Compositions and methods for taxol biosynthesis

Abstract

The taxadiene synthase gene of Pacific yew has been cloned and its nucleic acid and polypeptide sequence is presented. Truncation or removal of the transit peptide increases expression of the cloned taxadiene synthase gene expression in E. coli cells.

Description

TECHNICAL FIELD

This invention is related to the field of detection of diterpenoid biosynthesis, particularly to the biosynthesis of taxoid compounds such as Taxol.

BACKGROUND ART

The highly functionalized diterpenoid Taxol (Wani et al., J. Am. Chem. Soc. 93:2325-2327, 1971) is well-established as a potent chemotherapeutic agent (Holmes et al., in Taxane Anticancer Agents: Basic Science and Current Status, Georg et al., eds., pp. 31-57, American Chemical Society, Washington, D.C., 1995; Arbuck and Blaylock, in Taxol: Science and Applications, Suffness, ed., pp. 379-415, CRC Press, Boca Raton, Fla., 1995). (Paclitaxel is the generic name for Taxol, a registered trademark of Bristol-Myers Squibb.)

The supply of Taxol from the original source, the bark of the Pacific yew (Taxus brevifolia Nutt.; Taxaceae) is limited. As a result, there have been intensive efforts to develop alternate means of production, including isolation from the foliage and other renewable tissues of plantation-grown Taxus species, biosynthesis in tissue culture systems, and semisynthesis of Taxol and its analogs from advanced taxane diterpenoid (taxoid) metabolites that are more readily available (Cragg et al., J. Nat. Prod. 56:1657-1668, 1993). Total synthesis of Taxol, at present, is not commercially viable (Borman, Chem. Eng. News 72(7):32-34, 1994), and it is clear that in the foreseeable future the supply of Taxol and its synthetically useful progenitors must rely on biological methods of production, either in Taxus plants or in cell cultures derived therefrom (Suffness, in Taxane Anticancer Agents: Basic Science and Current Status, Georg et al., eds., American Chemical Society, Washington, D.C., 1995, pp. 1-17).

The biosynthesis of Taxol involves the initial cyclization of geranylgeranyl diphosphate, the universal precursor of diterpenoids (West, in Biosynthesis of Isoprenoid Compounds, Porter and Spurgeon, eds., vol. 1, pp. 375-411, Wiley & Sons, New York, N.Y., 1981), to taxa-4(5),11(12)-diene (Koepp et al., J. Biol. Chem. 270:8686-8690, 1995) followed by extensive oxidative modification of this olefin (Koepp et al., J. Biol. Chem. 270:8686-8690, 1995; Croteau et al., in Taxane Anticancer Agents: Basic Science and Current Status, Georg et al., eds., pp. 72-80, American Chemical Society, Washington, D.C., 1995) and elaboration of the side chains (FIG. 1) (Floss and Mocek, in Taxol: Science and Applications, Suffness, ed., pp. 191-208, CRC Press, Boca Raton, Fla., 1995).

Taxa-4(5),11(12)-diene synthase ("taxadiene synthase"), the enzyme responsible for the initial cyclization of geranylgeranyl diphosphate, to delineate the taxane skeleton, has been isolated from T. brevifolia stem tissue, partially purified, and characterized (Hezari et al., Arch. Biochem. Biophys. 322:437-444, 1995).

Although taxadiene synthase resembles other plant terpenoid cyclases in general enzymatic properties (Hezari et al., Arch. Biochem. Biophys. 322:437-444, 1995), it has proved extremely difficult to purify in sufficient amounts for antibody preparation or microsequencing, thwarting this approach toward cDNA cloning.

SUMMARY OF THE INVENTION

We have cloned and sequenced the taxadiene synthase gene of Pacific yew.

One embodiment of the invention includes isolated polynucleotides comprising at least 15 consecutive nucleotides, preferably at least 20, more preferably at least 25, and most preferably at least 30 consecutive nucleotides of a native taxadiene synthase gene, e.g., the taxadiene synthase gene of Pacific yew. Such polynucleotides are useful, for example, as probes and primers for obtaining homologs of the taxadiene synthase gene of Pacific yew by, for example, contacting a nucleic acid of a taxoid-producing organism with such a probe or primer under stringent hybridization conditions to permit the probe or primer to hybridize to a taxadiene synthase gene of the organism, then isolating the taxadiene synthase gene of the organism to which the probe or primer hybridizes.

Another embodiment of the invention includes isolated polynucleotides comprising a sequence that encodes a polypeptide having taxadiene synthase biological activity. Preferably, the polypeptide-encoding sequence has at least 70%, preferably at least 80%, and more preferably at least 90% nucleotide sequence similarity with a native Pacific yew taxadiene synthase polynucleotide gene.

In preferred embodiments of such polynucleotides, the polypeptide-encoding sequence encodes a polypeptide having only conservative amino acid substitutions to the native Pacific yew taxadiene synthase polypeptide, except, in some embodiments, for amino acid substitutions at one or more of: cysteine residues 329, 650, 719, and 777; histidine residues 370, 415, 579, and 793; a DDXXD motif (SEQ ID NO:3); a DXXDD motif (SEQ ID NO:4); a conserved arginine; and a RWWK element (SEQ ID NO:1 and SEQ ID NO:2). Preferably, the encoded polypeptide has only conservative amino acid substitutions to or is completely homologous with the native Pacific yew taxadiene synthase polypeptide. In addition, the encoded polypeptide preferably lacks at least part of the transit peptide. Also included are cells, particularly plant cells, and transgenic plants that include such polynucleotides and the encoded polypeptides.

Another embodiment of the invention includes isolated polypeptides having taxadiene synthase activity, preferably having at least 70%, more preferably at least 80%, and most preferably at least 90% homology with a native taxadiene synthase polypeptide. Also included are isolated polypeptides that comprise at least 10, preferably at least 20, more preferably at least 30 consecutive amino acids of a native Pacific yew taxadiene synthase, and most preferably the mature Pacific yew taxadiene synthase polypeptide (i.e., lacking only the transit peptide).

Another embodiment of the invention includes antibodies specific for a native Pacific yew taxadiene synthase polypeptide.

Another embodiment of the invention includes methods of expressing a taxadiene synthase polypeptide in a cell, e.g., a taxoid-producing cell, by culturing a cell that includes an expressible polynucleotide encoding a taxadiene synthase polypeptide under conditions suitable for expression of the polypeptide, preferably resulting in the production of the taxoid at levels that are higher than would be expected from an otherwise similar cell that lacks the expressible polynucleotide.

The foregoing and other objects and advantages of the invention will become more apparent from the following detailed description and accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows steps in the biosynthesis of Taxol, including the initial cyclization of geranylgeranyl diphosphate to taxa-4(5),11(12)-diene, followed by extensive oxidative modification and elaboration of the side chains.

FIG. 2 shows the nucleotide and predicted amino acid sequence of Pacific yew taxadiene synthase clone pTb 42.1 (SEQ ID NO:1 and SEQ ID NO:2). The start and stop codons are underlined. The locations of regions employed for primer synthesis are double underlined. The DDMAD and DSYDD motifs (SEQ ID NO:3 and SEQ ID NO:4, respectively) are in boldface. Conserved histidines (H) and cysteines (C) and an RWWK element are indicated by boxes. Truncation sites for removal of part or all of the transit peptide are indicated by a triangle (.tangle-soliddn.).

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

A homology-based cloning strategy using the polymerase chain reaction (PCR) was employed to isolate a cDNA encoding taxadiene synthase. A set of degenerate primers was constructed based on consensus sequences of related monoterpene, sesquiterpene, and diterpene cyclases. Two of these primers amplified a 83 base pair (bp) fragment that was cyclase-like in sequence and that was employed as a hybridization probe to screen a cDNA library constructed from poly(A).sup.+ RNA extracted from Pacific yew stems. Twelve independent clones with insert size in excess of two kilobase pairs (kb) were isolated and partially sequenced.

One of these cDNA isolates was functionally expressed in Escherichia coli, yielding a protein that was catalytically active in converting geranylgeranyl diphosphate to a diterpene olefin that was confirmed to be taxa-4(5),11(12)-diene by combined capillary gas chromatography-mass spectrometry (Satterwhite and Croteau, J. Chromatography 452:61-73, 1988).

The taxa-4(5),11(12)-diene synthase cDNA sequence specifies an open reading frame of 2586 nucleotides (SEQ ID NO:1). The deduced polypeptide sequence (SEQ ID NO:2) contains 862 amino acid residues and has a molecular weight of 98,303, compared to about 79,000 previously determined for the mature native enzyme. It therefore appears to be full-length and includes a long presumptive plastidial targeting peptide. Sequence comparisons with monoterpene, sesquiterpene, and diterpene cyclases of plant origin indicate a significant degree of similarity between these enzymes; the taxadiene synthase most closely resembles (46% identity, 67% similarity) abietadiene synthase, a diterpene cyclase from grand fir.

USES OF THE TAXADIENE SYNTHASE GENE

Increasing Taxol Biosynthesis in Transformed Cells

The committed step of Taxol (paclitaxel) biosynthesis is the initial cyclization of geranylgeranyl diphosphate, a ubiquitous isoprenoid intermediate, catalyzed by taxadiene synthase, a diterpene cyclase. The product of this reaction is the parent olefin with a taxane skeleton, taxa-4(5),11(12)-diene. For a review of taxoids and taxoid biochemistry, see, e.g., Kingston et al., "The Taxane Diterpenoids," Progress in the Chemistry of Organic Natural Products, vol. 61, Springer Verlag, New York, 1993, pp. 1-206.

The committed cyclization step of the target pathway is a slow step in the extended biosynthetic sequence leading to Taxol and related taxoids (Koepp et al., J. Biol. Chem. 270:8686-8690, 1995; Hezari et al., Arch. Biochem. Biophys. 322:437-444, 1995). The yield of Taxol and related taxoids (e.g., cephalomannine, baccatins, taxinines, among others) in cells of an organism capable of taxoid biosynthesis is increased by the expression in such cells of a recombinant taxadiene synthase gene.

This approach to increasing taxoid biosynthesis can be used in any organism that is capable of taxoid biosynthesis. Taxol synthesis is known to take place, for example, in the Taxaceae, including Taxus species from all over the world (including, but not limited to, T. brevifolia, T. baccata, T. x media, T. cuspidata, T. canadensis, and T. chinensis), as well as in certain microorganisms. Taxol may also be produced by a fungus, Taxomyces andreanae (Stierle et al., Science 260:214, 1993).

Agrobacterium tumefaciens-mediated transformation of Taxus species has been described and the resulting callus cultures shown to produce Taxol (Han et al., Plant Sci. 95:187-196, 1994).

Taxol can be isolated from cells transformed with the taxadiene synthase gene by conventional methods. The production of callus and suspension cultures of Taxus, and the isolation of Taxol and related compounds from such cultures, has been described (for example, in Fett-Netto et al., Bio/Technology 10:1572-1575, 1992).

Biosynthesis of Taxoids in Microorganisms

As discussed below, taxadiene synthase activity was observed in transformed E. coli host cells expressing recombinant taxadiene synthase. Taxadiene synthase does not require extensive post-translational modification, as provided, for example, in mammalian cells, for enzymatic function. As a result, functional taxadiene synthase can be expressed in a wide variety of host cells.

Geranylgeranyl diphosphate, a substrate of taxadiene synthase, is produced in a wide variety of organisms, including bacteria and yeast that synthesize carotenoid pigments (e.g., Serratia spp. and Rhodotorula spp.). Introduction of vectors capable of expressing taxadiene synthase in such microorganisms permits the production of large amounts of taxa-4(5),11(12)-diene and related compounds having the taxane backbone. The taxane backbone thus produced is useful as a chemical feedstock. Simple taxoids, for example, would be useful as perfume fixatives.

Cloning Taxadiene Synthase Homologs and Related Genes

The availability of the taxadiene synthase gene from Pacific yew makes possible the cloning of homologs of taxadiene synthase from other organisms capable of taxoid biosynthesis, particularly Taxus spp. Although the proportion of common taxoids varies with the species or cultivar of yew tested, apparently all Taxus species synthesize taxoids, including Taxol, to some degree (see, e.g., Mattina and Palva, J. Environ. Hort. 10:187-191, 1992; Miller, J. Natural Products 43:425-437, 1980). Taxol may also be produced by a fungus, Taxomyces andreanae (Stierle et al., Science 260:214, 1993).

A taxadiene synthase gene can be isolated from any organism capable of producing Taxol or related taxoids by using primers or probes based on the Pacific yew taxadiene synthase gene sequence or antibodies specific for taxadiene synthase by conventional methods.

Modified Forms of Taxadiene Synthase Gene and Polypeptide

Knowledge of the taxadiene synthase gene sequence permits the modification of the sequence, as described more fully below, to produce variant forms of the gene and the polypeptide gene product. For example, the plastidial transit peptide can be removed and/or replaced by other transit peptides to allow the gene product to be directed to various intracellular compartments or exported from a host cell.

Definitions and Methods

The following definitions and methods are provided to better define the present invention and to guide those of ordinary skill in the art in the practice of the present invention. Definitions of common terms in molecular biology may also be found in Rieger et al., Glossary of Genetics: Classical and Molecular, 5th edition, Springer-Verlag, New York, 1991; and Lewin, Genes V, Oxford University Press, New York, 1994.

The term "plant" encompasses any plant and progeny thereof. The term also encompasses parts of plants, including seed, cuttings, tubers, fruit, flowers, etc.

A "reproductive unit" of a plant is any totipotent part or tissue of the plant from which one can obtain a progeny of the plant, including, for example, seeds, cuttings, buds, bulbs, somatic embryos, cultured cell (e.g., callus or suspension cultures), etc.

Nucleic Acids

Nucleic acids (a term used interchangeably with "polynucleotides" herein) that are useful in the practice of the present invention include the isolated taxadiene synthase gene, its homologs in other plant species, and fragments and variants thereof.

The term "taxadiene synthase gene" refers to a nucleic acid that contains a taxa-4(5),11(12)-diene synthase sequence, preferably a nucleic acid that encodes a polypeptide having taxadiene synthase enzymatic activity. This term relates primarily to the isolated full-length taxadiene synthase cDNA from Pacific yew discussed above and shown in FIG. 2 (SEQ ID NO:1) and the corresponding genomic sequence (including flanking or internal sequences operably linked thereto, including regulatory elements and/or intron sequences).

This term also encompasses alleles of the taxadiene synthase gene from Pacific yew.

"Native". The term "native" refers to a naturally-occurring ("wild-type") nucleic acid or polypeptide.

"Homolog". A "homolog" of the taxadiene synthase gene is a gene sequence encoding a taxadiene synthase isolated from an organism other than Pacific yew.

"Isolated". An "isolated" nucleic acid is one that has been substantially separated or purified away from other nucleic acid sequences in the cell of the organism in which the nucleic acid naturally occurs, i.e., other chromosomal and extrachromosomal DNA and RNA, by conventional nucleic acid-purification methods. The term also embraces recombinant nucleic acids and chemically synthesized nucleic acids.

Fragments, Probes, and Primers

A fragment of a taxadiene synthase nucleic acid according to the present invention is a portion of the nucleic acid that is less than full-length and comprises at least a minimum length capable of hybridizing specifically with the taxadiene synthase nucleic acid of FIG. 2 (SEQ ID NO:1) under stringent hybridization conditions. The length of such a fragment is preferably 15-17 nucleotides or more.

Nucleic acid probes and primers can be prepared based on the taxadiene synthase gene sequence provided in FIG. 2 (SEQ ID NO:1). A "probe" is an isolated DNA or RNA attached to a detectable label or reporter molecule, e.g., a radioactive isotope, ligand, chemiluminescent agent, or enzyme. "Primers" are isolated nucleic acids, generally DNA oligonucleotides 15 nucleotides or more in length, that are annealed to a complementary target DNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand, then extended along the target DNA strand by a polymerase, e.g., a DNA polymerase. Primer pairs can be used for amplification of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR) or other conventional nucleic-acid amplification methods.

Methods for preparing and using probes and primers are described, for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, ed. Sambrook et al., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989; Current Protocols in Molecular Biology, ed. Ausubel et al., Greene Publishing and Wiley-Interscience, New York, 1987 (with periodic updates); and Innis et al., PCR Protocols: A Guide to Methods and Applications, Academic Press: San Diego, 1990. PCR-primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5,.COPYRGT. 1991, Whitehead Institute for Biomedical Research, Cambridge, Mass.).

Nucleotide Sequence Similarity

Nucleotide sequence "similarity" is a measure of the degree to which two polynucleotide sequences have identical nucleotide bases at corresponding positions in their sequence when optimally aligned (with appropriate nucleotide insertions or deletions). Sequence similarity can be determined using sequence analysis software such as the Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, Madison, Wis. Preferably, a variant form of a taxadiene synthase polynucleotide has at least 70%, more preferably at least 80%, and most preferably at least 90% nucleotide sequence similarity with a native taxadiene synthase gene, particularly with a native Pacific yew taxadiene synthase, as provided in FIG. 2 (SEQ ID NO:1).

Operably Linked

A first nucleic-acid sequence is "operably" linked with a second nucleic-acid sequence when the first nucleic-acid sequence is placed in a functional relationship with the second nucleic-acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences are contiguous and, where necessary to join two protein coding regions, in reading frame.

"Recombinant". A "recombinant" nucleic acid is an isolated polypeptide made by an artificial combination of two otherwise separated segments of sequence, e.g., by chemical synthesis or by the manipulation of isolated segments of nucleic acids by genetic engineering techniques.

Techniques for nucleic-acid manipulation are described generally in, for example, Sambrook et al. (1989) and Ausubel et al. (1987, with periodic updates). Methods for chemical synthesis of nucleic acids are discussed, for example, in Beaucage and Carruthers, Tetra. Letts. 22:1859-1862, 1981, and Matteucci et al., J. Am. Chem. Soc. 103:3185, 1981. Chemical synthesis of nucleic acids can be performed, for example, on commercial automated oligonucleotide synthesizers.

Preparation of Recombinant or Chemically Synthesized Nucleic Acids; Vectors, Transformation, Host Cells

Natural or synthetic nucleic acids according to the present invention can be incorporated into recombinant nucleic-acid constructs, typically DNA constructs, capable of introduction into and replication in a host cell. Such a construct preferably is a vector that includes a replication system and sequences that are capable of transcription and translation of a polypeptide-encoding sequence in a given host cell. For the practice of the present invention, conventional compositions and methods for preparing and using vectors and host cells are employed, as discussed, inter alia, in Sambrook et al., 1989, or Ausubel et al., 1987.

A "transformed" or "transgenic" cell, tissue, organ, or organism is one into which a foreign nucleic acid, has been introduced. A "transgenic" or "transformed" cell or organism also includes (1) progeny of the cell or organism and (2) progeny produced from a breeding program employing a "transgenic" plant as a parent in a cross and exhibiting an altered phenotype resulting from the presence of the "transgene," i.e., the recombinant taxadiene synthase nucleic acid.

Nucleic-Acid Hybridization; "Stringent Conditions"; "Specific"

The nucleic-acid probes and primers of the present invention hybridize under stringent conditions to a target DNA sequence, e.g., to the taxadiene synthase gene.

The term "stringent conditions" is functionally defined with regard to the hybridization of a nucleic-acid probe to a target nucleic acid (i.e., to a particular nucleic-acid sequence of interest) by the hybridization procedure discussed in Sambrook et al., 1989, at 9.52-9.55.

Hybridization of Radiolabeled Probes to Nucleic Acids Immobilized on Nitrocellulose Filters or Nylon Membranes

Although the method given below deals with RNA or DNA immobilized on nitrocellulose filters, only slight modifications are required to adapt the procedure to nylon membranes. These modifications are noted at the appropriate places in the text.

1. Prepare the prehybridization solution appropriate for the task at hand. Approximately 0.2 ml of prehybridization solution will be required for each square centimeter of nitrocellulose filter or nylon membrane The prehybridization solution should be filtered through a 0.45-micron disposable cellulose acetate filter (Schleicher and Schuell Uniflow syringe filter No 57240 or equivalent). Prehybridization solutions For detection of low-abundance sequences: Either 6.times.SSC (or 6.times.SSPE) 5.times.Denhardt's reagent 0.5% SDS 100 .mu.g/ml denatured, fragmented salmon sperm DNA or 6.times.SSC (or 6.times.SSPE) 5.times.Denhardt's reagent 0.5% SDS 100 .mu.g/ml denatured, fragmented salmon sperm DNA 50% formamide For preparation of Denhardt's reagent and denatured, fragmented salmon sperm DNA, see Table 9.1. Formamide: Many batches of reagent-grade formamide are sufficiently pure to be used without further treatment. However, if any yellow color is present, the formamide should be deionized by stirring on a magnetic stirrer with Dowex XG8 mixed-bed resin for 1 hour and filtering twice through Whatman No. 1 paper. Deionized formamide should be stored in small aliquots under nitrogen at -70.degree. C. For detection of moderate- or high-abundance sequences: Either 6.times.SSC (or 6.times.SSPE) 0.05.times.BLOTTO or 6.times.SSC (or 6.times.SSPE) 0.05:.times.BLOTTO 50% formamide For preparation of BLOTTO, see Table 9.1.

When .sup.32 P-labeled cDNA or RNA is used as a probe, poly(A).sup.+ RNA at a concentration of 1 .mu.g/ml may be included in the prehybridization and hybridization solutions to prevent the probe from binding to T-rich sequences that are found fairly commonly in eukaryotic DNA.

2. Float the nitrocellulose filter or nylon membrane containing the target DNA on the surface of a tray of 6.times.SSC (or 6.times.SSPE) until it becomes thoroughly wetted from beneath. Submerge the filter for 2 minutes. 3. Slip the wet filter into a heat-sealable bag (e.g., Sears Seal-A-Meal or equivalent). Add 0.2 ml of prehybridization solution for each square centimeter of nitrocellulose filter or nylon membrane. Squeeze as much air as possible from the bag. Seal the open end of the bag with the heat sealer. Incubate the bag for 1-2 hours submerged at the appropriate temperature (68.degree. C. for aqueous solvents; 42.degree. C. for solvents containing 50% formamide). Often, small bubbles of air form on the surface of the filter as the temperature of the prehybridization solution increases. It is important that these bubbles be removed by occasionally agitating the fluid in the bag; otherwise, the components of the prehybridization solution will not be able to coat the filter evenly. This problem can be minimized by heating the prehybridization solution to the appropriate temperature before adding it to the bag. 4. If the radiolabeled probe is double-stranded, denature it by heating for 5 minutes at 100.degree. C. Single-stranded probe need not be denatured. Chill the probe rapidly in ice water. Alternatively, the probe may be denatured by adding 0.1 volume of 3 N NaOH. After 5 minutes at room temperature, transfer the probe to ice water and add 0.05 volume of 1 M Tris.Cl (pH 7.2) and 0.1 volume of 3 N HCl. Store the probe in ice water until it is needed. For Southern hybridization of mammalian genomic DNA where each lane of the gel contains 10 .mu.g of DNA, 10-20 ng/ml radiolabeled probe (sp. act.=10.sup.9 cpm/.mu.g or greater) should be used. For Southern hybridization of fragments of cloned DNA where each band of the restriction digest contains 10 ng of DNA or more, much less probe is required. Typically, hybridization is carried out for 6-8 hours using 1-2 ng/ml radiolabeled probe (sp. act=10.sup.9 cpm/.mu.g or greater). 5. Working quickly, remove the bag containing the filter from the water bath. Open the bag by cutting off one corner with scissors. Add the denatured probe to the prehybridization solution, and then squeeze as much air as possible from the bag. Reseal the bag with the heat sealer so that as few bubbles as possible are trapped in the bag. To avoid radioactive contamination of the water bath, the resealed bag should be sealed inside a second, noncontaminated bag. When using nylon membranes, the prehybridization solution should be completely removed from the bag and immediately replaced with hybridization solution. The probe is then added and the bag is resealed. Hybridization solution for nylon membranes 6.times.SSC (or 6.times.SSPE) 0.5% SDS 100 .mu.g/ml denatured, fragmented salmon sperm DNA 50% formamide (if hybridization is to be carried out at 42.degree. C.) 6. Incubate the bag submerged in a water bath set at the appropriate temperature for the required period of hybridization. 7. Wearing gloves, remove the bag from the water bath and immediately cut off one corner. Pour out the hybridization solution into a container suitable for disposal, and then cut the bag along the length of three sides. Remove the filter and immediately submerge it in a tray containing several hundred milliliters of 2.times.SSC and 0.5% SDS at room temperature. Important: Do not allow the filter to dry out at any stage during the washing procedure. 8. After 5 minutes, transfer the filter to a fresh tray containing several hundred milliliters of 2.times.SSC and 0.1% SDS and incubate for 15 minutes at room temperature with occasional gentle agitation. If short oligonucleotides are used as probes, washing should be carried out only for brief periods (1-2 minutes) at the appropriate temperature. For a discussion of the stability of hybrids involving oligonucleotides, see Chapter 11. 9. Transfer the filter to a flat-bottom plastic box containing several hundred milliliters of fresh 0.1.times.SSC and 0.5% SDS. Incubate the filter for 30 minutes to 1 hour at 37.degree. C. with gentle agitation. 10. Replace the solution with fresh 0.1.times.SSC and 0.5% SDS, and transfer the box to a water bath set at 68.degree. C. for an equal period of time. Monitor the amount of radioactivity on the filter using a hand-held minimonitor. The parts of the filter that do not contain DNA should not emit a detectable signal. You should not expect to pick up a signal on the minimonitor from filters containing mammalian DNA that has been hybridized to single-copy probes. 11. Briefly wash the filter with 0.1.times.SSC at room temperature. Remove most of the liquid from the filter by placing it on a pad of paper towels. 12. Place the damp filter on a sheet of Saran Wrap. Apply adhesive dot labels marked with radioactive ink to several asymmetric locations on the Saran Wrap. These markers serve to align the autoradiograph with the filter. Cover the labels with Scotch Tape. This prevents contamination of the film holder or intensifying screen with the radioactive ink. Radioactive ink is made by mixing a small amount of .sup.32 P with waterproof black drawing ink, We find it convenient to make the ink in three grades: very hot (>2000 cps on a hand-held minimonitor), hot (>500 cps on a hand-held minimonitor), and cool (>50 cps on a hand-held minimonitor). Use a fiber-tip pen to apply ink of the desired hotness to the adhesive labels. Attach radioactive-warning tape to the pen, and store it in an appropriate place. 13. Cover the filter with a second sheet of Saran Wrap, and expose the filter to X-ray film (Kodak XAR-2 or equivalent) to obtain an autoradiographic image (see Appendix E). The exposure time should be determined empirically. However, single-copy sequences in mammalian genomic DNA can usually be detected after 16-24 hours of exposure at -70.degree. C. with an intensifying screen. See also, Sambrook et al., 1989 at 9.47-9.52, 9.56-9.58 Kanehisa, Nucl. Acids Res. 12:203-213, 1984; and Wetmur and Davidson, J. Mol. Biol. 31:349-370, 1968.

Regarding the amplification of a target nucleic-acid sequence (e.g., by PCR) using a particular amplification primer pair, stringent conditions are conditions that permit the primer pair to hybridize only to the target nucleic-acid sequence to which a primer having the corresponding wild-type sequence (or its complement) would bind and preferably to produce a unique amplification product.

The term "specific for (a target sequence)" indicates that a probe or primer hybridizes under stringent conditions only to the target sequence in a sample comprising the target sequence.

Nucleic-acid Amplification

As used herein, "amplified DNA" refers to the product of nucleic-acid amplification of a target nucleic-acid sequence. Nucleic-acid amplification can be accomplished by any of the various nucleic-acid amplification methods known in the art, including the polymerase chain reaction (PCR). A variety of amplification methods are known in the art and are described, inter alia, in U.S. Pat. Nos. 4,683,195 and 4,683,202 and in PCR Protocols: A Guide to Methods and Applications, Innis et al., eds., Academic Press, San Diego, 1990.

Methods of Making cDNA Clones Encoding Taxadiene Synthase or Homologs Thereof

Based upon the availability of the taxadiene synthase cDNA as disclosed herein, other taxadiene synthase genes (e.g., alleles and homologs of taxadiene synthase) can be readily obtained from a wide variety of plants by cloning methods known in the art.

One or more primer pairs based on the taxadiene synthase sequence can be used to amplify such taxadiene synthase genes or their homologs by the polymerase chain reaction (PCR) or other conventional amplification methods. Alternatively, the disclosed taxadiene synthase cDNA or fragments thereof can be used to probe a cDNA or genomic library made from a given plant species by conventional methods.

Cloning of the Taxadiene Synthase Genomic Sequence and Homologs Thereof

The availability of the taxadiene synthase cDNA sequence enables those skilled in the art to obtain a genomic clone corresponding to the taxadiene synthase cDNA (including the promoter and other regulatory regions and intron sequences) and the determination of its nucleotide sequence by conventional methods.

Virtually all Taxus species synthesize taxoids, including Taxol, to some degree (see, e.g., Mattina and Palva, J. Environ. Hort. 10:187-191, 1992; Miller, J. Natural Products 43:425-437, 1980). Any organism that produces taxoids would be expected to express a homolog of taxadiene synthase. Taxadiene synthase genes can be obtained by hybridization of a Pacific yew taxadiene synthase probe to a cDNA or genomic library of a target species. Such a homolog can also be obtained by PCR or other amplification method from genomic DNA or RNA of a target species using primers based on the taxadiene synthase sequence shown in FIG. 2 (SEQ ID NO:1). Genomic and cDNA libraries from yew or other plant species can be prepared by conventional methods.

Primers and probes based on the sequence shown in FIG. 2 (SEQ ID NO:1) can be used to confirm (and, if necessary, to correct) the taxadiene synthase sequence by conventional methods.

Nucleotide-Sequence Variants of Taxadiene Synthase cDNA and Amino Acid Sequence Variants of Taxadiene Synthase Protein

Using the nucleotide and the amino-acid sequence of the taxadiene synthase protein disclosed herein, those skilled in the art can create DNA molecules and polypeptides that have minor variations in their nucleotide or amino acid sequence.

"Variant" DNA molecules are DNA molecules containing minor changes in the native taxadiene synthase sequence, i.e., changes in which one or more nucleotides of a native taxadiene synthase sequence is deleted, added, and/or substituted, preferably while substantially maintaining taxadiene synthase activity. Variant DNA molecules can be produced, for example, by standard DNA mutagenesis techniques or by chemically synthesizing the variant DNA molecule or a portion thereof. Such variants preferably do not change the reading frame of the protein-coding region of the nucleic acid and preferably encode a protein having no change, only a minor reduction, or an increase in taxadiene synthase biological function.

Amino-acid substitutions are preferably substitutions of single amino-acid residues. DNA insertions are preferably of about 1 to 10 contiguous nucleotides and deletions are preferably of about 1 to 30 contiguous nucleotides. Insertions and deletions are preferably insertions or deletions from an end of the protein-coding or non-coding sequence and are preferably made in adjacent base pairs. Substitutions, deletions, insertions or any combination thereof can be combined to arrive at a final construct.

Preferably, variant nucleic acids according to the present invention are "silent" or "conservative" variants. "Silent" variants are variants of a native taxadiene synthase sequence or a homolog thereof in which there has been a substitution of one or more base pairs but no change in the amino-acid sequence of the polypeptide encoded by the sequence. "Conservative" variants are variants of the native taxadiene synthase sequence or a homolog thereof in which at least one codon in the protein-coding region of the gene has been changed, resulting in a conservative change in one or more amino acid residues of the polypeptide encoded by the nucleic-acid sequence, i.e., an amino acid substitution. A number of conservative amino acid substitutions are listed below. In addition, one or more codons encoding cysteine residues can be substituted for, resulting in a loss of a cysteine residue and affecting disulfide linkages in the taxadiene synthase polypeptide.

______________________________________Original Residue Conservative Substitutions______________________________________Ala Ser Arg Lys Asn Gln, His Asp Glu Cys Ser Gln Asn Glu Asp Gly Pro His Asn; Gln Ile Leu, Val Leu Ile; Val Lys Arg; Gln; Glu Met Leu; Ile Phe Met; Leu; Tyr Ser Thr Thr Ser Trp Tyr Tyr Trp; Phe Val Ile; Leu______________________________________

Substantial changes in function are made by selecting substitutions that are less conservative than those listed above, e.g., causing changes in: (a) the structure of the polypeptide backbone in the area of the substitution; (b) the charge or hydrophobicity of the polypeptide at the target site; or (c) the bulk of an amino acid side chain. Substitutions generally expected to produce the greatest changes in protein properties are those in which: (a) a hydrophilic residue, e.g., seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g., leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histadyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine.

The taxadiene synthase gene sequence can be modified as follows:

(1) To Improve Expression Efficiency and Redirect the Targeting of the Expressed Polypeptide

For expression in non-plant hosts (or to direct the expressed polypeptide to a different intracellular compartment in a plant host), the native gene sequence can be truncated from the 5' end to remove the sequence encoding the plastidial transit peptide of approximately 137 amino acids (i.e., to approximately 138S), leaving the sequence encoding the mature taxadiene synthase polypeptide of about 725 amino acids. In addition, one or more codons can be changed, for example, to conform the gene to the codon usage bias of the host cell for improved expression. Enzymatic stability can be altered by removing or adding one or more cysteine residues, thus removing or adding one or more disulfide bonds.

(2) To Alter Catalytic Efficiency

As discussed below, the aspartate-rich (I,L,V)XDDXX(XX)D motif(s) (SEQ ID NO:6) found in most prenyltransferases and terpenoid cyclases, and thought to play a role in substrate binding, is also present in taxadiene synthase, as is a related DXXDD motif (FIG. 2, SEQ ID NO:1 and SEQ ID NO:4). Histidine and cysteine residues have been implicated at the active sites of several terpenoid cyclases of plant origin. Histidines residues 370, 415 and 793 and cysteines at residues 329, 650 and 777 of taxadiene synthase are conserved among the plant terpenoid cyclase genes.

One or more conserved histidine and cysteine residues (as discussed below), or semi-conserved residues such as conserved cysteine residues (e.g., residues 329, 650, 719, and 777) and histidine residues (e.g., residues 370, 415, 579, and 793), can be mutagenized to alter enzyme kinetics. In addition, residues adjacent to these conserved histidine and cysteine residues can also be altered to increase the cysteine or histidine content to improve charge stabilization. By increasing the aspartate content of the DDXXD and DXXDD motifs (SEQ ID NO:3 and SEQ ID NO:14, respectively) (where D is aspartate and X is any amino acid), which are likely to be involved in substrate/intermediate binding, it is also possible to increase the enzymatic rate (i.e., the rate-limiting ionization step of the enzymatic reaction). Arginines have been implicated in binding or catalysis, and conserved arginine residues are also good targets for mutagenesis. Changing the conserved DDXXD and/or DXXDD motifs (SEQ ID NO:3 and SEQ ID NO:4, respectively) (e.g., the aspartate residues thereof) by conventional site-directed mutagenesis methods to match those of other known enzymes can also lead to changes in the kinetics or substrate specificity of taxadiene synthase. Additionally, product formation can be altered by mutagenesis of the RWWK element (SEQ ID NO:5) (residues 564 to 567), which includes aromatic residues that may play a role in stabilizing carbocationic reaction intermediates.

(3) To Modify Substrate Utilization

The enzyme, particularly the active site, can be modified to allow the enzyme to bind shorter (e.g., C.sub.10) or longer (e.g., C.sub.25) chains than geranylgeranyl diphosphate. Substrate size utilization can be altered by increasing or decreasing the size of the hydrophobic patches to modify the size of the hydrophobic pocket of the enzyme. Similar effects can be achieved by domain swapping.

(4) To Change Product Outcome

Directed mutagenesis of conserved aspartate and arginine residues can be used to permit the enzyme to produce different diterpene skeletons with, for example, one, two, or three rings.

See, e.g., Cane et al., Biochemistry 34:2480-2488, 1995; Joly and Edwards, J. Biol. Chem. 268:26983-26989, 1993; Marrero et al., J. Biol. Chem. 267:533-536, 1992; and Song and Poulter, Proc. Natl. Acad. Sci. USA 91:3044-3048, 1994).

Expression of Taxadiene Synthase Nucleic Acids in Host Cells

DNA constructs incorporating a taxadiene synthase gene or fragment thereof according to the present invention preferably place the taxadiene synthase protein coding sequence under the control of an operably linked promoter that is capable of expression in a host cell. Various promoters suitable for expression of heterologous genes in plant cells are known in the art, including constitutive promoters, e.g. the cauliflower mosaic virus (CaMV) 35S promoter, which is expressed in many plant tissues, organ- or tissue-specific promoters, and promoters that are inducible by chemicals such as methyl jasminate, salicylic acid, or safeners, for example. A variety of other promoters or other sequences useful in constructing expression vectors are available for expression in bacterial, yeast, mammalian, insect, amphibian, avian, or other host cells.

Nucleic Acids Attached to a Solid Support

The nucleic acids of the present invention can be free in solution or attached by conventional means to a solid support, such as a hybridization membrane (e.g., nitrocellulose or nylon), a bead, or other solid supports known in the art.

Polypeptides

The term "taxadiene synthase protein" (or polypeptide) refers to a protein encoded by a taxadiene synthase gene, including alleles, homologs, and variants thereof, for example. A taxadiene synthase polypeptide can be produced by the expression of a recombinant taxadiene synthase nucleic acid or be chemically synthesized. Techniques for chemical synthesis of polypeptides are described, for example, in Merrifield, J. Amer. Chem. Soc. 85:2149-2156, 1963.

Polypeptide Sequence Identity and Similarity

Ordinarily, taxadiene synthase polypeptides encompassed by the present invention have at least about 70% amino acid sequence "identity" (or homology) compared with a native taxadiene synthase polypeptide, preferably at least about 80% identity, and more preferably at least about 90% identity to a native taxadiene synthase polypeptide. Preferably, such polypeptides also possess characteristic structural features and biological activity of a native taxadiene synthase polypeptide.

Amino acid sequence "similarity" is a measure of the degree to which aligned amino acid sequences possess identical amino acids or conservative amino acid substitutions at corresponding positions.

A taxadiene synthase "biological activity" includes taxadiene synthase enzymatic activity as determined by conventional protocols (e.g., the protocol described in Hezari et al., Arch. Biochem. Biophys. 322:437-444, 1995, incorporated herein by reference). Other biological activities of taxadiene synthase include, but are not limited to substrate binding, immunological activity (including the capacity to elicit the production of antibodies that are specific for taxadiene synthase), etc.

Polypeptide identity (homology) or similarity is typically analyzed using sequence analysis software such as the Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, Madison, Wis.). Polypeptide sequence analysis software matches polypeptide sequences using measures of identity assigned to various substitutions, deletions, substitutions, and other modifications.

"Isolated," "Purified," "Homogeneous" Polypeptides

A polypeptide is "isolated" if it has been separated from the cellular components (nucleic acids, lipids, carbohydrates, and other polypeptides) that naturally accompany it. Such a polypeptide can also be referred to as "pure" or "homogeneous" or "substantially" pure or homogeneous. Thus, a polypeptide which is chemically synthesized or recombinant (i.e., the product of the expression of a recombinant nucleic acid, even if expressed in a homologous cell type) is considered to be isolated. A monomeric polypeptide is isolated when at least 60-90% by weight of a sample is composed of the polypeptide, preferably 95% or more, and more preferably more than 99%. Protein purity or homogeneity is indicated, for example, by polyacrylamide gel electrophoresis of a protein sample, followed by visualization of a single polypeptide band upon staining the polyacrylamide gel; high pressure liquid chromatography; or other conventional methods.

Protein Purification

The polypeptides of the present invention can be purified by any of the means known in the art. Various methods of protein purification are described, e.g., in Guide to Protein Purification, ed. Deutscher, Meth. Enzymol. 185, Academic Press, San Diego, 1990; and Scopes, Protein Purification: Principles and Practice, Springer Verlag, New York, 1982.

Variant Forms of Taxadiene Synthase Polypeptides; Labeling

Encompassed by the taxadiene synthase polypeptides according to an embodiment of the present invention are variant polypeptides in which there have been substitutions, deletions, insertions or other modifications of a native taxadiene synthase polypeptide. The variants substantially retain structural and/or biological characteristics and are preferably silent or conservative substitutions of one or a small number of contiguous amino acid residues. Preferably, such variant polypeptides are at least 70%, more preferably at least 80%, and most preferably at least 90% homologous to a native taxadiene synthase polypeptide.

The native taxadiene synthase polypeptide sequence can be modified by conventional methods, e.g., by acetylation, carboxylation, phosphorylation, glycosylation, ubiquitination, and labeling, whether accomplished by in vivo or in vitro enzymatic treatment of a taxadiene synthase polypeptide or by the synthesis of a taxadiene synthase polypeptide using modified amino acids.

There are a variety of conventional methods and reagents for labeling polypeptides and fragments thereof. Typical labels include radioactive isotopes, ligands or ligand receptors, fluorophores, chemiluminescent agents, and enzymes. Methods for labeling and guidance in the choice of labels appropriate for various purposes are discussed, e.g., in Sambrook et al. (1989) and Ausubel et al. (1987 with periodic updates).

Polypeptide Fragments

The present invention also encompasses fragments of taxadiene synthase polypeptides that lack at least one residue of a native full-length taxadiene synthase polypeptide yet retain at least one of the biological activities characteristic of taxadiene synthase, e.g., taxadiene synthase enzymatic activity or possession of a characteristic immunological determinant. As an additional example, an immunologically active fragment of a taxadiene synthase polypeptide is capable of raising taxadiene synthase-specific antibodies in a target immune system (e.g., murine or rabbit) or of competing with taxadiene synthase for binding to taxadiene synthase-specific antibodies, and is thus useful in immunoassays for the presence of taxadiene synthase polypeptides in a biological sample. Such immunologically active fragments typically have a minimum size of 7 to 17 amino acids. Fragments preferably comprise at least 10, more preferably at least 20, and most preferably at least 30 consecutive amino acids of a native taxadiene synthase polypeptide.

Fusion Polypeptides

The present invention also provides fusion polypeptides including, for example, heterologous fusion polypeptides, i.e., a taxadiene synthase polypeptide sequence or fragment thereof and a heterologous polypeptide sequence, e.g., a sequence from a different polypeptide. Such heterologous fusion polypeptides thus exhibit biological properties (such as ligand-binding, catalysis, secretion signals, antigenic determinants, etc.) derived from each of the fused sequences. Fusion partners include, for example, immunoglobulins, beta galactosidase, trpE, protein A, beta lactamase, alpha amylase, alcohol dehydrogenase, yeast alpha mating factor, and various signal and leader sequences which, e.g., can direct the secretion of the polypeptide. Fusion polypeptides are typically made by the expression of recombinant nucleic acids or by chemical synthesis.

Polypeptide Sequence Determination

The sequence of a polypeptide of the present invention can be determined by various methods known in the art. In order to determine the sequence of a polypeptide, the polypeptide is typically fragmented, the fragments separated, and the sequence of each fragment determined. To obtain fragments of a taxadiene synthase polypeptide, the polypeptide can be digested with an enzyme such as trypsin, clostripain, or Staphylococcus protease, or with chemical agents such as cyanogen bromide, o-iodosobenzoate, hydroxylamine or 2-nitro-5-thiocyanobenzoate. Peptide fragments can be separated, e.g., by reversed-phase high-performance liquid chromatography (HPLC) and analyzed by gas-phase sequencing.

Antibodies

The present invention also encompasses polyclonal and/or monoclonal antibodies that are specific for taxadiene synthase, i.e., bind to taxadiene synthase and are capable of distinguishing the taxadiene synthase polypeptide from other polypeptides under standard conditions. Such antibodies are produced and assayed by conventional methods.

For the preparation and use of antibodies according to the present invention, including various immunoassay techniques and applications, see, e.g., Goding, Monoclonal Antibodies: Principles and Practice, 2d ed, Academic Press, New York, 1986; and Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1988. Taxadiene synthase-specific antibodies are useful, for example in: purifying taxadiene synthase polypeptides; cloning taxadiene synthase homologs from Pacific yew or other plant species from an expression library; antibody probes for protein blots and immunoassays; etc.

Taxadiene synthase polypeptides and antibodies can be labeled by conventional techniques. Suitable labels include radionuclides, enzymes, substrates, cofactors, inhibitors, fluorescent agents, chemiluminescent agents, magnetic particles, etc.

Plant Transformation and Regeneration

Any well-known method can be employed for plant cell transformation, culture, and regeneration can be employed in the practice of the present invention. Methods for introduction of foreign DNA into plant cells include, but are not limited to: transfer involving the use of Agrobacterium tumefaciens and appropriate Ti vectors, including binary vectors; chemically induced transfer (e.g., with polyethylene glycol); biolistics; and microinjection. See, e.g., An et al., Plant Molecular Biology Manual A3:1-19, 1988.

The invention will be better understood by reference to the following Examples, which are intended to merely illustrate the best mode now known for practicing the invention. The scope of the invention is not to be considered limited thereto, however.

EXAMPLE 1

Cloning and Sequencing of a cDNA Encoding Taxa-4(5),11(12)-diene Synthase

Materials and Methods

Plants, Substrates, and Standards

Four-year-old T. brevifolia saplings in active growth were maintained in a greenhouse. [1-.sup.3 H]Geranylgeranyl diphosphate (120 Ci/mol) was prepared as described previously (LaFever et al., Arch. Biochem. Biophys. 313:139-149, 1994), and authentic (.+-.)-taxa-4(5),11(12)-diene was prepared by total synthesis (Rubenstein, J. Org. Chem. 60:7215-7223, 1995).

Library Construction

Total RNA was extracted from T. brevifolia stem using the procedures of Lewinsohn and associates (Lewinsohn et al., Plant Mol. Biol. Rep. 12:20-25, 1991) developed for woody gymnosperm tissue. Poly(A).sup.+ RNA was purified by chromatography on oligo(dT)-cellulose (Pharmacia) and 5 .mu.g of the resulting mRNA was utilized to construct a .lambda.ZAP II cDNA library according to the manufacturer's instructions (Stratagene).

PCR-Based Probe Generation and Library Screening

Comparison of six available sequences for monoterpene, sesquiterpene, and diterpene cyclases from higher plants (Facchini and Chappell, Proc. Natl. Acad. Sci. USA 89:11088-11092, 1992; Colby et al., J. Biol. Chem. 268:23016-23024, 1993; Mau and West, Proc. Natl. Acad. Sci. USA 91:8497-8501, 1994; Back and Chappell, J. Biol. Chem. 270:7375-7381, 1995; Sun and Karmiya, Plant Cell 6:1509-1518, 1994; and Bensen et al., Plant Cell 7:75-84, 1995) allowed definition of eleven homologous regions for which consensus degenerate primers were synthesized. All twenty primers (the most carboxy terminal primer, the most amino terminal primer, and nine internal primers in both directions) were deployed in all possible combinations with a broad range of amplification conditions using CsCl-purified T. brevifolia stem library phage DNA as template (Innis and Gelfand, in PCR Protocols (Innis et al., eds), pp. 3-12, 253-258, Academic Press, San Diego, Calif., 1990; Sambrook et al., 1989).

Analysis of PCR products by gel electrophoresis (Sambrook et al., 1989) indicated that only the combination of primers CC7.2F and CC3R (see FIG. 2 and SEQ ID NO:1) generated a specific DNA fragment (.about.80 bp). This DNA fragment was cloned into pT7Blue (Novagen) and sequenced (DyeDeoxy Terminator Cycle Sequencing, Applied Biosystems), and shown to be 83 bp in length. PCR was used to prepare approximately 1 .mu.g of this material for random hexamer labeling with [.alpha.-.sup.32 P]dATP (Tabor et al., in Current Protocols in Molecular Biology, Ausubel et al., Sections 3.5.9-3.5.10, 1987) and use as a hybridization probe to screen filter lifts of 3.times.10.sup.5 plaques grown in E. coli LE392 using standard protocols (Britten and Davidson, in Nucleic Acid Hybridisation, Hames and Higgins, eds., pp. 3-14, IRL Press, Oxford, 1988).

Of the plaques affording positive signals (102 total), 50 were purified through two additional cycles of hybridization. Thirty-eight pure clones were in vivo excised as Bluescript phagemids. The insert size was determined by PCR using T3 and T7 promoter primers, and the twelve largest clones (insert>2 kb) were partially sequenced.

cDNA Expression in E. coli

All of the partially sequenced, full-length inserts were either out of frame or bore premature stop sites immediately upstream of the presumptive methionine start codon. The latter complication likely resulted from hairpin-primed second-strand cDNA synthesis (Old and Primrose, Principles of Gene Manipulation, 4th ed., pp. 3435, Blackwell Scientific, London, 1989). The 2.7-kb insert from pTb42 was cloned into frame by PCR using the thermostable, high fidelity, blunting polymerase Pful (Stratagene) and the FRM42 primer (downstream of false stop codons) and T7 promoter primer. The resulting blunt fragment was ligated into EcoRV-digested pBluescript SK(-) (Stratagene), yielding pTb42.1, and transformed into E. coli XL1-Blue (Stratagene).

To evaluate functional expression of terpene cyclase activity, E. coli XL1-Blue cells harboring pTb42.1 were grown (to A.sub.600 =0.4) on 5 ml LB medium supplemented with 100 .mu.g/ml ampicillin and 12.5 .mu.g/ml tetracycline before induction with 200 .mu.M IPTG and subsequent growth for 4 h at 25.degree. C. Bacteria were harvested by centrifugation (1800 g, 10 min), resuspended in taxadiene synthase assay buffer (Hezari et al., Arch. Biochem. Biophys. 322:437-444, 1995), disrupted by brief sonication at 0-4.degree. C., and the resulting suspension centrifuged (18,000 g, 10 min) to pellet debris. The supernatant was assayed for taxadiene synthase activity by an established protocol (Hezari et al., Arch. Biochem. Biophys. 322:437-444, 1995) in the presence of 15 .mu.M [1-.sup.3 H]geranylgeranyl diphosphate and 1 mM MgCl.sub.2, with incubation at 31.degree. C. for 4 h. The reaction products were extracted with pentane and the extract purified by column chromatography on silica gel as previously described (Hezari et al., Arch. Biochem. Biophys. 322:437-444, 1995) to afford the olefin fraction, an aliquot of which was counted by liquid scintillation spectrometry to determine .sup.3 H incorporation. Control experiments with transformed E. coli bearing the plasmid with out-of-frame inserts were also carried out.

The identity of the olefin product of the recombinant enzyme was verified by capillary radio-gas chromatography ("capillary radio-GC") (Croteau and Satterwhite, J. Chromatogr. 500:349-354, 1990) as well as capillary gas chromatography-mass spectrum/spectrometry ("capillary GC-MS") using methods described previously (Koepp et al., J. Biol. Chem. 270:8686-8690, 1995) and authentic taxa-4(5),11(12)-diene (Rubenstein, J. Org. Chem. 60:7215-7223, 1995). For GC-MS analysis (Hewlett-Packard 6890 GC-MSD), selected diagnostic ions were monitored: m/z 272 [P.sup.+ ]; 257 [P.sup.+ -15 (CH.sub.3)]; 229 [P.sup.+ -43 (C.sub.3 H.sub.7)]; 121, 122, 123 [C-ring fragment cluster]; and 107 [m/z 122 base peak-15 (CH.sub.3)]. The origin of the highly characteristic C-ring double cleavage fragment ion [base peak, m/z 122(C.sub.9 H.sub.14)] has been described (Koepp et al., J. Biol. Chem. 270:8686-8690, 1995).

Results and Discussion

cDNA Isolation and Characterization

In general characteristics (molecular weight, divalent metal ion requirement, kinetic constants, etc.), taxadiene synthase resembles other terpenoid cyclases from higher plants; however, the low tissue titers of the enzyme and its instability under a broad range of fractionating conditions impeded purification of the protein to homogeneity (Hezari et al., Arch. Biochem. Biophys. 322:437-444, 1995). A 10 .mu.g sample of the electrophoretically-purified cyclase, prepared by standard analytical procedures (Schagger and von Jagow, Anal. Biochem. 166:368-379, 1987; Towbin et al., Proc. Natl. Acad. Sci. USA 76:350-4354, 1979), failed to provide amino-terminal sequence via Edman degradation. Repeated attempts at trypsinization and CNBr cleavage of comparable protein samples also failed to provide sequenceable peptides, in large part because of very low recoveries.

As an alternate approach to cDNA library screening using protein-based oligonucleotide probes, a PCR-based strategy was developed that was founded on a set of degenerate primers for PCR amplification designed to recognize highly-conserved regions of six higher plant terpene cyclases whose nucleotide sequences are known. Three of these cyclases, (-)-limonene synthase (a monoterpene cyclase from spearmint) (Colby et al., J. Biol. Chem. 268:23016-23024, 1993), epi-aristolochene synthase (a sesquiterpene cyclase from tobacco) (Facchini and Chappell, Proc. Natl. Acad. Sci. USA 89:11088-11092, 1992; Back and Chappell, J. Biol. Chem. 270:7375-7381, 1995), and casbene synthase (a diterpene cyclase from castor bean) (Mau and West, Proc. Natl. Acad. Sci. USA 91:8497-8501, 1994), exploit reaction mechanisms similar to taxadiene synthase in the cyclization of the respective geranyl (C.sub.10), farnesyl (C.sub.15), and geranylgeranyl (C.sub.20) diphosphate substrates (Lin et al., Biochemistry, in press). Kaurene synthase A from Arabidopsis thaliana (Sun and Karmiya, Plant Cell 6:1509-1518, 1994) and maize (Bensen et al., Plant Cell 7:75-84, 1995) and (-)-abietadiene synthase from grand fir (Abies grandis; Stofer Vogel, Wildung, Vogel, and Croteau, manuscript in preparation) exploit a quite different mechanism that involves protonation of the terminal double bond of geranylgeranyl diphosphate to initiate cyclization to the intermediate copalyl diphosphate followed, in the case of abietadiene synthase, by the more typical ionization of the diphosphate ester function to initiate a second cyclization sequence to the product olefin (LaFever et al., Arch. Biochem. Biophys. 313:139-149, 1994). The latter represents the only gymnosperm terpene cyclase sequence presently available.

Comparison of deduced amino acid sequences between all of the cyclases targeted eleven regions for PCR primer construction. Testing of all twenty primers in all combinations under a broad range of amplification conditions, followed by product analysis by gel electrophoresis, revealed that only one combination of primers [CC7.2 (forward) with CC3 (reverse), see FIG. 2 for locations] yielded a specific DNA fragment (83 bp) using T. brevifolia library phage as template. Primer CC3 delineates a region of strong homology between (-)-limonene synthase (Colby et al., J. Biol. Chem. 268:23016-23024, 1993), epi-aristolochene synthase (Facchini and Chappell, Proc. Natl. Acad. Sci. USA 89:11088-11092, 1992) and casbene synthase (Mau and West, Proc. Natl. Acad. Sci. USA 91:8497-8501, 1994). Primer CC7.2 was selected based on sequence comparison of the angiosperm diterpene cyclases (Mau and West, Proc. Natl. Acad. Sci. USA 91:8497-8501, 1994; Sun and Karmiya, Plant Cell 6:1509-1518, 1994; Bensen et al., Plant Cell 7:75-84, 1995) to the recently acquired cDNA clone encoding a gymnosperm diterpene cyclase, (-)-abietadiene synthase from grand fir (Stofer Vogel, Wildung, Vogel, and Croteau, manuscript in preparation).

The 83 bp fragment was cloned and sequenced, and thus demonstrated to be cyclase-like. This PCR product was .sup.32 P-labeled for use as a hybridization probe and employed in high stringency screening of 3.times.10.sup.5 plaques which yielded 102 positive signals. Fifty of these clones were purified through two additional rounds of screening, in vivo excised and the inserts sized. The twelve clones bearing the largest inserts (>2.0 kb) were partially sequenced, indicating that they were all representations of the same gene. Four of these inserts appeared to be full-length.

cDNA Expression in E. coli

All four of the full-length clones that were purified were out of frame or had stop sites immediately upstream of the starting methionine codon resulting from hairpin-primed second strand cDNA synthesis. The insert from pTb42 was cloned into frame by PCR methods, the blunt fragment was ligated into the EcoRV-site of pBluescript SK(-), yielding pTb42.1, and transformed into E. coli XL1-Blue.

Transformed E. coli were grown in LB medium supplemented with antibiotics and induced with IPTG. The cells were harvested and homogenized, and the extracts were assayed for taxadiene synthase activity using standard protocols with [1-.sup.3 H]geranylgeranyl diphosphate as substrate (Hezari et al., Arch. Biochem. Biophys. 322:437-444, 1995). The olefin fraction isolated from the reaction mixture contained a radioactive product (.about.1 nmol) that was coincident on capillary radio-GC with authentic taxa-4(5),11(12)-diene (Rt=19.40.+-.0.13 min).

The identification of this diterpene olefin was confirmed by capillary GC-MS analysis. The retention time (12.73 min. vs. 12.72 min.) and selected ion mass spectrum (Table I) of the diterpene olefin product was identical to that of authentic (.+-.)-taxa-4(5),11(12)-diene (Rubenstein, J. Org. Chem. 60:7215-7223, 1995). The origin of the selected diagnostic ions shown in Table I, which account for most of full spectrum abundance, are described herein and elsewhere (Koepp et al., J. Biol. Chem. 270:8686-8690, 1995). Because of different sample sizes, the total abundance of the authentic standard (2.96 E.sup.5) was approximately twice that of the biosynthetic olefin (1.42 E.sup.5). This, and variation in background between runs, probably account for minor differences in relative abundances of the high mass fragments.

TABLE 1______________________________________GC-MS Analysis of the Diterpene Olefin Synthesized by Recombinant Taxadiene Synthase ("Product") Compared to Authentic Taxa-4 (5), 11 (12) -diene ("Standard") Relative Abundance (%)m/z Product Standard______________________________________107 15.3 15.3 121 14.3 14.3 122 58.1 57.8 123 10.2 10.3 229 0.56 0.71 257 0.35 0.45 272 1.19 1.17______________________________________

Since identically prepared extracts of control cultures of E. coli that were transformed with pBluescript bearing an out-of-frame insert were incapable of transforming geranylgeranyl diphosphate to detectable levels of diterpene olefin, these results confirm that clone pTb42.1 encodes the taxadiene synthase from Pacific yew.

Sequence Analysis

Both strands of the inserts from pTb42 and pTb42.1 were sequenced. No mistakes were incorporated by Pfu polymerase. The pTb42.1 taxadiene synthase cDNA is 2700 nucleotides in length and contains a complete open reading frame of 2586 nucleotides (FIG. 2 and SEQ ID NO:1). The deduced amino acid sequence (SEQ ID NO:1 and SEQ ID NO:2) indicates the presence of a putative plastidial transit peptide of approximately 137 amino acids and a mature protein of about 725 residues (.about.82.5' kDa), based on the size of the native (mature) enzyme (.about.79 kDa) as estimated by gel permeation chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis ("SDS-PAGE") (Hezari et al., Arch. Biochem. Biophys. 322:437-444, 1995), the characteristic amino acid content and structural features of such aminoterminal targeting sequences, and their cleavage sites (Keegstra et al., Annu. Rev. Plant Physiol. Plant Mol. Biol. 40:471-501, 1989; von Heijne et al., Eur. J. Biochem. 180:535-545, 1989), and the fact that diterpene biosynthesis is localized exclusively within plastids (West et al., Rec. Adv. Phytochem. 13:163-198, 1979; Kleinig, Annu. Rev. Plant Physiol. Plant Mol. Biol. 40:39-59, 1989). The transit peptide/mature protein junction and thus the exact lengths of both moieties are unknown, because the amino terminus of the mature protein is apparently blocked and has not yet been identified.

Pairwise sequence comparison (Feng and Doolittle, Methods Enzymol. 183:375-387, 1990; Genetics Computer Group, Program Manual for the Wisconsin Packet, Version 8, Genetics Computer Group, Madison, Wis., 1994) with other terpene cyclases from higher plants revealed a significant degree of sequence similarity at the amino acid level. The taxadiene synthase from yew showed 32% identity and 55% similarity to (-)-limonene synthase from spearmint (Colby et al., J. Biol. Chem. 268:23016-23024, 1993), 30% identity and 54% similarity to epi-aristolochene synthase from tobacco (Facchini and Chappell, Proc. Natl. Acad. Sci. USA 89:11088-11092, 1992), 31% identity and 56% similarity to casbene synthase from castor bean (Mau and West, Proc. Natl. Acad. Sci. USA 91:8497-8501, 1994), and 33% identity and 56% similarity to kaurene synthase A from Arabidopsis thaliana and maize (Sun and Karmiya, Plant Cell 6:1509-1518, 1994; Bensen et al., Plant Cell 7:75-84, 1995), and 45% identity and 67% similarity to (-)-abietadiene synthase from grand fir (Stofer Vogel, Wildung, Vogel, and Croteau, manuscript in preparation). Pairwise comparison of other members within this group show roughly comparable levels of identity (30-40%) and similarity (50-60%). These terpenoid synthases represent a broad range of cyclase types from diverse plant families, supporting the suggestion of a common ancestry for this class of enzymes (Colby et al., J. Biol. Chem. 268:23016-23024, 1993; Mau and West, Proc. Natl. Acad. Sci. USA 91:8497-8501, 1994; Back and Chappell, J. Biol. Chem. 270:7375-7381, 1995; McGarvey and Croteau, Plant Cell 7:1015-1026, 1995; Chappell, Annu. Rev. Plant Physiol. Plant Mol. Biol. 46:521-547, 1995).

The amino acid sequence of taxadiene synthase (SEQ ID NO:1 and SEQ ID NO:2) does not closely resemble (identity .about.20%; similarity .about.40%) that of any of the microbial sesquiterpene cyclases that have been determined recently (Hohn and Beremand, Gene (Amst.) 79:131-136, 1989; Proctor and Hohn, J. Biol. Chem. 268:4543-4548, 1993; Cane et al., Biochemistry 33:5846-5857, 1994), nor does the taxadiene synthase sequence resemble any of the published sequences for prenyltransferases (Chen et al., Protein Sci. 3:600-607, 1994; Scolnik and Bartley, Plant Physiol. 104:1469-1470, 1994; Attucci et al. Arch. Biochem. Biophys. 321:493-500, 1995), a group of enzymes that, like the terpenoid cyclases, employ allylic diphosphate substrates and exploit similar electrophilic reaction mechanisms (Poulter and Rilling, in Biosynthesis of Isoprenoid Compounds, Porter and Spurgeon, eds., vol. 1, pp. 161-224, Wiley & Sons, New York, N.Y., 1981). The aspartate-rich (I,L,V)XDDXX(XX)D motif(s) (SEQ ID NO:6) found in most prenyltransferases and terpenoid cyclases (Facchini and Chappell, Proc. Natl. Acad. Sci. USA 89:11088-11092, 1992; Colby et al., J. Biol. Chem. 268:23016-23024, 1993; Mau and West, Proc. Natl. Acad. Sci. USA 91:8497-8501, 1994; Back and Chappell, J. Biol. Chem. 270:7375-7381, 1995; Hohn and Beremand, Gene (Amst.) 79:131-136, 1989; Proctor and Hohn, J. Biol. Chem. 268:4543-4548, 1993; Cane et al., Biochemistry 33:5846-5857, 1994; Chen et al., Protein Sci. 3:600-607, 1994; Scolnik and Bartley, Plant Physiol. 104:1469-1470, 1994; Attucci et al. Arch. Biochem. Biophys. 321:493-500, 1995; Abe and Prestwich, J. Biol. Chem. 269:802-804, 1994), and thought to play a role in substrate binding (Chen et al., Protein Sci. 3:600-607, 1994; Abe and Prestwich, J. Biol. Chem. 269:802-804, 1994; Marrero et al., J. Biol. Chem. 267:21873-21878, 1992; Joly and Edwards, J. Biol. Chem. 268:26983-26989, 1993; Tarshis et al., Biochemistry 33:10871-10877, 1994), is also present in taxadiene synthase, as is a related DXXDD motif (FIG. 2; SEQ ID NO:1 and SEQ ID NO:4). Histidine and cysteine residues have been implicated at the active sites of several terpenoid cyclases of plant origin (Rajaonarivony et al., Arch. Biochem. Biophys. 299:77-82, 1992; Savage et al. , Arch. Biochem. Biophys. 320:257-265, 1995). A search of the aligned sequences revealed that three histidines (at positions 370, 415 and 793) and three cysteines (at positions 329, 650 and 777) of taxadiene synthase are conserved among the plant terpenoid cyclase genes. The taxadiene synthase from yew most closely resembles the abietadiene synthase from grand fir rather than the casbene synthase from castor bean (Mau and West, Proc. Natl. Acad. Sci. USA 91:8497-8501, 1994), which catalyzes a similar type of cyclization reaction but is phylogenetically quite distant. The abietadiene synthase from grand fir is the only other terpenoid cyclase sequence from a gymnosperm now available (Stofer Vogel, Wildung, Vogel, and Croteau, in preparation), and these two diterpene cyclases from the coniferales share several regions of significant sequence homology, one of which was fortuitously chosen for primer construction and proved to be instrumental in the acquisition of a PCR-derived probe that led to the cloning of taxadiene synthase.

EXAMPLE 3

Expression of Taxadiene Synthase Genes Truncated to Remove Transit Peptide Sequences

The native taxadiene synthase gene sequence was truncated from the 5' end to removing part or all of the sequence that encodes the plastidial transit peptide of approximately 137 amino acids (the mature taxadiene synthase polypeptide is about 725 amino acids.) Deletion mutants were produced that remove amino acid residues from the amino terminus up to residue 31 (Glu), 39 (Ser), 49 (Ser), 54 (Gly), 79 (Val), or 82 (Ile). These mutants were expressed in E. coli calls and cell extracts were assayed for taxadiene synthase activity as described above. In preliminary experiments, expression of truncation mutants up was increased over wild-type taxadiene synthase by up to about 50%, with further truncation past residues 83-84 apparently decreasing taxadiene synthase activity.

Truncation of at least part of the plastidial transit peptide improves taxadiene synthase expression. Moreover, removing this sequence improves purification of taxadiene synthase, since the transit peptide is recognized by E. coli chaperonins, which co-purify with the enzyme and complicate purification, and because the taxadiene synthase preprotein tends to form inclusion bodies when expressed in E. coli.

The actual cleavage site for removal of the transit peptide may not be at the predicted cleavage site between residue 136 (Ser) and residue 137 (Pro). A transit peptide of 136 residues appears quite long, and other (monoterpene) synthases have a tandem pair of arginines (Arg-Arg) at about residue 60 (Met). Truncation immediately amino-terminal to the tandem pair of arginines of these synthases has resulted in excellent expression in E. coli. Taxadiene synthase lacks an Arg-Arg element. Also, truncation beyond residues 83-84 leads to lower activity.

This invention has been detailed both by example and by direct description. It should be apparent that one having ordinary skill in the relevant art would be able to surmise equivalents to the invention as described in the claims which follow but which would be within the spirit of the foregoing description. Those equivalents are to be included within the scope of this invention.

__________________________________________________________________________# SEQUENCE LISTING - - - - (1) GENERAL INFORMATION: - - (iii) NUMBER OF SEQUENCES: 6 - - - - (2) INFORMATION FOR SEQ ID NO:1: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 2700 ba - #se pairs (B) TYPE: nucleic a - #cid (C) STRANDEDNESS: doub - #le stranded (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #1: - - TTCCCCTGCC TCTCTGGAGA A - # - # - #21 - - ATG GCT CAG CTC TCA TTT AAT GCA GCG CTG AA - #G ATG AAC GCA TTG GGG 69 Met Ala Gln Leu Ser Phe Asn Ala Ala Leu Ly - #s Met Asn Ala Leu Gly 5 - # 10 - # 15 - - AAC AAG GCA ATC CAC GAT CCA ACG AAT TGC AG - #A GCC AAA TCT GAG CGC 117 Asn Lys Ala Ile His Asp Pro Thr Asn Cys Ar - #g Ala Lys Ser Glu Arg 20 - # 25 - # 30 - - CAA ATG ATG TGG GTT TGC TCC AGA TCA GGG CG - #A ACC AGA GTA AAA ATG 165 Gln Met Met Trp Val Cys Ser Arg Ser Gly Ar - #g Thr Arg Val Lys Met 35 - # 40 - # 45 - - TCG AGA GGA AGT GGT GGT CCT GGT CCT GTC GT - #A ATG ATG AGC AGC AGC 213 Ser Arg Gly Ser Gly Gly Pro Gly Pro Val Va - #l Met Met Ser Ser Ser 50 - # 55 - # 60 - - ACT GGC ACT AGC AAG GTG GTT TCC GAG ACT TC - #C AGT ACC ATT GTG GAT 261 Thr Gly Thr Ser Lys Val Val Ser Glu Thr Se - #r Ser Thr Ile Val Asp 65 - #70 - #75 - #80 - - GAT ATC CCT CGA CTC TCC GCC AAT TAT CAT GG - #C GAT CTG TGG CAC CAC 309 Asp Ile Pro Arg Leu Ser Ala Asn Tyr His Gl - #y Asp Leu Trp His His 85 - # 90 - # 95 - - AAT GTT ATA CAA ACT CTG GAG ACA CCG TTT CG - #T GAG AGT TCT ACT TAC 357 Asn Val Ile Gln Thr Leu Glu Thr Pro Phe Ar - #g Glu Ser Ser Thr Tyr 100 - # 105 - # 110 - - CAA GAA CGG GCA GAT GAG CTG GTT GTG AAA AT - #T AAA GAT ATG TTC AAT 405 Gln Glu Arg Ala Asp Glu Leu Val Val Lys Il - #e Lys Asp Met Phe Asn 115 - # 120 - # 125 - - GCG CTC GGA GAC GGA GAT ATC AGT CCG TCT GC - #A TAC GAC ACT GCG TGG 453 Ala Leu Gly Asp Gly Asp Ile Ser Pro Ser Al - #a Tyr Asp Thr Ala Trp 130 - # 135 - # 140 - - GTG GCG AGG CTG GCG ACC ATT TCC TCT GAT GG - #A TCT GAG AAG CCA CGG 501 Val Ala Arg Leu Ala Thr Ile Ser Ser Asp Gl - #y Ser Glu Lys Pro Arg 145 1 - #50 1 - #55 1 -#60 - - TTT CCT CAG GCC CTC AAC TGG GTT TTC AAC AA - #C CAG CTC CAG GATGGA 549 Phe Pro Gln Ala Leu Asn Trp Val Phe Asn As - #n Gln Leu Gln Asp Gly 165 - # 170 - # 175 - - TCG TGG GGT ATC GAA TCG CAC TTT AGT TTA TG - #C GAT CGA TTG CTT AAC 597 Ser Trp Gly Ile Glu Ser His Phe Ser Leu Cy - #s Asp Arg Leu Leu Asn 180 - # 185 - # 190 - - ACG ACC AAT TCT GTT ATC GCC CTC TCG GTT TG - #G AAA ACA GGG CAC AGC 645 Thr Thr Asn Ser Val Ile Ala Leu Ser Val Tr - #p Lys Thr Gly His Ser 195 - # 200 - # 205 - - CAA GTA CAA CAA GGT GCT GAG TTT ATT GCA GA - #G AAT CTA AGA TTA CTC 693 Gln Val Gln Gln Gly Ala Glu Phe Ile Ala Gl - #u Asn Leu Arg Leu Leu 210 - # 215 - # 220 - - AAT GAG GAA GAT GAG TTG TCC CCG GAT TTC CA - #A ATA ATC TTT CCT GCT 741 Asn Glu Glu Asp Glu Leu Ser Pro Asp Phe Gl - #n Ile Ile Phe Pro Ala 225 2 - #30 2 - #35 2 -#40 - - CTG CTG CAA AAG GCA AAA GCG TTG GGG ATC AA - #T CTT CCT TAC GATCTT 789 Leu Leu Gln Lys Ala Lys Ala Leu Gly Ile As - #n Leu Pro Tyr Asp Leu 245 - # 250 - # 255 - - CCA TTT ATC AAA TAT TTG TCG ACA ACA CGG GA - #A GCC AGG CTT ACA GAT 837 Pro Phe Ile Lys Tyr Leu Ser Thr Thr Arg Gl - #u Ala Arg Leu Thr Asp 260 - # 265 - # 270 - - GTT TCT GCG GCA GCA GAC AAT ATT CCA GCC AA - #C ATG TTG AAT GCG TTG 885 Val Ser Ala Ala Ala Asp Asn Ile Pro Ala As - #n Met Leu Asn Ala Leu 275 - # 280 - # 285 - - GAA GGT CTC GAG GAA GTT ATT GAC TGG AAC AA - #G ATT ATG AGG TTT CAA 933 Glu Gly Leu Glu Glu Val Ile Asp Trp Asn Ly - #s Ile Met Arg Phe Gln 290 - # 295 - # 300 - - AGT AAA GAT GGA TCT TTC CTG AGC TCC CCT GC - #C TCC ACT GCC TGT GTA 981 Ser Lys Asp Gly Ser Phe Leu Ser Ser Pro Al - #a Ser Thr Ala Cys Val 305 3 - #10 3 - #15 3 -#20 - - CTG ATG AAT ACA GGG GAC GAA AAA TGT TTC AC - #T TTT CTC AAC AATCTG 1029 Leu Met Asn Thr Gly Asp Glu Lys Cys Phe Th - #r Phe Leu Asn Asn Leu 325 - # 330 - # 335 - - CTC GAC AAA TTC GGC GGC TGC GTG CCC TGT AT - #G TAT TCC ATC GAT CTG 1077 Leu Asp Lys Phe Gly Gly Cys Val Pro Cys Me - #t Tyr Ser Ile Asp Leu 340 - # 345 - # 350 - - CTG GAA CGC CTT TCG CTG GTT GAT AAC ATT GA - #G CAT CTC GGA ATC GGT 1125 Leu Glu Arg Leu Ser Leu Val Asp Asn Ile Gl - #u His Leu Gly Ile Gly 355 - # 360 - # 365 - - CGC CAT TTC AAA CAA GAA ATC AAA GGA GCT CT - #T GAT TAT GTC TAC AGA 1173 Arg His Phe Lys Gln Glu Ile Lys Gly Ala Le - #u Asp Tyr Val Tyr Arg 370 - # 375 - # 380 - - CAT TGG AGT GAA AGG GGC ATC GGT TGG GGC AG - #A GAC AGC CTT GTT CCA 1221 His Trp Ser Glu Arg Gly Ile Gly Trp Gly Ar - #g Asp Ser Leu Val Pro 385 3 - #90 3 - #95 4 -#00 - - GAT CTC AAC ACC ACA GCC CTC GGC CTG CGA AC - #T CTT CGC ATG CACGGA 1269 Asp Leu Asn Thr Thr Ala Leu Gly Leu Arg Th - #r Leu Arg Met His Gly 405 - # 410 - # 415 - - TAC AAT GTT TCT TCA GAC GTT TTG AAT AAT TT - #C AAA GAT GAA AAC GGG 1317 Tyr Asn Val Ser Ser Asp Val Leu Asn Asn Ph - #e Lys Asp Glu Asn Gly 420 - # 425 - # 430 - - CGG TTC TTC TCC TCT GCG GGC CAA ACC CAT GT - #C GAA TTG AGA AGC GTG 1365 Arg Phe Phe Ser Ser Ala Gly Gln Thr His Va - #l Glu Leu Arg Ser Val 435 - # 440 - # 445 - - GTG AAT CTT TTC AGA GCT TCC GAC CTT GCA TT - #T CCT GAC GAA AGA GCT 1413 Val Asn Leu Phe Arg Ala Ser Asp Leu Ala Ph - #e Pro Asp Glu Arg Ala 450 - # 455 - # 460 - - ATG GAC GAT GCT AGA AAA TTT GCA GAA CCA TA - #T CTT AGA GAG GCA CTT 1461 Met Asp Asp Ala Arg Lys Phe Ala Glu Pro Ty - #r Leu Arg Glu Ala Leu 465 4 - #70 4 - #75 4 -#80 - - GCA ACG AAA ATC TCA ACC AAT ACA AAA CTA TT - #C AAA GAG ATT GAGTAC 1509 Ala Thr Lys Ile Ser Thr Asn Thr Lys Leu Ph - #e Lys Glu Ile Glu Tyr 485 - # 490 - # 495 - - GTG GTG GAG TAC CCT TGG CAC ATG AGT ATC CC - #A CGC TTA GAA GCC AGA 1557 Val Val Glu Tyr Pro Trp His Met Ser Ile Pr - #o Arg Leu Glu Ala Arg 500 - # 505 - # 510 - - AGT TAT ATT GAT TCA TAT GAC GAC AAT TAT GT - #A TGG CAG AGG AAG ACT 1605 Ser Tyr Ile Asp Ser Tyr Asp Asp Asn Tyr Va - #l Trp Gln Arg Lys Thr 515 - # 520 - # 525 - - CTA TAT AGA ATG CCA TCT TTG AGT AAT TCA AA - #A TGT TTA GAA TTG GCA 1653 Leu Tyr Arg Met Pro Ser Leu Ser Asn Ser Ly - #s Cys Leu Glu Leu Ala 530 - # 535 - # 540 - - AAA TTG GAC TTC AAT ATC GTA CAA TCT TTG CA - #T CAA GAG GAG TTG AAG 1701 Lys Leu Asp Phe Asn Ile Val Gln Ser Leu Hi - #s Gln Glu Glu Leu Lys 545 5 - #50 5 - #55 5 -#60 - - CTT CTA ACA AGA TGG TGG AAG GAA TCC GGC AT - #G GCA GAT ATA AATTTC 1749 Leu Leu Thr Arg Trp Trp Lys Glu Ser Gly Me - #t Ala Asp Ile Asn Phe 565 - # 570 - # 575 - - ACT CGA CAC CGA GTG GCG GAG GTT TAT TTT TC - #A TCA GCT ACA TTT GAA 1797 Thr Arg His Arg Val Ala Glu Val Tyr Phe Se - #r Ser Ala Thr Phe Glu 580 - # 585 - # 590 - - CCC GAA TAT TCT GCC ACT AGA ATT GCC TTC AC - #A AAA ATT GGT TGT TTA 1845 Pro Glu Tyr Ser Ala Thr Arg Ile Ala Phe Th - #r Lys Ile Gly Cys Leu 595 - # 600 - # 605 - - CAA GTC CTT TTT GAT GAT ATG GCT GAC ATC TT - #T GCA ACA CTA GAT GAA 1893 Gln Val Leu Phe Asp Asp Met Ala Asp Ile Ph - #e Ala Thr Leu Asp Glu 610 - # 615 - # 620 - - TTG AAA AGT TTC ACT GAG GGA GTA AAG AGA TG - #G GAT ACA TCT TTG CTA 1941 Leu Lys Ser Phe Thr Glu Gly Val Lys Arg Tr - #p Asp Thr Ser Leu Leu 625 6 - #30 6 - #35 6 -#40 - - CAT GAG ATT CCA GAG TGT ATG CAA ACT TGC TT - #T AAA GTT TGG TTCAAA 1989 His Glu Ile Pro Glu Cys Met Gln Thr Cys Ph - #e Lys Val Trp Phe Lys 645 - # 650 - # 655 - - TTA ATG GAA GAA GTA AAT AAT GAT GTG GTT AA - #G GTA CAA GGA CGT GAC 2037 Leu Met Glu Glu Val Asn Asn Asp Val Val Ly - #s Val Gln Gly Arg Asp 660 - # 665 - # 670 - - ATG CTC GCT CAC ATA AGA AAA CCC TGG GAG TT - #G TAC TTC AAT TGT TAT 2085 Met Leu Ala His Ile Arg Lys Pro Trp Glu Le - #u Tyr Phe Asn Cys Tyr 675 - # 680 - # 685 - - GTA CAA GAA AGG GAG TGG CTT GAA GCC GGG TA - #T ATA CCA ACT TTT GAA 2133 Val Gln Glu Arg Glu Trp Leu Glu Ala Gly Ty - #r Ile Pro Thr Phe Glu 690 - # 695 - # 700 - - GAG TAC TTA AAG ACT TAT GCT ATA TCA GTA GG - #C CTT GGA CCG TGT ACC 2181 Glu Tyr Leu Lys Thr Tyr Ala Ile Ser Val Gl - #y Leu Gly Pro Cys Thr 705 7 - #10 7 - #15 7 -#20 - - CTA CAA CCA ATA CTA CTA ATG GGT GAG CTT GT - #G AAA GAT GAT GTTGTT 2229 Leu Gln Pro Ile Leu Leu Met Gly Glu Leu Va - #l Lys Asp Asp Val Val 725 - # 730 - # 735 - - GAG AAA GTG CAC TAT CCC TCA AAT ATG TTT GA - #G CTT GTA TCC TTG AGC 2277 Glu Lys Val His Tyr Pro Ser Asn Met Phe Gl - #u Leu Val Ser Leu Ser 740 - # 745 - # 750 - - TGG CGA CTA ACA AAC GAC ACC AAA ACA TAT CA - #G GCT GAA AAG GCT CGA 2325 Trp Arg Leu Thr Asn Asp Thr Lys Thr Tyr Gl - #n Ala Glu Lys Ala Arg 755 - # 760 - # 765 - - GGA CAA CAA GCC TCA GGC ATA GCA TGC TAT AT - #G AAG GAT AAT CCA GGA 2373 Gly Gln Gln Ala Ser Gly Ile Ala Cys Tyr Me - #t Lys Asp Asn Pro Gly 770 - # 775 - # 780 - - GCA ACT GAG GAA GAT GCC ATT AAG CAC ATA TG - #T CGT GTT GTT GAT CGG 2421 Ala Thr Glu Glu Asp Ala Ile Lys His Ile Cy - #s Arg Val Val Asp Arg 785 7 - #90 7 - #95 8 -#00 - - GCC TTG AAA GAA GCA AGC TTT GAA TAT TTC AA - #A CCA TCC AAT GATATC 2469 Ala Leu Lys Glu Ala Ser Phe Glu Tyr Phe Ly - #s Pro Ser Asn Asp Ile 805 - # 810 - # 815 - - CCA ATG GGT TGC AAG TCC TTT ATT TTT AAC CT - #T AGA TTG TGT GTC CAA 2517 Pro Met Gly Cys Lys Ser Phe Ile Phe Asn Le - #u Arg Leu Cys Val Gln 820 - # 825 - # 830 - - ATC TTT TAC AAG TTT ATA GAT GGG TAC GGA AT - #C GCC AAT GAG GAG ATT 2565 Ile Phe Tyr Lys Phe Ile Asp Gly Tyr Gly Il - #e Ala Asn Glu Glu Ile 835 - # 840 - # 845 - - AAG GAC TAT ATA AGA AAA GTT TAT ATT GAT CC - #A ATT CAA GTA TGA 2610 Lys Asp Tyr Ile Arg Lys Val Tyr Ile Asp Pr - #o Ile Gln Val 850 - # 855 - # 860 - - TATATCATGT AAAACCTCTT TTTCATGATA AATTGACTTA TTATTGTATT GG -#CAAAAAAA 2670 - - AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA - # - # 2700 - - - - (2) INFORMATION FOR SEQ ID NO: 2: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 862 amino - #acid residues (B) TYPE: amino aci - #d (C) STRANDEDNESS: sing - #le stranded (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #2: - - Met Ala Gln Leu Ser Phe Asn Ala Ala Leu Ly - #s Met Asn Ala Leu Gly 5 - # 10 - # 15 - - Asn Lys Ala Ile His Asp Pro Thr Asn Cys Ar - #g Ala Lys Ser Glu Arg 20 - # 25 - # 30 - - Gln Met Met Trp Val Cys Ser Arg Ser Gly Ar - #g Thr Arg Val Lys Met 35 - # 40 - # 45 - - Ser Arg Gly Ser Gly Gly Pro Gly Pro Val Va - #l Met Met Ser Ser Ser 50 - # 55 - # 60 - - Thr Gly Thr Ser Lys Val Val Ser Glu Thr Se - #r Ser Thr Ile Val Asp 65 - #70 - #75 - #80 - - Asp Ile Pro Arg Leu Ser Ala Asn Tyr His Gl - #y Asp Leu Trp His His 85 - # 90 - # 95 - - Asn Val Ile Gln Thr Leu Glu Thr Pro Phe Ar - #g Glu Ser Ser Thr Tyr 100 - # 105 - # 110 - - Gln Glu Arg Ala Asp Glu Leu Val Val Lys Il - #e Lys Asp Met Phe Asn 115 - # 120 - # 125 - - Ala Leu Gly Asp Gly Asp Ile Ser Pro Ser Al - #a Tyr Asp Thr Ala Trp 130 - # 135 - # 140 - - Val Ala Arg Leu Ala Thr Ile Ser Ser Asp Gl - #y Ser Glu Lys Pro Arg 145 1 - #50 1 - #55 1 -#60 - - Phe Pro Gln Ala Leu Asn Trp Val Phe Asn As - #n Gln Leu Gln AspGly 165 - # 170 - # 175 - - Ser Trp Gly Ile Glu Ser His Phe Ser Leu Cy - #s Asp Arg Leu Leu Asn 180 - # 185 - # 190 - - Thr Thr Asn Ser Val Ile Ala Leu Ser Val Tr - #p Lys Thr Gly His Ser 195 - # 200 - # 205 - - Gln Val Gln Gln Gly Ala Glu Phe Ile Ala Gl - #u Asn Leu Arg Leu Leu 210 - # 215 - # 220 - - Asn Glu Glu Asp Glu Leu Ser Pro Asp Phe Gl - #n Ile Ile Phe Pro Ala 225 2 - #30 2 - #35 2 -#40 - - Leu Leu Gln Lys Ala Lys Ala Leu Gly Ile As - #n Leu Pro Tyr AspLeu 245 - # 250 - # 255 - - Pro Phe Ile Lys Tyr Leu Ser Thr Thr Arg Gl - #u Ala Arg Leu Thr Asp 260 - # 265 - # 270 - - Val Ser Ala Ala Ala Asp Asn Ile Pro Ala As - #n Met Leu Asn Ala Leu 275 - # 280 - # 285 - - Glu Gly Leu Glu Glu Val Ile Asp Trp Asn Ly - #s Ile Met Arg Phe Gln 290 - # 295 - # 300 - - Ser Lys Asp Gly Ser Phe Leu Ser Ser Pro Al - #a Ser Thr Ala Cys Val 305 3 - #10 3 - #15 3 -#20 - - Leu Met Asn Thr Gly Asp Glu Lys Cys Phe Th - #r Phe Leu Asn AsnLeu 325 - # 330 - # 335 - - Leu Asp Lys Phe Gly Gly Cys Val Pro Cys Me - #t Tyr Ser Ile Asp Leu 340 - # 345 - # 350 - - Leu Glu Arg Leu Ser Leu Val Asp Asn Ile Gl - #u His Leu Gly Ile Gly 355 - # 360 - # 365 - - Arg His Phe Lys Gln Glu Ile Lys Gly Ala Le - #u Asp Tyr Val Tyr Arg 370 - # 375 - # 380 - - His Trp Ser Glu Arg Gly Ile Gly Trp Gly Ar - #g Asp Ser Leu Val Pro 385 3 - #90 3 - #95 4 -#00 - - Asp Leu Asn Thr Thr Ala Leu Gly Leu Arg Th - #r Leu Arg Met HisGly 405 - # 410 - # 415 - - Tyr Asn Val Ser Ser Asp Val Leu Asn Asn Ph - #e Lys Asp Glu Asn Gly 420 - # 425 - # 430 - - Arg Phe Phe Ser Ser Ala Gly Gln Thr His Va - #l Glu Leu Arg Ser Val 435 - # 440 - # 445 - - Val Asn Leu Phe Arg Ala Ser Asp Leu Ala Ph - #e Pro Asp Glu Arg Ala 450 - # 455 - # 460 - - Met Asp Asp Ala Arg Lys Phe Ala Glu Pro Ty - #r Leu Arg Glu Ala Leu 465 4 - #70 4 - #75 4 -#80 - - Ala Thr Lys Ile Ser Thr Asn Thr Lys Leu Ph - #e Lys Glu Ile GluTyr 485 - # 490 - # 495 - - Val Val Glu Tyr Pro Trp His Met Ser Ile Pr - #o Arg Leu Glu Ala Arg 500 - # 505 - # 510 - - Ser Tyr Ile Asp Ser Tyr Asp Asp Asn Tyr Va - #l Trp Gln Arg Lys Thr 515 - # 520 - # 525 - - Leu Tyr Arg Met Pro Ser Leu Ser Asn Ser Ly - #s Cys Leu Glu Leu Ala 530 - # 535 - # 540 - - Lys Leu Asp Phe Asn Ile Val Gln Ser Leu Hi - #s Gln Glu Glu Leu Lys 545 5 - #50 5 - #55 5 -#60 - - Leu Leu Thr Arg Trp Trp Lys Glu Ser Gly Me - #t Ala Asp Ile AsnPhe 565 - # 570 - # 575 - - Thr Arg His Arg Val Ala Glu Val Tyr Phe Se - #r Ser Ala Thr Phe Glu 580 - # 585 - # 590 - - Pro Glu Tyr Ser Ala Thr Arg Ile Ala Phe Th - #r Lys Ile Gly Cys Leu 595 - # 600 - # 605 - - Gln Val Leu Phe Asp Asp Met Ala Asp Ile Ph - #e Ala Thr Leu Asp Glu 610 - # 615 - # 620 - - Leu Lys Ser Phe Thr Glu Gly Val Lys Arg Tr - #p Asp Thr Ser Leu Leu 625 6 - #30 6 - #35 6 -#40 - - His Glu Ile Pro Glu Cys Met Gln Thr Cys Ph - #e Lys Val Trp PheLys 645 - # 650 - # 655 - - Leu Met Glu Glu Val Asn Asn Asp Val Val Ly - #s Val Gln Gly Arg Asp 660 - # 665 - # 670 - - Met Leu Ala His Ile Arg Lys Pro Trp Glu Le - #u Tyr Phe Asn Cys Tyr 675 - # 680 - # 685 - - Val Gln Glu Arg Glu Trp Leu Glu Ala Gly Ty - #r Ile Pro Thr Phe Glu 690 - # 695 - # 700 - - Glu Tyr Leu Lys Thr Tyr Ala Ile Ser Val Gl - #y Leu Gly Pro Cys Thr 705 7 - #10 7 - #15 7 -#20 - - Leu Gln Pro Ile Leu Leu Met Gly Glu Leu Va - #l Lys Asp Asp ValVal 725 - # 730 - # 735 - - Glu Lys Val His Tyr Pro Ser Asn Met Phe Gl - #u Leu Val Ser Leu Ser 740 - # 745 - # 750 - - Trp Arg Leu Thr Asn Asp Thr Lys Thr Tyr Gl - #n Ala Glu Lys Ala Arg 755 - # 760 - # 765 - - Gly Gln Gln Ala Ser Gly Ile Ala Cys Tyr Me - #t Lys Asp Asn Pro Gly 770 - # 775 - # 780 - - Ala Thr Glu Glu Asp Ala Ile Lys His Ile Cy - #s Arg Val Val Asp Arg 785 7 - #90 7 - #95 8 -#00 - - Ala Leu Lys Glu Ala Ser Phe Glu Tyr Phe Ly - #s Pro Ser Asn AspIle 805 - # 810 - # 815 - - Pro Met Gly Cys Lys Ser Phe Ile Phe Asn Le - #u Arg Leu Cys Val Gln 820 - # 825 - # 830 - - Ile Phe Tyr Lys Phe Ile Asp Gly Tyr Gly Il - #e Ala Asn Glu Glu Ile 835 - # 840 - # 845 - - Lys Asp Tyr Ile Arg Lys Val Tyr Ile Asp Pr - #o Ile Gln Val 850 - # 855 - # 860 - - - - (2) INFORMATION FOR SEQ ID NO: 3: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 5 amino - #acid residues (B) TYPE: amino aci - #d (C) STRANDEDNESS: sing - #le stranded (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #3: - - Asp Asp Xaa Xaa Asp 5 - - - - (2) INFORMATION FOR SEQ ID NO: 4: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 5 amino - #acid residues (B) TYPE: amino aci - #d (C) STRANDEDNESS: sing - #le stranded (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #4: - - Asp Xaa Xaa Asp Asp 5 - - - - (2) INFORMATION FOR SEQ ID NO: 5: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 4 amino - #acid residues (B) TYPE: amino aci - #d (C) STRANDEDNESS: sing - #le stranded (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #5: - - Arg Trp Trp Lys - - - - (2) INFORMATION FOR SEQ ID NO: 6: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 9 amino - #acid residues (B) TYPE: amino aci - #d (C) STRANDEDNESS: sing - #le stranded (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #6: - - Xaa Xaa Asp Asp Xaa Xaa Xaa Xaa Asp__________________________________________________________________________

Claims

1. An isolated polynucleotide comprising a sequence that encodes a polypeptide with taxadiene synthase activity, wherein the complement of the polynucleotide hybridizes under stringent conditions with a nucleic acid sequence as shown in SEQ ID NO:1, wherein stringent conditions comprise wash conditions of 0.1.times.SSC and 0.5% SDS at a temperature of 68.degree. C.

2. The isolated nucleic acid molecule of claim 1, comprising nucleotides 22-2610 of SEQ ID NO:1.

3. The polynucleotide of claim 1 wherein the polypeptide-encoding sequence encodes a polypeptide having SEQ ID NO:2 except for an amino acid substitution at at least one location selected from the group consisting of: cysteine residues 329, 650, 719, and 777; histidine residues 370, 415, 579, and 793; a DDXXD motif; a DXXDD motif; a conserved arginine; and a RWWK element.

4. The polynucleotide of claim 1 wherein the polypeptide-encoding sequence encodes a polypeptide that lacks at least part of a transit peptide sequence of a native Pacific yew taxadiene synthase polypeptide.

5. A recombinant nucleic acid molecule comprising a promoter sequence operably linked to the nucleic acid molecule of claim 1.

6. A transformed cell comprising the polynucleotide of claim 1.

7. A transformed plant cell comprising the polynucleotide of claim 1.

8. A transgenic plant comprising the polynucleotide of claim 1.

9. A method of expressing a taxadiene synthase polypeptide in a transformed cell, the method comprising the steps of:

providing a transformed taxoid-producing cell that comprises an expressible polynucleotide that encodes a taxadiene synthase polypeptide having taxadiene synthase activity according to claim 1; and

culturing the cell under conditions suitable for the expression of the polypeptide wherein expression of the polypeptide causes the cell to produce a higher level of a taxoid than an otherwise similar cell that lacks the expressible polynucleotide.

10. A cell transformed with the recombinant nucleic acid molecule of claim 5.

11. A transgenic plant comprising the recombinant nucleic acid molecule of claim 5.

12. An isolated nucleic acid molecule encoding a protein wherein the protein comprises an amino acid sequence as shown in SEQ ID NO:2.

13. A recombinant nucleic acid molecule comprising a promoter sequence operably linked to the nucleic acid molecule of claim 12.

14. A cell transformed with the recombinant nucleic acid molecule of claim 13.

15. A transgenic plant comprising the recombinant nucleic acid molecule of claim 13.

16. An isolated polynucleotide comprising at least 7 consecutive nucleotides of the sequence comprising nucleotides 22-2610 of SEQ ID NO:1.

17. The isolated polynucleotide of claim 16 comprising at least 30 consecutive nucleotides.

18. A transformed cell comprising the polynucleotide of claim 16.

19. A transformed plant cell comprising the polynucleotide of claim 16.

20. A transgenic plant comprising the polynucleotide of claim 1.

21. An isolated polynucleotide comprising a least 30 consecutive nucleotides SEQ ID NO:1 comprising a sequence that encodes a polypeptide having taxadiene synthase activity.

22. An oligonucleotide comprising a nucleotide sequence of at least 7 contiguous nucleotides nucleotides 22-2610 of the sequence as shown in SEQ ID NO:1.

23. The oligonucleotide of claim 22 comprising at least 30 contiguous nucleotides.