Molecular Devices) at OD340 every 15 sec for 10 min. A Biomek® 2000 Workstation was utilized to add/mix reagents to the 96-well plates. Sixteen out of 1056 clones screened showed improved ketoreductase activity. Activity was confirmed by assaying these sixteen (10 replicas for each clone) for activity against the substrate 3,4-methylenedioxyphenyl acetone. Out of the sixteen, nine variants exhibited statistically significant higher potency than parental control. These variants exhibited 1.8 to 14.9-fold greater volumetric potency than the parental control (see Tables 2 and 3).

2TABLE 2Mutation ProfileMutation Frequency:0.28%(46)Mutation Bias:Location:A or T: 76%(35)G or C 24%(11)Transitions: 70%(32)Transversions: 30%(14)Mutation Types:Silent:28.3%(13)Missense:67.4%(31)Nonsense: 4.3% (2)Clones Screened: 100%(1056) Variants = Control Activity 11%(113) Variants > Control Activity 3%(30)Variants < Control Activity 86%(913)

[0124]

3

TABLE 3

Effects of DNA and Amino Acid Substitutions on Volumetric Potency of Ketoreductase Expression

Nucleotide

Codon
Amino Acid
Amino Acid

Mutant
Position*
Mutation
Position
Position**
Substitution
Fold improvement1
Stat. confidence2

7E8
574
T to C
3
137
silent
14.9
99.96%

733
T to C
3
190
silent

862
T to C
3
233
silent

1008
A to G
2
282
Lys to Arg

4D4
382
A to T
3
73
silent
11.3
99.99

740
A to G
1
193
Ile to Val

910
A to G
3
249
silent

8C5
469
T to C
3
102
silent
8.3
99.6

871
T to C
3
236
silent

1036
T to C
3
291
silent

7E10
307
A to T
3
48
silent
8.0
99.95

649
T to C
3
162
silent

913
T to C
3
250
Asn to Lys

5H3
889
A to G
3
242
silent
6.2
99.74

1138
T to C
3
325
silent

1C5
868
T to C
3
235
silent
5.7
99.67

8D12
574
T to A
3
137
silent
4.0
99.32

838
T to A
3
225
silent

5C4
1004
T to C
1
281
silent
3.8
98.9

1008
A to G
2
282
Lys to Arg

8F5
896
A to G
1
245
Ile to Val
1.8
97.69

974
T to C
1
271
silent

1024
T to G
3
287
silent

*in reference to SEQ ID NO: 1

**in reference to SEQ ID NO: 2

1
ketoreductase activity as compared to control (host expressing SEQ ID NO: 1).

2
statistical confidence that host carrying mutant sequence shows volumetric potency different from control (wild-type).

[0125]

	Number	Date	Country
Parent	09182985	Oct 1998	US
Child	09415277	Oct 1999	US

KETOREDUCTASE GENE AND PROTEIN FROM YEAST

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