# Patent

## Title
Cis-prenyltransferases from plants

## Abstract

This invention pertains to nucleic acid fragments encoding plant proteins that are homologs to the cis-prenyltransferases UPP synthase from the bacterium Micrococcus luteus or Dedol-PP synthase from yeast Saccharomyces cerevisiae. More specifically, this invention pertains to cis-prenyltransferase homologs from wheat, grape, soybean, rice, African daisy, rubber tree latex and pot marigold.

## Background
CROSS REFERENCE TO RELATED APPLICATION
This application is a continuation of Ser. No. 10/700,171 filed Sep. 21, 2000, which is a divisional of non-provisional application Ser. No. 09/655,908 filed Sep. 6, 2000, now U.S. Pat. No. 6,645,747, which claimed priority to provisional application 60/155,046 filed Sep. 21, 1999, all of which are hereby incorporated by reference.


FIELD OF THE INVENTION
This invention is in the field of plant molecular biology. This invention pertains to nucleic acid fragments from plants encoding proteins that are homologs of the undecaprenyl diphosphate and dehydrodolichyl diphosphate synthases (cis-prenyltransferases) previously identified only in microbes. More specifically, this invention pertains to homologs from wheat, grape, soybean, rice, African daisy, rubber tree and pot marigold.
BACKGROUND OF THE INVENTION
Plants synthesize a variety of hydrocarbons built up of isoprene units (C5H8), termed polyisoprenoids (Tanaka, Y. In Rubber and Related Polyprenols. Methods in Plant Biochemistry; Dey, P. M. and Harborne, J. B., Eds., Academic Press: San Diego, (1991) 7:519-536). Those with from 45 to 115 carbon atoms, and varying numbers of cis-and trans- (Z- and E-) double bonds, are termed polyprenols, while those of longer chain length are termed rubbers (Tanaka, Y., In Minor Classes of Terpenoids. Methods in Plant Biochemistry; Dey, P. M. and Harborne, J. B., Eds., Academic Press: San Diego, (1991) 7:537-542). The synthesis of these compounds is carried out by a family of enzymes termed prenyltransferases, which catalyze the sequential addition of C5 units to an initiator molecule.
The initiator molecules themselves are derived from isoprene units through the action of distinct prenyltransferases, and are allylic terpenoid diphosphates such as dimethylallyldiphosphate (DMAPP), but more usually the C10 compound geranyl diphosphate (GPP), the C15 compound farnesyl diphosphate (FPP) or the C20 compound geranylgeranyl diphosphate (GGPP). Genes encoding the enzymes which synthesize these allylic terpenoid diphosphates have been cloned from a number of organisms, including plants, and all of these genes encode polypeptides with conserved regions of homology (McGarvey, et al., (1995) Plant Cell 7:1015-1026; Chappell, (1995) Annu. Rev. Plant Physiol. Plant Mol. Biol. 46:521-547). All of these gene products condense isoprene units in the trans-configuration. Prenyltransferases which condense isoprene units in a cis-configuration have not been identified in higher animals or plants, nor have prenyltransferases catalyzing extension of the polyisoprenoid chain beyond the C20 compound geranylgeranyl diphosphate.
A gene encoding octaprenyl diphosphate (OPP) synthase from the bacterium E. coli was identified (Asai, et al., (1994) Biochem. Biophys. Res. Commun. 202:340-345), and more recently, genes encoding bacterial undecaprenyl diphosphate (UPP) synthases (Shimizu, et al., (1998) J. Biol. Chem. 273:19476-19481; Apfel, et al., (1999) J. Bacteriol. 181:483-492) and yeast dehydrodolichyl diphosphate (Dedol-PP) synthase (Sato, et al., (1999) Mol. Cell. Biol. 19:471-483) were identified. OPP synthase generates the all-trans polyisoprenoid side chain of biological quinones (ubiquinone-8, menaquinone-8 and dimethylmenaquinone-8), and its primary structure contains regions of similarity with GPP, FPP and GGPP synthases. UPP synthase and Dedol-PP synthase generate cis-polyisoprenoids, and their primary structures are related to each other but distinct from those of OPP, GPP, FPP and GGPP synthases.
There are several suggested functions for plant polyisoprenoids. Terpenoid quinones are most likely involved in photophosphorylation and respiratory chain phosphorylation. Rubbers have been implicated in plant defense against herbivory, possibly serving to repel and entrap insects and seal wounds in a manner analogous to plant resins. The specific roles of the C45-C115 polyprenols remain unidentified, although as with most secondary metabolites they too most likely function in plant defense. Short-chain polyprenols may also be involved in protein glycosylation in plants, by analogy with the role of dolichols in animal metabolism.
The problem to be solved is to identify new plant genes having utility in plant defense mechanisms. Applicants have solved the stated problem by the identification of plant genes encoding plant cis-prenyltransferases. The present invention presents genes with significant homology to the bacterial UPP synthase and yeast Dedol-PP synthase from plants. The present invention shows that such genes are present in a range of plant species, including economically important crop plants such as cereals and the rubber tree Hevea brasiliensis, and thus are likely to be ubiquitous in plants.
This invention pertains to the identification and characterization of EST sequences from wheat, grape, soybean, rice, African daisy, rubber tree and pot marigold encoding cis-prenyltransferase proteins from these species.
SUMMARY OF THE INVENTION
It is an object of the present invention to provide an isolated nucleic acid fragment encoding a plant cis-prenyltransferase protein selected from the group consisting of: (a) an isolated nucleic acid fragment encoding all or a substantial portion of the amino acid sequence selected from the group consisting of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18 and SEQ ID NO: 20; (b) an isolated nucleic acid fragment that is substantially similar to an isolated nucleic acid fragment encoding all or a substantial portion of the amino acid sequence selected from the group consisting of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18 and SEQ ID NO: 20; (c) an isolated nucleic acid fragment encoding a polypeptide, the polypeptide having at least 41% identity with the amino acid sequence set forth in SEQ ID NO: 24; (d) an isolated nucleic acid fragment encoding having at least 50% identity with nucleic acid sequence as set forth in SEQ ID NO: 23; (e) an isolated nucleic acid molecule that hybridizes with a nucleic acid sequence of (a) (b), (c) or (d) under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and washed with 0.2×SSC, 0.5% SDS; (f) an isolated nucleic acid fragment that hybridizes with a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17 and SEQ ID NO: 19 under the following hybridization conditions 0.1×SSC, 0.1% SDS, 65° C. and washed with 0.2×SSC, 0.5% SDS; and (g) an isolated nucleic acid fragment that is complementary to (a), (b), (c), (d), (e) or (f).
The invention further provides polypeptides encoded by the isolated nucleic acid fragments of the present invention, such as are presented in SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18 and SEQ ID NO: 20.
In another embodiment the invention provides a chimeric gene comprising the isolated nucleic acid fragment of the present invention operably linked to suitable regulatory sequences.
The invention additionally provides a method of altering the level of expression of a plant cis-prenyltransferase protein in a host cell comprising: (a) transforming a host cell with the chimeric gene of the present invention and; (b) growing the transformed host cell produced in step (a) under conditions that are suitable for expression of the chimeric gene resulting in production of altered levels of a plant cis-prenyltransferase protein in the transformed host cell relative to expression levels of an untransformed host cell. The invention further provides that where the cis-prenyltransferase protein is expressed in a transformed plant that the defense mechanism of the plant will be modulated.
The invention additionally provides transformed host cells comprising the chimeric genes of the present invention.
In an alternative embodiment the invention provides methods of obtaining a nucleic acid fragment encoding all or a substantial portion of the amino acid sequence encoding a plant cis-prenyltransferase protein using portions of the present nucleic acid sequences as hybridization probes or as primers.



BRIEF DESCRIPTION OF THE DRAWINGS AND SEQUENCE DESCRIPTIONS
FIG. 1 shows a scheme for synthesis of GPP, FPP and GGPP from IPP and the synthesis of polyprenols from GPP, FPP and GGPP.
FIG. 2 shows an alignment of coding regions of cDNAs encoding homologs of bacterial undecaprenyl phosphate synthases from different plant species with those of a bacterial (Micrococcus luteus) and two yeast (rer2, srt1) genes.
FIG. 3 shows an alignment of the deduced amino acid sequences of plant cis-prenyltransferases.
FIG. 4 shows an alignment of the proteins derived from the partial plant cDNAs shown in FIG. 2, with the deduced amino acid sequences of a bacterial (Micrococcus luteus) and two yeast (rer2, srt1) genes.
FIG. 5A depicts the chromatogram (diode array detector response at 210 nm) generated by LC-MS analysis of non-saponifiable material extracted from wild-type arabidopsis leaves.
FIG. 5B depicts the chromatogram (diode array detector response at 210 nm) generated by LC-MS analysis of non-saponifiable material extracted from leaves of arabidopsis transformed with a 35S::Hpt3 construct.
FIG. 5C depicts the chromatogram (diode array detector response at 210 nm) generated by LC-MS analysis of non-saponifiable material extracted from leaves of arabidopsis transformed with a 35S::rr1 construct.
FIG. 5D depicts the chromatogram (diode array detector response at 210 nm) generated by LC-MS analysis of non-saponifiable material extracted from leaves of arabidopsis transformed with a 35S::Apt5 construct.
FIG. 5E depicts the chromatogram (diode array detector response at 210 nm) generated by LC-MS analysis of non-saponifiable material extracted from leaves of arabidopsis transformed with a 35S::rr1 construct.
FIG. 6A depicts the extracted ion chromatogram for dodecaprenol (mass detector response to ions with m/z 816 to 818) generated by LC-MS analysis of non-saponifiable material extracted from wild-type arabidopsis leaves.
FIG. 6B depicts the extracted ion chromatogram for dodecaprenol (mass detector response to ions with m/z 816 to 818) generated by LC-MS analysis of non-saponifiable material extracted from leaves of arabidopsis transformed with a 35S::Hpt3 construct.
FIG. 6C depicts the extracted ion chromatogram for dodecaprenol (mass detector response to ions with m/z 816 to 818) generated by LC-MS analysis of non-saponifiable material extracted from leaves of arabidopsis transformed with a 35S::rr1 construct.
FIG. 6D depicts the extracted ion chromatogram for dodecaprenol (mass detector response to ions with m/z 816 to 818) generated by LC-MS analysis of non-saponifiable material extracted from leaves of arabidopsis transformed with a 35S::Apt5 construct.
FIG. 6E depicts the extracted ion chromatogram for dodecaprenol (mass detector response to ions with m/z 816 to 818) generated by LC-MS analysis of non-saponifiable material extracted from leaves of arabidopsis transformed with a 35S::Sl1 construct.



The invention can be more fully understood from the following detailed description and the accompanying sequence descriptions which form part of this application.
The following sequence descriptions and sequences listings attached hereto comply with the rules governing nucleotide and/or amino acid sequence disclosures in patent applications as set forth in 37 C.F.R. §1.821-1.825 (“Requirements for Patent Applications Containing Nucleotide Sequences and/or Amino Acid Sequence Disclosures—the Sequence Rules”) and are consistent with World Intellectual Property Organization (WIPO) Standard ST2.5 (1998) and the sequence listing requirements of the EPO and PCT (Rules 5.2 and 49.5 (a-bis), and Section 208 and Annex C of the Administration Instructions). The Sequence Descriptions contain the one letter code for nucleotide sequence characters and the three letter codes for amino acids as defined in conformity with the IUPAC-IYUB standards described in Nucleic Acids Res. 13:3021-3030 (1985) and in the Biochemical Journal 219:345-373 (1984) which are herein incorporated by reference.
SEQ ID NO: 1 is the nucleotide sequence for the African daisy clone dms2c.pk005.c7.
SEQ ID NO: 2 is the deduced amino acid sequence for the African daisy dms2c.pk005.c7, encoded by SEQ ID NO: 1.
SEQ ID NO: 3 is the nucleotide sequence for the Pot Marigold clone ecs1c.pk009.p19.
SEQ ID NO: 4 is the deduced amino acid sequence for the Pot Marigold clone ecs1c.pk009.p19, encoded by SEQ ID NO: 3.
SEQ ID NO: 5 is the nucleotide sequence for the Hevea clone ehb2c.pk001.i10.
SEQ ID NO: 6 is the deduced amino acid sequence for the Hevea clone ehb2c.pk001.i10, encoded by SEQ ID NO: 5.
SEQ ID NO: 7 is the nucleotide sequence for the Hevea clone ehb2c.pk001.d17.
SEQ ID NO: 8 is the deduced amino acid sequence for the Hevea clone ehb2c.pk001.d17, encoded by SEQ ID NO: 7.
SEQ ID NO: 9 is the nucleotide sequence for the Hevea clone ehb2c.pk001.o18.
SEQ ID NO: 10 is the deduced amino acid sequence for the Hevea clone ehb2c.pk001.o18, encoded by SEQ ID NO: 9.
SEQ ID NO: 11 is the nucleotide sequence for the grape clone vdb1c.pk001.k23.
SEQ ID NO: 12 is the deduced amino acid sequence for the grape clone vdb1c.pk001.k23, encoded by SEQ ID NO: 11.
SEQ ID NO: 13 is the nucleotide sequence for the rice clone rl0n.pk117.i23.
SEQ ID NO: 14 is the deduced amino acid sequence for the rice clone rl0n.pk 117.i23, encoded by SEQ ID NO: 13.
SEQ ID NO: 15: is the nucleotide sequence for clone the rice clone rr1.pk0050.h8.
SEQ ID NO: 16 is the deduced amino acid sequence for rr1.pk0050.h8, encoded by SEQ ID NO: 15.
SEQ ID NO: 17 is the nucleotide sequence for the soybean clone sl1.pk0128.h7.
SEQ ID NO: 8 is the deduced amino acid sequence for the soybean clone sl1.pk0128.h7, encoded by SEQ ID NO: 7.
SEQ ID NO: 19 is the nucleotide sequence for the wheat clone wdk5c.pk005.f22.
SEQ ID NO: 20 is the deduced amino acid sequence for the wheat clone wdk5c.pk005.f22, encoded by SEQ ID NO: 19.
SEQ ID NO: 21 is the conserved Domain I.
SEQ ID NO: 22 is the conserved Domain V.
SEQ ID NO: 23 is the nucleotide sequence encoding a bacterial undecaprenyl phosphate synthase isolated from Micrococcus luteus. 
SEQ ID NO: 24 is the deduced amino acid sequence of a bacterial undecaprenyl phosphate synthase isolated from Micrococcus luteus. 
SEQ ID NO: 25 is the nucleotide sequence encoding a yeast undecaprenyl phosphate synthase isolated from the yeast strain rer2.
SEQ ID NO: 26 is the deduced amino acid sequence of a yeast undecaprenyl phosphate synthase isolated from the yeast strain rer2.
SEQ ID NO: 27 is the nucleotide sequence encoding a yeast undecaprenyl phosphate synthase isolated from the yeast strain srt1.
SEQ ID NO: 28 is the deduced amino acid sequence of a yeast undecaprenyl phosphate synthase isolated from the yeast strain srt1.
SEQ ID NOS: 29-36 are primers used for the transformation of arabidopsis with various cis-prenyltransferases genes.
SEQ ID NO: 37 is the nucleotide sequence of the Apt5 arabidopsis cis-prenyl transferase homolog.
DETAILED DESCRIPTION OF THE INVENTION
The present invention reports the isolation and characterization of cDNAs corresponding to genes homologous with microbial cis-prenyltransferases as ESTs from wheat, grape, soybean, rice, African daisy, rubber and marigold. No such homologs have been described previously in these species. The level of expression of the genes described here can be altered in the plant by methods of cosuppression and overexpression. As they are previously undescribed genes involved in synthesizing a family of molecules with fundamental cellular roles as well as roles in plant defense, this can lead to novel phenotypes that are expected to be beneficial for crop protection, production or as industrial sources of polyisoprenoids. In addition, if the reduction in expression of one of the genes leads to a growth or developmental defect in the plant, this gene can be used as a novel herbicide target. All isolated proteins can be used as tools to study the elaboration of polymeric cis-isoprenoids by plants. This can lead to the identification of additional proteins that can be used as described above. Any related EST sequences can be directly used for the above described applications in crop plants.
The following definitions are provided for the full understanding of terms and abbreviations used in this specification:
“Polymerase chain reaction” is abbreviated PCR
“Expressed sequence tag” is abbreviated EST
“Open reading frame” is abbreviated ORF
“SDS polyacrylamide gel electrophoresis” is abbreviated SDS-PAGE
“UPPS” is the abbreviation for the specific undecaprenyl diphosphate synthases isolated from bacteria.
“OPPS” is the abbreviation for the specific octaprenyl diphosphate synthases isolated from bacteria.
“Dedol-PP” is dehydrodolichol diphosphate
“DMAPP” is dimethyl allyl diphosphate
“IPP” is isopentenyl diphosphate
“GPP” is geranyl diphosphate
“FPP” is farnesyl diphosphate
“GGPP” is geranylgeranyl diphosphate
The term “cis-prenyltransferase” refers generally to a class of enzymes capable of catalyzing the sequential addition of C5 units to polyprenols and rubbers. Two examples of cis-prenyltransferases are the undecaprenyl diphosphate and dehydrodolichyl diphosphate synthases.
The terms “isolated nucleic acid fragment” or “isolated nucleic acid molecule” refer to a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases. An isolated nucleic acid fragment or an isolated nucleic acid molecule in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA, or synthetic DNA.
The terms “host cell” and “host organism” refer to a cell capable of receiving foreign or heterologous genes and expressing those genes to produce an active gene product. Suitable host cells include microorganisms such as bacteria and fungi, as well as plant cells.
The term “plant defense response” refers to the ability of a plant to deter tissue damage by insects, pathogens such as fungi, bacteria or viruses, as well as herbivores.
The term “fragment” refers to a DNA or amino acid sequence comprising a subsequence of the nucleic acid sequence or protein of the present invention. However, an active fragment of the present invention comprises a sufficient portion of the protein to maintain activity.
As used herein, “substantially similar” refers to nucleic acid fragments wherein changes in one or more nucleotide bases result in substitution of one or more amino acids, but do not affect the functional properties of the protein encoded by the DNA sequence. “Substantially similar” also refers to nucleic acid fragments wherein changes in one or more nucleotide bases do not affect the ability of the nucleic acid fragment to mediate alteration of gene expression by antisense or co-suppression technology. “Substantially similar” also refers to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of one or more nucleotide bases that do not substantially affect the functional properties of the resulting transcript vis-à-vis the ability to mediate alteration of gene expression by antisense or co-suppression technology or alteration of the functional properties of the resulting protein molecule. It is therefore understood that the invention encompasses more than the specific exemplary sequences.
For example, it is well known in the art that antisense suppression and co-suppression of gene expression may be accomplished using nucleic acid fragments representing less that the entire coding region of a gene, and by nucleic acid fragments that do not share 100% identity with the gene to be suppressed. Moreover, alterations in a gene which result in the production of a chemically equivalent amino acid at a given site, but do not effect the functional properties of the encoded protein, are well known in the art. Thus, a codon for the amino acid alanine, a hydrophobic amino acid, may be substituted by a codon encoding another less hydrophobic residue (such as glycine) or a more hydrophobic residue (such as valine, leucine, or isoleucine). Similarly, changes which result in substitution of one negatively charged residue for another (such as aspartic acid for glutamic acid) or one positively charged residue for another (such as lysine for arginine) can also be expected to produce a functionally equivalent product. Nucleotide changes which result in alteration of the N-terminal and C-terminal portions of the protein molecule would also not be expected to alter the activity of the protein. Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products. Moreover, the skilled artisan recognizes that substantially similar sequences encompassed by this invention are also defined by their ability to hybridize, under stringent conditions (0.1×SSC, 0.1% SDS, 65° C.), with the sequences exemplified herein. Preferred substantially similar nucleic acid fragments of the instant invention are those nucleic acid fragments whose DNA sequences are at least 80% identical to the DNA sequence of the nucleic acid fragments reported herein. More preferred nucleic acid fragments are at least 90% identical to the identical to the DNA sequence of the nucleic acid fragments reported herein. Most preferred are nucleic acid fragments that are at least 95% identical to the DNA sequence of the nucleic acid fragments reported herein.
A “substantial portion” of an amino acid or nucleotide sequence comprising enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., (1993) J. Mol. Biol. 215:403-410; see also, www.ncbi.nlm.nih.gov/BLAST/). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a “substantial portion” of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence. The instant specification teaches partial or complete amino acid and nucleotide sequences encoding one or more particular fungal proteins. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above.
The term “sequence analysis software” refers to any computer algorithm or software program that is useful for the analysis of nucleotide or amino acid sequences. “Sequence analysis software” may be commercially available or independently developed. Typical sequence analysis software will include but is not limited to the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.), BLASTP, BLASTN, BLASTX (Altschul, et al., (1990) J. Mol. Biol. 215:403-410, Vector NTI (InforMax Inc. 6110 Executive Boulevard, Suite 400, North Bethesda, Md.) and DNASTAR (DNASTAR Inc. 1228 S. Park Street, Madison, Wis.). Within the context of this application it will be understood that where sequence analysis software is used for analysis, that the results of the analysis will be based on the “default values” of the program referenced, unless otherwise specified. As used herein “default vales” will mean any set of values or parameters which originally load with the software when first initialized.
The term “percent identity”, as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. “Identity” and “similarity” can be readily calculated by known methods, including but not limited to those described in: Computational Molecular Biology (Lesk, A. M., ed.) Oxford University Press, New York (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.) Academic Press, New York (1993); Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., eds.) Humana Press, New Jersey (1994); Sequence Analysis in Molecular Biology (von Heinje, G., ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux, J., eds.) Stockton Press, New York (1991). Preferred methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using the Megalign program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequences was performed using the Clustal method of alignment (Higgins and Sharp (1989) CABIOS. 5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwise alignments using the Clustal method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5.
Suitable nucleic acid fragments (isolated polynucleotides of the present invention) encode polypeptides that are at least about 70% identical, preferably at least about 80% identical to the amino acid sequences reported herein. Preferred nucleic acid fragments encode amino acid sequences that are about 85% identical to the amino acid sequences reported herein. More preferred nucleic acid fragments encode amino acid sequences that are at least about 90% identical to the amino acid sequences reported herein. Most preferred are nucleic acid fragments that encode amino acid sequences that are at least about 95% identical to the amino acid sequences reported herein. Suitable nucleic acid fragments not only have the above homologies but typically encode a polypeptide having at least 50 amino acids, preferably at least 100 amino acids, more preferably at least 150 amino acids, still more preferably at least 200 amino acids, and most preferably at least 250 amino acids.
“Codon degeneracy” refers to divergence in the genetic code permitting variation of the nucleotide sequence without effecting the amino acid sequence of an encoded polypeptide. Accordingly, the present invention relates to any nucleic acid fragment that encodes all or a substantial portion of present proteins as set forth in SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18 and SEQ ID NO: 20. The skilled artisan is well aware of the “codon-bias” exhibited by a specific host cell to use nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.
The term “complementary” is used to describe the relationship between nucleotide bases that are hybridizable to one another. Hence with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine.
A nucleic acid molecule is “hybridizable” to another nucleic acid molecule, such as a cDNA, genomic DNA, or RNA, when a single stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule under the appropriate conditions of temperature and solution ionic strength. Hybridization and washing conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989), particularly Chapter 11 and Table 11.1 therein (entirely incorporated herein by reference). The conditions of temperature and ionic strength determine the “stringency” of the hybridization. Stringency conditions can be adjusted to screen for moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms. Post-hybridization washes determine stringency conditions. One set of preferred conditions uses a series of washes starting with 6×SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2×SSC, 0.5% SDS at 45° C. for 30 min, and then repeated twice with 0.2×SSC, 0.5% SDS at 50° C. for 30 min. A more preferred set of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2×SSC, 0.5% SDS was increased to 60° C. Another preferred set of highly stringent conditions uses two final washes in 0.1×SSC, 0.1% SDS at 65° C. Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see, Sambrook, et al., supra, 9.50-9.51). For hybridizations with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see, Sambrook, et al., supra, 11.7-11.8). In one embodiment the length for a hybridizable nucleic acid is at least about 10 nucleotides. Preferable a minimum length for a hybridizable nucleic acid is at least about 15 nucleotides; more preferably at least about 20 nucleotides; and most preferably the length is at least 30 nucleotides. Furthermore, the skilled artisan will recognize that the temperature and wash solution salt concentration may be adjusted as necessary according to factors such as length of the probe.
“Synthetic genes” can be assembled from oligonucleotide building blocks that are chemically synthesized using procedures known to those skilled in the art. These building blocks are ligated and annealed to form gene segments which are then enzymatically assembled to construct the entire gene. “Chemically synthesized”, as related to a sequence of DNA, means that the component nucleotides were assembled in vitro. Manual chemical synthesis of DNA may be accomplished using well established procedures, or automated chemical synthesis can be performed using one of a number of commercially available machines. Accordingly, the genes can be tailored for optimal gene expression based on optimization of nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful gene expression if codon usage is biased towards those codons favored by the host. Determining preferred codons can be based on a survey of genes derived from the host cell where sequence information is available.
“Gene” refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” refers to any gene, not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign” gene refers to a gene not normally found in the host organism, but which is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. A “transgene” is a gene that has been introduced into the genome by a transformation procedure.
“Coding sequence” refers to a DNA sequence that codes for a specific amino acid sequence. “Regulatory sequences” refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns and polyadenylation recognition sequences.
“Promoter” refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3′ to a promoter sequence. The promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. Accordingly, an “enhancer” is a DNA sequence which can stimulate promoter activity and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue-specificity of a promoter. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. Promoters which cause a gene to be expressed in most cell types at most times are commonly referred to as “constitutive promoters”. New promoters of various types useful in plant cells are constantly being discovered; numerous examples may be found in the compilation by Okamuro and Goldberg, (Biochem. Plants 15:1-82 (1989)). It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths may have identical promoter activity.
The “translation leader sequence” refers to a DNA sequence located between the promoter sequence of a gene and the coding sequence. The translation leader sequence is present in the fully processed mRNA upstream of the translation start sequence. The translation leader sequence may affect processing of the primary transcript to mRNA, mRNA stability or translation efficiency. Examples of translation leader sequences have been described (Turner, et al., (1995) Mol. Biotech. 3:225).
The “3′non-coding sequences” refer to DNA sequences located downstream of a coding sequence and include polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor. The use of different 3′ non-coding sequences is exemplified by Ingelbrecht, et al., (Plant Cell 1:671-680 (1989)).
“RNA transcript” refers to the product resulting from RNA polymerase-catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is referred to as the primary transcript or it may be a RNA sequence derived from posttranscriptional processing of the primary transcript and is referred to as the mature RNA. “Messenger RNA” (mRNA) refers to the RNA that is without introns and that can be translated into protein by the cell. “cDNA” refers to a double-stranded DNA that is complementary to and derived from mRNA. “Sense” RNA refers to RNA transcript that includes the mRNA and so can be translated into protein by the cell. “Antisense RNA” refers to a RNA transcript that is complementary to all or part of a target primary transcript or mRNA and that blocks the expression of a target gene (U.S. Pat. No. 5,107,065). The complementarity of an antisense RNA may be with any part of the specific gene transcript, i.e., at the 5′ non-coding sequence, 3′ non-coding sequence, introns or the coding sequence. “Functional RNA” refers to antisense RNA, ribozyme RNA or other RNA that is not translated yet has an effect on cellular processes.
The term “operably-linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably-linked with a coding sequence when it affects the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably-linked to regulatory sequences in sense or antisense orientation.
The term “expression” refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid fragment of the invention. Expression may also refer to translation of mRNA into a polypeptide. “Antisense inhibition” refers to the production of antisense RNA transcripts capable of suppressing the expression of the target protein. “Overexpression” refers to the production of a gene product in transgenic organisms that exceeds levels of production in normal or non-transformed organisms. “Co-suppression” refers to the production of sense RNA transcripts capable of suppressing the expression of identical or substantially similar foreign or endogenous genes (U.S. Pat. No. 5,231,020).
“Altered levels” refers to the production of gene product(s) in organisms in amounts or proportions that differ from that of normal or non-transformed organisms.
“Mature” protein refers to a post-translationally processed polypeptide; i.e., one from which any pre- or propeptides present in the primary translation product have been removed. “Precursor” protein refers to the primary product of translation of mRNA; i.e., with pre- and propeptides still present. Pre- and propeptides may be but are not limited to intracellular localization signals.
A “chloroplast transit peptide” is an amino acid sequence which is translated in conjunction with a protein and directs the protein to the chloroplast or other plastid types present in the cell in which the protein is made. “Chloroplast transit sequence” refers to a nucleotide sequence that encodes a chloroplast transit peptide. A “signal peptide” is an amino acid sequence which is translated in conjunction with a protein and directs the protein to the secretory system (Chrispeels, (1991) Ann. Rev. Plant Phys. Plant Mol. Biol. 42:21-53). If the protein is to be directed to a vacuole, a vacuolar targeting signal (supra) can further be added, or if to the endoplasmic reticulum, an endoplasmic reticulum retention signal (supra) may be added. If the protein is to be directed to the nucleus, any signal peptide present should be removed and instead a nuclear localization signal included (Raikhel, et al., (1992) Plant Phys. 100:1627-1632).
“Transformation” refers to the transfer of a nucleic acid fragment into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic” organisms. Examples of methods of plant transformation include Agrobacterium-mediated transformation (De Blaere, et al., (1987)Meth. Enzymol. 143:277) and particle-accelerated or “gene gun” transformation technology (Klein, et al., (1987) Nature, London 327:70-73; U.S. Pat. No. 4,945,050).
Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described more fully in Sambrook, et al., Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1989 (hereinafter, “Sambrook., et al.”).
Unique plant homologs of microbial cis-prenyltransferase proteins, involved in the synthesis of poly-cis-isoprenoids, have been isolated from wheat, grape, soybean, rice, African daisy, rubber and marigold. Comparison of their random cDNA sequences to the GenBank database using the BLAST algorithm, well known to those skilled in the art, revealed that these proteins have no significant homologies to other identified proteins in plants. The nucleotide sequences of the present homolog cDNAs are provided in SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17 and SEQ ID NO: 19. Other poly-cis-isoprenoid synthase genes and proteins from other plants can now be identified by comparison of random cDNA sequences to the present cis-prenyltransferase sequences provided herein.
The present sequences were identified by comparison to public as well as internal database. Strong correlation was seen between the instant sequences and the cis-prenyltransferase genes and proteins isolated from Micrococcus luteus Shimizu, N, Koyama, T and Ogura, K, (1998) J. Biol. Chem. 273:19476-19481 and Saccharomyces cerevisiae. Accordingly it is an object of the present invention to provide nucleic acid molecules encoding plant cis-prenyltransferase proteins where the nucleic acid sequence is at least 50% identical to the bacterial undecaprenyl diphosphate synthase gene isolated from Micrococcus luteus where a correlation of at least 80% is preferred. Similarly the invention provides plant cis-prenyltransferase proteins where the amino acid sequence is at least 41% identical to the bacterial undecaprenyl diphosphate synthase protein isolated from Micrococcus luteus where a correlation of at least 70% is preferred.
The nucleic acid fragments of the present invention may be used to isolate cDNAs and genes encoding a homologous prenyltransferases from the same or other plant species. Isolating homologous genes using sequence-dependent protocols is well known in the art. Examples of sequence-dependent protocols include, but are not limited to, methods of nucleic acid hybridization and methods of DNA and RNA amplification as exemplified by various uses of nucleic acid amplification technologies (e.g., polymerase chain reaction (PCR) or ligase chain reaction).
For example, other cis-prenyltransferase genes, (and particularly undecaprenyl diphosphate and dehydrodolichyl diphosphate syntheses) either as cDNAs or genomic DNAs, could be isolated directly by using all or a portion of the present nucleic acid fragments as DNA hybridization probes to screen libraries from any desired plant using methodology well known to those skilled in the art. Specific oligonucleotide probes based upon the present cis-prenyltransferase sequences can be designed and synthesized by methods known in the art (Sambrook, et al., supra). Moreover, the entire sequences can be used directly to synthesize DNA probes by methods known to the skilled artisan such as random primers, DNA labeling, nick translation, or end-labeling techniques, or RNA probes using available in vitro transcription systems. In addition, specific primers can be designed and used to amplify a part of or full-length of the present sequences. The resulting amplification products can be labeled directly during amplification reactions or labeled after amplification reactions, and used as probes to isolate full length cDNA or genomic fragments under conditions of appropriate stringency.
In addition, two short segments of the present nucleic acid fragment may be used in PCR protocols to amplify longer nucleic acid fragments encoding homologous genes from DNA or RNA. The polymerase chain reaction may also be performed on a library of cloned nucleic acid fragments wherein the sequence of one primer is derived from the present nucleic acid fragments, and the sequence of the other primer takes advantage of the presence of the polyadenylic acid tracts to the 3′ end of the mRNA precursor encoding plant UPPS homologs.
Alternatively, the second primer sequence may be based upon sequences derived from the cloning vector. For example, the skilled artisan can follow the RACE protocol (Frohman, et al., (1988) Proc. Natl. Acad. Sci. USA 85:8998) to generate cDNAs by using PCR to amplify copies of the region between a single point in the transcript and the 3′ or 5′ end. Primers oriented in the 3′ and 5′ directions can be designed from the present sequences. Using commercially available 3′ RACE or 5′ RACE systems (BRL), specific 3′ or 5′ cDNA fragments can be isolated (Ohara, et al., (1989) Proc. Natl. Acad. Sci., USA 86:5673; Loh, et al., (1989) Science 243:217). Products generated by the 3′ and 5′ RACE procedures can be combined to generate full-length cDNAs (Frohman, et al., (1989) Techniques 1:165).
Finally, availability of the present nucleotide and deduced amino acid sequences facilitates immunological screening of cDNA expression libraries. Synthetic peptides representing portions of the present amino acid sequences may be synthesized. These peptides can be used to immunize animals to produce polyclonal or monoclonal antibodies with specificity for peptides or proteins comprising the amino acid sequences. These antibodies can be then be used to screen cDNA expression libraries to isolate full-length cDNA clones of interest (Lerner, et al., (1984) Adv. Immunol. 36:1; Sambrook, et al., supra).
The nucleic acid fragments of the present invention may also be used to create transgenic plants in which the present cis-prenyltransferase protein is present at higher or lower levels than normal. Alternatively, in some applications, it might be desirable to express the present cis-prenyltransferase protein in specific plant tissues and/or cell types, or during developmental stages in which they would normally not be encountered. The expression of full-length plant cis-prenyltransferase cDNAs (i.e., any of the sequences below or related sequences incorporating an appropriate in-frame ATG start codon) in a bacterial (e.g., E. coli), yeast (e.g., Saccharomyces cerevisiae, Pichia pastoralis) or plant yields a mature protein capable of the synthesis of cis-polyisoprenoids from substrate IPP. The presence of an initiator allylic isoprenoid diphosphate (DMAPP, GPP, FPP or GGPP) enhances this activity.
It is contemplated that transgenic plants expressing the present cis-prenyltransferase sequences will have altered or modulated defense mechanisms against various pathogens and natural predators. For example, various latex proteins are known to be antigenic and recognized by IgE antibodies, suggesting their role in immunolgical defense (Yagami, et al., Journal of Allergy and Clinical Immunology, (1998) 101(3):379-385. Additionally it has been shown that a significant portion of the latex isolated from Hevea brasiliensis contains chitinases/lysozymes, which are capable of degrading the chitin component of fungal cell walls and the peptidoglycan component of bacterial cell walls (Martin, (1991) Plant Physiol (Bethesda), 95(2):469-476). It is therefore an object of the present invention to provide transgenic plants having altered, modulated or increased defenses towards various pathogens and herbivores.
The plant species suitable for expression of the present sequences may be (but are not limited to) tobacco (Nicotiana spp.), tomato (Lycopersicon spp.), potato (Solanum spp.), hemp (Cannabis spp.), sunflower (Helianthus spp.), sorghum (Sorghum vulgare), wheat (Triticum spp.), maize (Zea mays), rice (Oryza sativa), rye (Secale cereale), oats (Avena spp.), barley (Hordeum vulgare), rapeseed (Brassica spp.), broad bean (Vicia faba), french bean (Phaseolus vulgaris), other bean species (Vigna spp.), lentil (Lens culinaris), soybean (Glycine max), arabidopsis (Arabidopsis thaliana), guayule (Parthenium argentatum), cotton (Gossypium hirsutum), petunia (Petunia hybrida), flax (Linum usitatissimum) and carrot (Daucus carota sativa).
Various methods of transforming cells of higher plants according to the present invention are available to those skilled in the art (see, EPO Publication Number 0 295 959 A2 and 0 318 341 A1). Such methods include those based on transformation vectors utilizing the Ti and Ri plasmids of Agrobacterium spp. It is particularly preferred to use the binary type of these vectors. Ti-derived vectors transform a wide variety of higher plants, including monocotyledonous and dicotyledonous plants (Sukhapinda, et al., (1987) Plant Mol. Biol. 8:209-216; Potrykus, et al., (1985) Mol. Gen. Genet. 199:183). Other transformation methods are available to those skilled in the art, such as direct uptake of foreign DNA constructs (see, EPO Publication Number 0 295 959 A2), techniques of electroporation (Fromm, et al., (1986) Nature (London) 319:791) or high-velocity ballistic bombardment with metal particles coated with the nucleic acid constructs (Kline, et al., (1987) Nature (London) 327:70). Once transformed, the cells can be regenerated by those skilled in the art.
Of particular relevance are the recently described methods to transform foreign genes into commercially important crops, such as rapeseed (De Block, et al., (1989) Plant Physiol. 91:694-701), sunflower (Everett, et al., (1987) Bio/Technology 5:1201), and soybean (Christou, et al., (1989) Proc. Natl. Acad. Sci. USA 86:7500-7504).
Overexpression of the present cis-prenyltransferase homologs may be accomplished by first constructing a chimeric gene in which their coding region is operably-linked to a promoter capable of directing expression of a gene in the desired tissues at the desired stage of development. For reasons of convenience, the chimeric gene may comprise promoter sequences and translation leader sequences derived from the same genes. 3′ Non-coding sequences encoding transcription termination signals must also be provided. The present chimeric genes may also comprise one or more introns in order to facilitate gene expression.
Plasmid vectors comprising the present chimeric genes can then be constructed. The choice of a plasmid vector depends upon the method that will be used to transform host plants. The skilled artisan is well aware of the genetic elements that must be present on the plasmid vector in order to successfully transform, select and propagate host cells containing the chimeric gene. The skilled artisan will also recognize that different independent transformation events will result in different levels and patterns of expression (Jones, et al., (1985) EMBO J. 4:2411-2418; De Almeida, et al., (1989) Mol. Gen. Genetics 218:78-86), and thus that multiple events must be screened in order to obtain lines displaying the desired expression level and pattern. Such screening may be accomplished by Southern analysis of DNA, Northern analysis of mRNA expression, Western analysis of protein expression, or phenotypic analysis.
For some applications it may be useful to direct the cis-prenyltransferase protein to different cellular compartments or to facilitate their secretion from the cell. The chimeric genes described above may be further modified by the addition of appropriate intracellular or extracellular targeting sequence to their coding regions. These include chloroplast transit peptides (Keegstra, et al., (1989) Cell 56:247-253), signal sequences that direct proteins to the endoplasmic reticulum (Chrispeels, et al., (1991) Ann. Rev. Plant Phys. Plant Mol. 42:21-53), and nuclear localization signal (Raikhel, (1992) et al., Plant Phys. 100:1627-1632). While the references cited give examples of each of these, the list is not exhaustive and more targeting signals of utility may be discovered in the future.
It may also be desirable to reduce or eliminate expression of the cis-prenyltransferase genes in plants for some applications. In order to accomplish this, chimeric genes designed for antisense or co-suppression of cis-prenyltransferase homologs can be constructed by linking the genes or gene fragments encoding parts of these enzymes to plant promoter sequences. Thus, chimeric genes designed to express antisense RNA for all or part of a UPPS homolog can be constructed by linking the cis-prenyltransferase homolog genes or gene fragments in reverse orientation to plant promoter sequences. The co-suppression or antisense chimeric gene constructs could be introduced into plants via well known transformation protocols wherein expression of the corresponding endogenous genes are reduced or eliminated.
The present cis-prenyltransferase homolog proteins may be produced in heterologous host cells, particularly in the cells of microbial hosts, and can be used to prepare antibodies to the proteins by methods well known to those skilled in the art. The antibodies would be useful for detecting the present cis-prenyltransferase proteins in situ in cells or in vitro in cell extracts. Preferred heterologous host cells for production of the present cis-prenyltransferase proteins are microbial hosts. Microbial expression systems and expression vectors containing regulatory sequences that direct high level expression of foreign proteins are well known to those skilled in the art. Any of these could be used to construct a chimeric gene for production of the present cis-prenyltransferase homologs. This chimeric gene could then be introduced into appropriate microorganisms via transformation to provide high level expression of the present cis-prenyltransferase proteins.
Microbial host cells suitable for the expression of the present cis-prenyltransferase proteins include any cell capable of expression of the chimeric genes encoding these proteins. Such cells will include both bacteria and fungi including, for example, the yeasts (e.g., Aspergillus, Saccharomyces, Pichia, Candida and Hansenula), members of the genus Bacillus as well as the enteric bacteria (e.g., Escherichia, Salmonella and Shigella). Methods for the transformation of such hosts and the expression of foreign proteins are well known in the art and examples of suitable protocols may be found In Manual of Methods for General Bacteriology; Gerhardt, et al., Eds.; American Society for Microbiology: Washington, D.C., 1994 or In Biotechnology: A Textbook of Industrial Microbiology, 2nd Edition, Brock, T. D., Ed.; Sinauer Associates, Inc.: Sunderland, Mass., 1989.
Vectors or cassettes useful for transforming suitable microbial host cells are well known in the art. Typically the vector or cassette contains sequences directing transcription and translation of the relevant gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Suitable vectors comprise a region 5′ of the gene which harbors transcriptional initiation controls and a region 3′ of the DNA fragment which controls transcriptional termination. It is most preferred when both control regions are derived from genes homologous to the transformed host cell, although such control regions need not be derived from the genes native to the specific species chosen as a production host.
Initiation control regions or promoters useful to drive expression of the genes encoding the cis-prenyltransferase proteins in the desired host cell are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving these genes is suitable for the present invention including but not limited to CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, TPI (useful for expression in Saccharomyces); AOX1 (useful for expression in Pichia); and lac, trp, IPL, IPR, T7, tac, and trc (useful for expression in E. coli). Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary; however, it is most preferred if included.
Additionally, the present cis-prenyltransferase proteins can be used as targets to facilitate the design and/or identification of inhibitors of cis-prenyltransferase homologs that may be useful as herbicides or fungicides. This could be achieved either through the rational design and synthesis of potent functional inhibitors that result from structural and/or mechanistic information that is derived from the purified present plant proteins, or through random in vitro screening of chemical libraries. It is anticipated that significant in vivo inhibition of any of the cis-prenyltransferase homolog proteins described herein may severely cripple cellular metabolism and likely result in plant (or fungal) death.
All or a portion of the nucleic acid fragments of the present invention may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to expression of the present cis-prenyltransferase homologs. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. For example, the present nucleic acid fragments may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Sambrook, et al., supra) of restriction-digested plant genomic DNA may be probed with the nucleic acid fragments of the present invention. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander, et al., (1987) Genomics 1:174-181) in order to construct a genetic map. In addition, the nucleic acid fragments of the present invention may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the present nucleic acid sequence in the genetic map previously obtained using this population (Botstein, et al., (1980) Am. J. Hum. Genet. 32:314-331).
The production and use of plant gene-derived probes for use in genetic mapping is described by Bernatzky, et al., (Plant Mol. Biol. Reporter 4:37-41 (1986)). Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.
Nucleic acid probes derived from the present nucleic acid sequences may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel, et al., Nonmammalian Genomic Analysis: A Practical Guide; Academic Press, 1996; pp. 319-346 and references cited therein).
In another embodiment, nucleic acid probes derived from the present nucleic acid sequence may be used in direct fluorescence in situ hybridization (FISH) mapping. Although current methods of FISH mapping favor use of large clones (several to several hundred kb), improvements in sensitivity may allow performance of FISH mapping using shorter probes.
A variety of nucleic acid amplification-based methods of genetic and physical mapping may be carried out using the present nucleic acid sequences. Examples include allele-specific amplification (Kazazian, et al. (1989), J. Lab. Clin. Med. 114:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield, (1993) et al., Genomics 16:325-332), allele-specific ligation (Landegren, et al., (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov, et al., (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter, et al., (1997) Nature Genetics 7:22-28) and Happy Mapping (Dear, et al., (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid fragment is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods using PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the present nucleic acid sequence. This, however, is generally not necessary for mapping methods.
Loss of function-mutant phenotypes may be identified for the present cDNA clones either by targeted gene disruption protocols or by identifying specific mutants for these genes contained in a population of plants carrying mutations in all possible genes (e.g., Ballinger, et al., (1989) Proc. Natl. Acad. Sci. USA 86:9402; Koes, et al., (1995) Proc. Natl. Acad. Sci. USA 92:8149; Bensen, et al., (1995) Plant Cell 7:75). The latter approach may be accomplished in two ways. First, short segments of the present nucleic acid fragments may be used in polymerase chain reaction protocols in conjunction with a mutation tag sequence primer on DNAs prepared from a population of plants in which Mutator transposons or some other mutation-causing DNA element has been introduced (see, Bensen, supra). The amplification of a specific DNA fragment with these primers indicates the insertion of the mutation tag element in or near the plant gene encoding the cis-prenyltransferase protein. Alternatively, the present nucleic acid fragment may be used as a hybridization probe against PCR amplification products generated from the mutation population using the mutation tag sequence primer in conjunction with an arbitrary genomic site primer, such as that for a restriction enzyme site-anchored synthetic adaptor. With either method, a plant containing a mutation in the endogenous gene encoding a cis-prenyltransferase protein can be identified and obtained. This mutant plant can then be used to determine or confirm the natural function of the cis-prenyltransferase gene product.
The present invention is further defined in the following Examples, in which all parts and percentages are by weight and degrees are Celsius, unless otherwise stated. It should be understood that these Examples, while indicating preferred embodiments of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usage and conditions.
EXAMPLES
General Methods
Standard recombinant DNA and molecular cloning techniques used here are well known in the art and are described by Sambrook, et al., Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989) (hereinafter, “Sambrook, et al.”); and by T. J. Silhavy, M. L. Bennan, and L. W. Enquist, Experiments with Gene Fusions, Cold Spring Harbor Laboratory Press, Cold Spring, N.Y. (1984) and by Ausubel, et al., Current Protocols in Molecular Biology, pub. by Greene Publishing Assoc. and Wiley-Interscience (1987).
Nucleotide and amino acid percent identity and similarity comparisons were made using the GCG suite of programs, applying default parameters unless indicated otherwise.
The meaning of abbreviations is as follows: “sec” means second(s), “min” means minute(s), “h” means hour(s), “d” means day(s), “μL” means microliter, “mL” means milliliters, “L” means liters, “mM” means millimolar, “M” means molar, and “mmol” means millimole(s).
Example 1
Composition of cDNA Libraries Used for Identification of cDNA Clones from Plant Species Encoding cis-Prenyltransferase Homologs
cDNA libraries representing mRNAs from wheat, grape, soybean, rice, African daisy, rubber tree latex and marigold tissues were prepared. The characteristics of the libraries are described in Table 1. cDNA libraries were prepared by any one of several methods. The cDNAs were introduced into plasmid vectors by first preparing the cDNA libraries in Uni-ZAP XR vectors according to the manufacturer's protocol (Stratagene Cloning Systems, La Jolla, Calif.). The Uni-ZAP XR libraries were converted into plasmid libraries according to the protocol provided by Stratagene. Upon conversion, cDNA inserts were contained in the plasmid vector pBluescript. In an alternate approach the cDNAs were introduced directly into precut Bluescript II SK(+) vectors (Stratagene) using T4 DNA ligase (New England Biolabs), followed by transfection into DH10B cells according to the manufacturer's protocol (GIBCO BRL Products). Once the cDNA inserts were in plasmid vectors, plasmid DNAs were prepared from randomly picked bacterial colonies containing recombinant pBluescript plasmids, or the insert cDNA sequences were amplified via polymerase chain reaction using primers specific for vector sequences flanking the inserted cDNA sequences. Amplified insert DNAs or plasmid DNAs were sequenced in dye-primer sequencing reactions to generate partial cDNA sequences (expressed sequence tags or “ESTs”; see, Adams, et al., (1991) Science 252:1651-1656. The resulting ESTs were analyzed using a Perkin Elmer Model 377 fluorescent sequencer.







TABLE 1







cDNA Libraries from Plants








Library
Species and Tissue





dms2c
African daisy (Dimorphotheca sinuata) developing seeds


ecs1c
pot marigold (Calendula officinalis) developing seeds


ehb2c
para rubber tree (Hevea brasiliensis, PR255) latex tapped in



2nd day of two day tapping cycle


Vdb1c
Grape (Vitis sp.) developing bud


rl0n
rice (Oryza sativa L.) fifteen day leaf (normalized)


rr1
rice (Oryza sativa L.) root of two week old developing



seedling


sl1
soybean (Glycine max L.) of two week old developing



seedlings treated with water


wdk5c
wheat (Triticum aestivum L.) developing kernel, thirty days



after anthesis









Example 2
Characterization of ESTs
ESTs encoding candidate cis-prenyltransferases were identified by conducting BLAST (Basic Local Alignment Search Tool; Altschul, et al., (1993) J. Mol. Biol. 215:403-410; see also, www.ncbi.nlm.nih.gov/BLAST/) searches for similarity to sequences contained in the BLAST “nr” database (comprising all non-redundant GenBank CDS translations, sequences derived from the 3-dimensional structure Brookhaven Protein Data Bank, the last major release of the SWISS-PROT protein sequence database, EMBL and DDBJ databases). The cDNA sequences obtained in Example 3 were analyzed for similarity to all publicly available DNA sequences contained in the “nr” database using the BLASTN algorithm provided by the National Center for Biotechnology Information (NCBI). The DNA sequences were translated in all reading frames and compared for similarity to all publicly available protein sequences contained in the “nr” database using the BLASTX algorithm (Gish, W. and States, D. J. (1993) Nature Genetics 3:266-272) provided by the NCBI. For convenience, the P-value (probability) of observing a match of a cDNA sequence to a sequence contained in the searched databases merely by chance as calculated by BLAST are reported herein as “pLog” values, which represent the negative of the logarithm of the reported P-value. Accordingly, the greater the pLog value, the greater the likelihood that the cDNA sequence and the BLAST “hit” represent homologous proteins.
Example 3
Identification and Characterization of cDNA Clones for cis-Prenyltransferases
cDNAs from the libraries listed in Table 1 were identified as cis-prenyltransferase homologs based on interrogation of the database described in Examples 1 and 2. cDNAs were thus identified by a number of methods, including the following: 1) keyword searches (e.g., “undecaprenyl”), 2) searches of the database using the TBLASTN algorithm provided by the National Center for Biotechnology Information (NCBI) and short fragments of conserved sequence present in bacterial undecaprenyl synthases, and 3) identification of further homologs of cDNAs discovered by 1 and 2 within the in-house database using the FASTA program. An alignment of the deduced amino acid sequence of the E. coli undecaprenyl pyrophosphate synthase gene with a number of other publicly-available sequences from bacteria, yeast (Saccharomyces cerevisiae) and one eukaryote (Caenorhabditis elegans) has been published (Apfel, et al., (1999) J. Bacteriol. 81:483-492). This alignment revealed five conserved domains. One of these (Domain I) is present at the 5′ end of the ORFs of these genes, and consists of the following sequence: HXXMDGNXRXA (X=any amino acid; (SEQ ID NO: 21)). Another (Domain V) is present towards the 3′ end of the ORFs, and consists of the following sequence: DLXIRTXGEXRXSNFLLWQXXYXE (where X=any amino acid; (SEQ ID NO: 22)). These sections of conserved sequence are likely to be diagnostic for the cis-prenyltransferase family of enzymes, and were used in the aforementioned TBLASTN searches.
Further homologs of cDNAs discovered by the first and second method within the in-house database were identified as sequences homologous by FASTA alignment with a specified sequence, either restricted to the same library, or across all libraries or across a library group. The cDNAs identified by these means are listed in Table 2.







TABLE 2







cDNAs Identified as cis-Prenyltransferase Homologs










Sequence identification number (SID)
Source







dms2c.pk005.c7
African Daisy



ecs1c.pk009.p19
pot marigold



ehb2c.pk001.i10
Hevea brasiliensis



ehb2c.pk001.d17
Hevea brasiliensis



ehb2c.pk001.o18
Hevea brasiliensis



Vdb1c.pk001.k23
grape



rl0n.pk117.i23
rice



rr1.pk0050.h8
rice



sl1.pk0128.h7
soybean



wdk5c.pk005.f22
wheat










Comparison of the nucleotide (SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17 and SEQ ID NO: 19) and deduced amino acid (SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18 and SEQ ID NO: 20) sequences of these ESTs with those of a representative bacterial cis-prenyltransferase (Micrococcus luteus UPPS; Shimizu, N., Koyama, T. and Ogura, K., (1998) J. Biol. Chem. 273:19476-19481) show them to exhibit >45% identity in nucleotide sequence and >30% identity in amino acid sequence. Table 3 lists the comparison of the cis-prenyltransferase sequences isolated from wheat, grape, soybean, rice, African daisy, rubber tree and pot marigold with the sequence of the Micrococcus luteus UPPS. FIG. 2 shows an alignment of the nucleotide sequence within the coding regions of these cDNAs with those of Micrococcus luteus UPPS and two yeast cis-prenyltransferase genes, rer2 (GenBank Accession Number AB013497) and srt1 (GenBank Accession Number AB013498) which indicates the extent of homology between the primary sequence of these cis-prenyltransferase genes from diverse species.







TABLE 3







Comparison of Grape, Rice, Soybean, Rubber tree and


African Daisy Sequences Against the Sequence of Micrococcus luteus


Undecaprenyl Pyrophosphate Synthase









Similarity Identified to M. luteus








cDNA/deduced
Gene5










protein
% Identity1
BLAST













sequence
NA2
AA2
algorithm
Score3
pLog4















dms2c.pk005.c7
50.13
39.024
Xnr
162
10.57


ecs1c.pk009.p19
50.40
38.938


ehb2c.pk001.i10
46.00
33.603
Xnr
71
1.48


ehb2c.pk001.d17
46.133
33.603
Xnr
161
10.46


ehb2c.pk001.o18
49.464
32.129


vdb1c.pk001.o18
46.559
34.413


rl0n.pk117.i23
45.652
33.186
Xnr
152
9.41


rr1.pk0050.h8
45.699
34.694


sl1.pk0128.h7
50.133
41.564


wdk5c.pk005.f22
43.067
38.00





1Comparison made using GCG GAP program, applying default values.


2AA is the abbreviation for amino acid sequence; NA is the abbreviation for nucleotide sequence.


3Score is the value assigned to a match between two sequences by the BLAST program.


4pLog is the negative of the logarithm of the reported P-value, the probability of observing a match of a cDNA sequence to a sequence contained in the searched databases merely by chance as calculated by BLAST.


5Given for those cDNAs where this similarity was detected by the initial BLAST search.






Example 4
Analysis of Deduced Amino Acid Sequence of cDNAs Identified as cis-Prenyltransferase Homologs in Plants
The plant cDNAs identified as described above were translated and the deduced amino acid sequences compared one to another using the GCG GAP program. Gap considers all possible alignments and gap positions between two sequences and creates a global alignment that maximizes the number of matched residues and minimizes the number and size of gaps. A scoring matrix is used to assign values for symbol matches. In addition, a gap creation penalty and a gap extension penalty are required to limit the insertion of gaps into the alignment. Gap uses the alignment method of Needleman and Wunsch (J. Mol. Biol. 48:443-453 (1970)). It is clear from this analysis (Table 4) that these sequences encode polypeptides with a minimum of 27.826% identity. The highest identities revealed by this analysis are between sequences from the same species, with two rice sequences exhibiting 90.668% identity and two rubber latex sequences 98.282% identity. The highest identity between sequences from different species was exhibited by the rice and grape sequences. In addition, alignment of the deduced amino acid sequence of these cDNAs together (FIG. 3) and with bacterial and yeast cis-prenyltransferases (FIG. 4) using the CLUSTALW program within the VECTOR NTI suite of programs reveals the presence of the conserved domains characteristic of this gene family (referred to in Example 2).







TABLE 4







Identity Comparison Using the GAP Program of the Deduced


Amino Acid Sequences from Plant cis-Prenyltransferases

















SEQ












ID
2
4
6
8
10
12
14
16
18
20




















2
100
48.684
31.907
33.858
31.923
52.669
33.043
30.545
58.537
50.965


4
48.684
100
30.701
30.702
33.333
46.222
33.186
33.186
48.246
45.133


6
31.907
30.701
100
99.655
78.547
32.296
47.773
46.182
33.588
31.679


8
33.858
30.702
99.655
100
78.201
32.296
47.773
46.182
33.588
31.679


10
31.923
33.333
78.547
78.201
100
29.502
46.154
44.891
32.067
30.943


12
52.669
46.222
32.296
32.296
29.502
100
33.478
31.250
53.398
48.450


14
33.043
33.186
47.773
47.773
46.154
33.478
100
100
32.051
37.627


16
30.545
33.186
46.182
46.182
44.891
31.250
100
100
29.643
30.916


18
58.537
48.246
33.588
33.588
32.061
53.398
32.051
29.643
100
50.775


20
50.965
45.133
90.943
31.679
30.943
48.450
37.627
30.916
50.775
100









Example 5
Transformation and Expression of Hevea cis-Prenyltransferase in Dandelion Plants
A chimeric gene comprising the Hevea cis-prenyltransferase gene (SEQ ID No: 5) in sense orientation is constructed by polymerase chain reaction (PCR) of the gene using appropriate oligonucleotide primers. Cloning sites (EcorI and KpnI) are incorporated into the oligonucleotides to provide proper orientation of the DNA fragment when inserted into the digested vector pML82. The binary vectors pML82 are transferred by a freeze/thaw method (Holsters, et al., (1978) Mol. Gen. Genet. 163:181-187) to the Agrobacterium tumefaciens strain LBA4404 and Agrobacterium rhizogenes ATCC 15834 (Hockema, et al., (1983) Nature 303:179-180).
Dandelion plants are transformed by co-cultivation of leaf and petiole explants with disarmed Agrobacterium tumefaciens strain LBA4404 and Agrobacterium rhizogenes strain ATCC 15834 carrying the appropriate binary vector.
Dandelion leaf and petiole explants from greenhouse are sterilized by stirring in 70% ethanol for 10 min and transferring to 5% Chlorox®, 0.01% Triton-X 100 for 30 min, and then rinsing thoroughly with sterile distilled water. Liquid cultures of Agrobacterium for plant transformation are grown overnight at 28° C. in Minimal A medium containing 100 mg/L kanamycin. The bacterial cells are pelleted by centrifugation and resuspended in liquid MS medium containing 1 mg/L BAP and 0.2 mg/L NAA to a density of A600=0.5, leaf and petiole explants are inoculated with the bacteria suspension for 10 min, blotted dry with sterile filter paper, then co-cultivated on solidified MS medium for two to four days (in case of the explants and strain LBA440 co-cultivation, use MS medium containing 0.5 mg/L BAP and 0.2 mg/L NAA). The co-cultivations are terminated by transferring the explants onto the same medium plus 200 mg/L cefotaxime and 50 mg/L kanamycin to kill the Agrobacteria, and to select for transformed plant cell growth.
The explants inoculated with LBA4404 strain are maintained at 27° C. under cool white fluorescent lamps with a 16/8 h light/dark photoperiod. After three to four weeks, excised shoots are transferred onto rooting medium (1⁄2 MS plus 0.2 mg/L NAA) containing the same concentrations of antibiotics as above. Once the transformed plants have established their root systems, they are transferred directly into wet Metro-Mix 350 soilless potting medium. The pots are covered with plastic bags which are removed when the plants are clearly growing (after about ten days).
The explants inoculated with ATCC 15834 strain are incubated at 27° C. under continuous dark. After ten to fifteen days, excised roots were transferred to the same plates for large production of the transformed roots.
Example 6
Expression of Plant cis-Prenyltransferase in Microbial Cells and Purification of Gene Product
Example 6 illustrates the expression of isolated full length genes encoding cis-prenyltransferase proteins in E. coli, using as an example the expression of clone ehb2c.pk001.o18.
Plasmid DNA from ehb2c.pk001.o18 is purified using QIAFilter cartridges (Qiagen Inc., 9600 De Soto Avenue, Chatsworth, Calif.) according to the manufacturer's instructions. Sequence is generated on an ABI Automatic sequencer using dye terminator technology (U.S. Pat. No. 5,366,860; EP Number 272007) using a combination of vector and insert-specific primers. Sequence editing is performed in either Vector NTI, DNAStar, or the Wisconsin GCG program (vide supra).
cDNA from the full length clone ehb2c.pk001.o18 encoding the instant cis-prenyltransferase enzyme is amplified with specific PCR primers designed to the 5′ and 3′ ends of the coding region and containing appropriate restriction enzyme digestion sites. The amplified DNA is inserted into the vector pET28b by ligation into restriction sites suitable for expression under the control of the T7/ac promoter according to the manufacturer's instructions (Novagen Inc., 597 Science Drive, Madison, Wis.). The vector is then used to transform BL21(DE3) competent E. coli hosts, and selected on LB agar plates containing 50 μg/mL kanamycin. Colonies arising from this transformation are grown overnight at 37° C. in Lauria Broth to an OD600 of approximately 0.5, and induced with 50 mM IPTG and allowed to grow for an additional 4.5 h. The culture is harvested, resuspended in buffer, lysed with a French press and cleared by centrifugation at 20,000×g. Centrifugation of the supernatant after 20,000×g centrifugation at 100,000×g for 1 h yielded a membrane fraction, which is resuspended in buffer to approximately 7 mg protein/mL. Proteins in this purified membrane fraction are examined on 4-12% SDS-PAGE Gels (Novex, 11040 Roselle Street, San Diego, Calif.) after staining with Gelcode reagent (Pierce, P.O. Box 117, Rockford, Ill.). By comparison of the stained gel with one prepared from similar preparations from E. coli cells not expressing the putative cis-prenyltransferase, the protein corresponding to ehb2c.pk001.o18 (molecular mass 34,044 Daltons) is present at a significant level in this purified membrane fraction. Isolation of membranes from microbial hosts containing expressed cis-prenyltransferase proteins as described in this example, or further purification (e.g., by chromatographic means following solubilization of the protein) provides sufficient enzyme protein for analysis by biochemical, chemical or physicochemical means.
Example 7
Expression of Plant cis-Prenyltransferases in Arabidopsis thaliana 
Chimeric genes comprising Hevea, rice and soybean cis-prenyltransferases (SEQ ID NO: 9, 15 and 17, respectively) in sense orientation were constructed by polymerase chain reaction (PCR) from plasmids containing the Hevea, rice or soybean cis-prenyltransferase homologs, for expression in Arabidopsis thaliana. 
The Hevea DNA (designated Hpt3) was amplified by PCR from clone ehb2c.pk001.o18, using oligonucleotide primers Hpt3/Xba I (5′-GCTCTAGAGAAGGTTAAGTCAGTTTAGCATCG-3′) (SEQ ID NO: 29), and Hpt3/Kpn I (5′-GGGGTACCTTATTTTAAATATTCCTTATGCTTCTCC-3′) (SEQ ID NO: 30). The amplified Hpt3 cDNAs were digested with XbaI and KpnI and separated on an agrose gel. The DNA fragment was isolated and purified using a QIAguick Gel Extraction Kit according to the manufacture's instructions (Qiagen, USA). The purified DNA fragment was cloned into the corresponding sites of the binary vector pBI-35S (vide infra).
The rice and soybean DNAs were similarly isolated by PCR. For these clones, BamHI and SacI cloning sites were incorporated into the oligonucleotide primers to provide proper orientation of the DNA fragment when inserted into the binary vector pGV827. The rice homolog was amplified from clone rr1.pk0050.h8 using primers JK1 (5′-GTGGATCCATGCTTGGCTCACTTATG-3′) (SEQ ID NO: 31) and JK2 (5′-TTGAGCTCTATCTCC TCCCAGGGAGG-3′) (SEQ ID NO: 32) and the soybean homologue was amplified from clone sl1.pk0128.h7 using primers JK3 (5′-ACGGATCCATGTTCTCGTTAAGACTCC-3′) (SEQ ID NO: 33) and JK4 (5′-TCGAGCTCTTATGAATGTCGACCACC-3′) (SEQ ID NO: 34). PCR products were cloned into the PGEM T-easy vector using a TA-cloning kit (Promega Corporation, 2800 Woods Hollow Road, Madison, Wis.) and these plasmids were then transformed into E. coli. 
In addition to the cis-prenyltransferase genes identified in in-house databases, several Arabidopsis thaliana genomic DNA fragments containing putative cis-prenyl transferase gene sequences were identified in public databases by conducting BLAST searches using the sequences of bacterial and yeast cis-prenyl transferases essentially as outlined in Example 3. One gene, designated Apt5 (SEQ ID NO: 37) from Arabidopsis thaliana chromosome 5 genomic DNA (GenBank Accession Number AB011483), contains an 813 nt open reading frame with no intron sequences which encodes a protein with 271 amino acids and extensive homology to the microbial and plant cis-prenyltransferase sequences described in Examples 3 and 4. It was decided to include this gene in our arabidopsis transformation experiments to determine the effect of overexpression of an endogenous gene. The Apt5 gene (SEQ ID NO: 37) was cloned by PCR amplification using Arabidopsis thaliana genomic DNA as a template. Primers were designed to include specific restriction sites at each end to facilitate in cloning. The Primers used were Apt5/XbaI (5′-CTAGTCTAGAATCTCCCCTCCGATAACCAAAAAATCC-3′) (SEQ ID NO: 35) and Apt5/KpnI (5′-GGGGTACCTAGGGTTTAACTTAGAAACTATTTAG-3′) (SEQ ID NO: 36). The amplified Apt5 gene (SEQ ID NO: 37) was digested with XbaI and KpnI and separated on an agrose gel. The DNA fragment, ca. 850 bp in length, was isolated and purified using a QIAguick Gel Extraction Kit according to the manufacture's instructions (Qiagen, USA). The purified DNA fragments were cloned into a pBluescript vector according to manufacturer's instructions (Stratagene, 11011 North Torry Pines Road, LaJolla, Calif.).
To verify integrity of the amplified DNAs, plasmids were isolated and purified using QIAFilter cartridges (Qiagen Inc., 9600 De Soto Avenue, Chatsworth, Calif.) according to the manufacturer's instructions. Sequence was generated on an ABI Automatic sequencer using dye terminator technology (U.S. Pat. No. 5,366,860; EP Number 272007) using a combination of vector-specific primers. Sequence editing was performed in either Vector NTI, DNAStar, or the Wisconsin GCG program (vide supra).
The plasmid, pBI-35S, containing Hpt3 gene was transformed into Argobacterium tumefaciens strain C58 using a freeze-thaw method (Holsters, et al., (1978) Mol. Gen. Genet. 163:181-187). Arabidopsis thaliana plants were transformed via Agrobacterium-mediated transformation (Clough S J, Bent A F; (1998) Plant Journal 16(6):735-43).
The plasmids encoding rice and soybean cis-prenyltransferases were digested with BamHI and SacI and the cDNA fragments encoding the instant cis-prenyltransferases were isolated by agarose gel purification. The fragments were ligated into a derivative of the binary vector pBIN19 (Frisch, et al., (1995) Complete sequence of the binary vector BIN19. Plant Molecular Biology 27:405-409) containing a 35S cauliflower mosaic virus promoter and the nopaline synthase 3′ translation termination sequence (nos) with appropriate restriction sites. The resulting rice and soybean gene expression constructs were termed 35S::rr1 and 35S::sl1, respectively. These plasmids were transformed into E. coli and the integrity of the binary vectors was confirmed by plasmid isolation and restriction enzyme digestion as described above. The plasmids were then transformed into the Agrobacterium tumefaciens strain C58C1 by a freeze/thaw method (Holsters, et al., (1978) Mol. Gen. Genet. 163:181-187). Agrobacterium lines bearing the binary vector constructs were selected using PCR and used to transform Arabidopsis thaliana using the floral dip method (Clough, S J, Bent, A F, (1998) Plant Journal 16(6):735-43).
A binary vector, pBI-35S, was constructed for expression of the Apt5 gene (SEQ ID NO: 37) in plants by ligating an 800 bp Hind III-Xba I CaMV 35 promoter DNA fragment (Guilley H, Dudley R K, Jonard, G, Balazs, E, Richards, K E, (1982) Transcription of Cauliflower mosaic virus DNA: detection of promoter sequences, and characterization of transcripts, Cell 30(3):763-73) into the corresponding sites of the vector pBIB/NPT (Detlef Becker (1990) Binary vectors which allow the exchange of plant selectable mekers and reporter genes. Nucleic Acids Research 18(1):203 to yield the binary vector pBI-35S.) The Xba I-Kpn I DNA fragment encoding the Apt5 gene (SEQ ID NO: 37) was then cloned into the pBI-35S vector, yielding the construct 35S::Apt5. This construct was transformed into Argobacterium tumefaciens strain C58 using a freeze-thaw method (Holsters, et al., (1978) Mol. Gen. Genet. 163:181-187). Arabidopsis thaliana plants were transformed via Agrobacterium-mediated transformation (Clough S J, Bent, A F, (1998) Plant Journal 16(6):735-43).
The seeds produced from infected plants were plated on agar plates containing 100 μg/ml kanamycin. Arabidopsis plants resistant to kanamycin were selected and planted into soil.
Example 8
Analysis of the Polyprenol Profile of Transgenic Plants
Heterozygous transgenic plants expressing either the rice, Hevea brasiliensis, Arabidopsis or soybean cis-prenyltransferase homologs described in Example 7 were grown at 19° C., with 18 hours of light/day. Rosette leaves were harvested, frozen in liquid nitrogen and then lyophilized. The dried leaf material was extracted overnight in 2 ml of chloroform:methanol (2:1 v/v); geranylgeraniol was added at 1 μg per 10 mg dry weight to act as an internal standard. The organic extracts were washed with 400 μl of water and the aqueous phase discarded. The extracts were then dried down under a stream of nitrogen, and, after redissolving in 1 ml of 2MKOH/50% methanol, saponified by heating at 70° C. for 2 hours. The saponification mixtures were extracted twice with hexane. A volume of these hexane extracts equivalent to 10 mg (dry weight) of leaf tissue was then analyzed by high-pressure combined liquid chromatography-mass spectrometry (LC_MS), using a Hewlett-Packard 1100 Series LC-MS in atmospheric pressure chemical ionization (APCI) mode.
Chromatography was conducted using a Zorbax C18 (2.1×150 mm; 5 μm) reverse-phase column with methanol:isopropanol:water (12:8:1) at a flow rate of 0.25 ml/min as initial solvent. Polyprenols were eluted by applying a gradient of isopropanol:hexane (1:4), and elution monitored at 210 nm. Polyprenols were identified by comparing their elution time and mass spectrum with those of authentic standards (Sigma, St. Louis, Mo.).
The data from these analyses indicated that expression of the soybean clone sl1.pk0128.h7 (SEQ ID NO: 17) and overexpression of the arabidopsis cis-prenyltransferase Apt5 caused significant alteration of the polyprenol composition of leaves of the transgenic arabidopsis plants. In both of these cases, dodecaprenol (a 60-carbon polyprenol (C60), composed of 12 isoprene units) was undetectable either by examination of the diode array detector (DAD; FIG. 5) response or by selective ion monitoring of the mass detector data (Table 5; FIG. 6).
FIG. 5 illustrates the LC-MS analysis of extracts from wild-type and transgenic arabidopsis leaves. Samples equivalent to 10 mg leaf dry weight were separated by reverse phase chromatography and polyprenol elution was monitored at 210 nm using a diode array detector (DAD). Elution of standard polyprenols (C45-C60) was indicated in the profile of the extract from wild-type arabidopsis. Similarly FIG. 6 the LC-MS analysis of the molecular ion for dodecaprenol (C60) in rosette leaves of arabidopsis.
In addition to this primary effect, the amounts of other polyprenols (45-, 50-, 55-carbon) were drastically reduced (FIG. 5) compared to extracts of wild-type plants (which contain significant amounts of all of these polyprenols; Table 5, FIG. 5). This effect was not seen in plants expressing the Hevea Hpt3 or rice clones. The data clearly indicates that overexpression of at least two of the genes identified in Examples 2 and 3, which by homology appear to encode plant cis-prenyltransferases, dramatically alters the phenotype of transgenic plants with regard to polyprenol composition.







TABLE 5







Polyprenol profiles of Transgenic Arabidopsis Leaves












polyprenol
Wild-type
35S::Hpt3
35S::rr1
35::Sl1
35S::Apt3





C45
+
+
+
+
+


m/z 612-


614


C50
+
+
+
+
+


m/z 680-


682


C55
+
+
+
+
+


m/z 748-


750


C60
+
+
+
−
−


m/z 816-


818









The presence of a particular polyprenol in extracts of wild type or transgenic arabidopsis leaves was determined by selective ion monitoring of the mass spectrometer output during chromatography of extracts. Presence is indicated by a ‘+’ symbol, absence by a ‘−’.

## Claims

1. An isolated polynucleotide encoding a plant cis-prenyltransferase enzyme selected from the group consisting of:
(a) a polynucleotide encoding the amino acid sequence as set forth in SEQ ID NO: 10;
(b) a polynucleotide that hybridizes with a nucleic acid sequence of (a) under the following conditions: 0.1×SSC, 0.1% SDS, 65° C., and washed with 0.2×SSC, 0.5% SDS; and
(c) a polynucleotide that is fully complementary to the polynucleotide of (a) or (b).

2. The polynucleotide of claim 1 as set forth in SEQ ID NO: 9.

3. A chimeric gene comprising the isolated polynucleotide of claim 1 operably linked to a suitable regulatory sequence.

4. A transformed host cell comprising the chimeric gene of claim 3.

5. The host cell according to claim 4 selected from the group consisting of tobacco (Nicotiana spp.), tomato (Lycopersicon spp.), potato (Solanum spp.), hemp (Cannabis spp.), sunflower (Helianthus spp.), sorghum (Sorghum vulgare), wheat (Triticum spp.), maize (Zea mays), rice (Oryza sativa), rye (Secale cereale), oats (Avena spp.), barley (Hordeum vulgare), rapeseed (Brassica spp.), broad bean (Vicia faba), french bean (Phaseolus vulgaris), other bean species (Vigna spp.), lentil (Lens culinaris), soybean (Glycine max), arabidopsis (Arabidopsis thaliana), guayule (Parthenium argentatum), cotton (Gossypium hirsutum), petunia (Petunia hybrida), flax (Linum usitatissimum); carrot (Daucus carota sativa); and rubber tree (Hevea brasiliensis).

6. A transformed plant regenerated from the transformed host cell of claim 4.