Dwarfism Genes And Dwarf Plants

  *US07420102B2*
  US007420102B2                                 
(12)United States Patent(10)Patent No.: US 7,420,102 B2
 Amasino et al. (45) Date of Patent:Sep.  2, 2008

(54)Dwarfism genes and dwarf plants 
    
(75)Inventors: Richard M Amasino,  Madison, WI (US); 
  Fritz M Schomburg,  Madison, WI (US); 
  Scott D Michaels,  Madison, WI (US); 
  Colleen M. Bizzell,  Middleton, WI (US) 
(73)Assignee:Wisconsin Alumni Research Foundation,  Madison, WI (US), Type: US Company 
(*)Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 U.S.C. 154(b) by 358 days. 
(21)Appl. No.: 11/152,892 
(22)Filed: Jun.  15, 2005 
(65)Prior Publication Data 
 US 2005/0251883 A1 Nov.  10, 2005 
 Related U.S. Patent Documents 
(62) .
Division of application No. 10/155,435, filed on May  23, 2002, now Pat. No. 6,921,849 .
 
(51)Int. Cl. C12N 015/29 (20060101); C12N 015/82 (20060101); A01H 005/00 (20060101)
(52)U.S. Cl. 800/298; 536/23.6; 435/320.1
(58)Field of Search  None

 
(56)References Cited
 
 U.S. PATENT DOCUMENTS
 5,939,539  A  8/1999    Lange et al.     
 6,198,021  B1  3/2001    Lange et al.     

 OTHER PUBLICATIONS
  
  Biemelt et al (2004, Plant Physiology 135:254-265). *
  Bowie et al, Science 247:1306-1310, 1990. *
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  Chasan, R., et al., “GA Biosynthesis: a glimpse at the genes.” Plant Cell, 7, 141-143, 1995.
  Coles, J.P., et al., “Modification of gibberellin production and plant development in Arabidopsis by sense and antisense . . . ” Plant J., 17(5), 547-556, 1999.
  Curtis, I.S., et al., “Induction of dwarfism in transgeneic Solanum dulcamara by over-expression of a gibberellin 20-oxidase . . . ” Plant J., 23(3), 329-338, 2000.
  Harberd, N.P., et al., “Gibbeerellin: inhibitor of an inhibitor of . . . ” BioEssays, 20, 1001-1008, 1998.
  Hedden, P., et al., “Genetic analysis of gibberellin biosynthesis.” Plant Physiol., 119, 365-370, 1999.
  Hedden, P., et al., “Gibberellin metabolism: new insights revealed by the genes.” Trends Plant Sci, 5(12), 523-530, 2000.
  Hedden, P., et al., “Gibberellin biosynthesis: enzymes, genes, and their regulation.” Annu. Rev. Plant Physiol. Plant Mol. Biol., 48, 431-60, 1997.
  Hedden, P., et al., “Manipulation of hormone biosynthetic genes in transgenic plants.” Curr. Opin. in Biotech., 11, 130-137, 2000.
  Hedden, P., “Recent advances in gibberellin biosynthesis.” J. Expt. Bot., 50(334), 553-563, 1999.
  Huang, S., et al., “Overexpression of 20-oxidase confers a gibberellin-overproduction phenotype in Arabidopsis.” Plant Physiol., 118, 773-781, 1998.
  Jones, R., et al., “Gibberellins 2000.” Trends Plant Sci., 5(8), 320-321, 2000.
  Martin, D.N., et al., “The Slender gene of pea encodes a gibberellin 2-oxidase.” Plant Physiol., 121, 775-781, 1999.
  Peng, J., et al., “‘Green revolution’ genes encode mutant gibberellin response modulators.” Nature, 400, 256-26, 1999.
  Phillips, A.L., “Gibberellins in Arabidopsis.” Plant Physiol. Biochem., 36(1-2), 115-124, 1998.
  Phillips, A.L., et al., “Isolation and expression of three gibberellin 20-oxidase cDNA clones from Arabidopsis.” Plant Physiol., 108, 1049-1057, 1995.
  Prescott, A.G., et al., “Dioxygenases: molecular structure and role in plant metabolism.” Annu. Rev. Plant Physiol. Plant Mol. Biol., 47, 245-71, 1996.
  Ross, J.J., et al., “Gibberellin mutants.” Physiol. Plantarum, 100, 550-560, 1997.
  Ross, J.J., “Recent Advances in the study of gibberellin mutants.” Plant Growth Regulation, 15, 193-206, 1994.
  Sakamoto, T., et al., “Expression of a gibberellin 2-oxidase gene around the shoot apex is related to phase transition in rice.” Plant Physiol., 125, 1508-1516, 2001.
  Silverstone, A.L., et al., “Gibberellins and the green revolution.” Trends Plant Sci., 5(1), 1-2, 2000.
  Thomas, S.G., et al., “Molecular cloning and functional expression of gibberellin 2-oxidases, multifunctional enzymes involved in gibberellin deactivation.” Proc. Natl. Acad. Sci. USA, 96, 4698-4703, 1999.
  Weigel, D., et al., “Activation tagging in Arabidopsis.” Plant Physiol., 122, 1003-1013, 2000.
  Yamaguchi, S., et al., “Gibberellin biosynthesis: its regulation by endogenous and environmental signals.” Plant Cell Physiol., 41(3), 251-257, 2000.
  GenBank Accession No. AC079284.
  Lin et al, (Jan. 2001, NCBI Accession No. AC079284).
 
 
     * cited by examiner
 
     Primary Examiner —Stuart F. Baum
     Art Unit — 1638
     Exemplary claim number — 1
 
(74)Attorney, Agent, or Firm — Quarles & Brady LLP

(57)

Abstract

The present invention discloses the function, the cDNA sequences, and the expressed amino acid sequences of two genes the expression of which reduced bioactive GA levels and the height of a plant. This information enables creation of dwarf transgenic plants or transgenic plants with a specific dwarf organ.
6 Claims, 2 Drawing Sheets, and 2 Figures


CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application is a divisional application of U.S. patent application Ser. No. 10/155,435, filed on May 23, 2002, now U.S. Pat. No. 6,921,849 which is herein incorporated by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

[0002] This invention was made with United States government support awarded by the following agency: DOE DE-FCO5-92QR22072. The United States has certain rights in this invention.

BACKGROUND OF THE INVENTION

[0003] Gibberellins (GAs) are a group of tetracyclic diterpene carboxylic acids involved in a variety of developmental processes. They were originally identified through their effect on stem elongation (Phillips, A. L., Plant Physiol. Biochem 36: 115-124, 1998), and are now implicated in all stages of the plant life cycle including seed germination, leaf expansion, floral induction, fruit maturation, and apical dominance (Harberd, N. P. et al., BioEssays 20: 1001-1008, 1998). There are at least 126 different GAs identified in plants, fungi, and bacteria; however, most are precursors or degradation products, which are inactive forms. The bioactive GAs in higher plants include GA1, GA3, GA4, and GA7 (Hedden, P. and A. L. Phillips, Trends Plant Sci. 5: 523-530, 2000).
[0004] The GA biosynthetic pathway has three different classes of enzymes that catalyze specific reactions in the synthesis of bioactive GAs: terpene cyclases, Cyt P450 monooxygenases, and 2-oxoglutarate-dependent dioxygenases (Yamaguchi, S. and Y. Kamiya, Plant Cell Physiol. 41: 251-257, 2000). The first set of reactions of the biosynthetic pathway, from trans-geranylgeranyl diphosphate (GGPP) to GA12-aldehyde, is the same in all systems that have been studied. GGPP is converted to ent-kaurene via the terpene cyclases. ent-kaurene is then oxidized by Cyt P450 monooxygenases to GA12-aldehyde, GA12 and then GA53. GA12 and GA53 are the initial substrates for the 2-oxoglutarate-dependent dioxygenases. The specific enzymatic steps for the synthesis of bioactive GAs from GA12 are species specific.
[0005] The last reactions producing bioactive GAs and the first breakdown reactions involve several types of dioxygenases. The nomenclature of these dioxygenases is variable throughout the literature. Herein, the most commonly used name is listed first, followed by any other names also used. GA 20-oxidases remove the C-20, whereas 3β-hydroxylases (also called 3-oxidases) introduce the 3β-hydroxyl group; both are steps on the way to bioactive GAs. GA 2-oxidases (also called 2β-hydroxylases) introduce a 2β-hydroxyl group resulting in inactive products that cannot be converted to active forms (Thomas, S. G. et al., Proc. Natl. Acad. Sci. USA 96: 4698-4703, 1999). GA 2-oxidases generally act on GAs with 19 carbons, although there is evidence of 2β-hydroxylation of C20-GAs (Hedden, P. and Y. Kamiya, Annu. Rev. Plant Physiol. Plant Mol. Biol. 48: 431-60, 1997).
[0006] GA-modifying enzymes produce a vast number of GAs, although most are precursors or inactive forms. Many dioxygenases have been shown to be multifunctional, catalyzing consecutive reactions in the pathway, or modifying different, but structurally similar, GAs. For example, GA5, a GA 20-oxidase, converts GA12 to GA15 to GA24 to GA9, and GA53 to GA20 (Yamaguchi, S. and Y. Kamiya, Plant Cell Physiol. 41: 251-257, 2000). This multifunctional property allows many different GAs to be formed from relatively few enzymes.
[0007] Several of the dioxygenases can be grouped into small gene families. In Arabidopsis, GA 20-oxidases and GA 3β-hydroxylases are each encoded by at least four genes, and GA 2-oxidases are claimed in one review to be encoded by at least six genes (Hedden, P. and A. L. Phillips, Trends Plant Sci. 5: 523-530, 2000). Although the three groups of dioxygenases act on similar GA substrates, cluster analysis shows that they are no more closely related to each other than to any other plant dioxygenase (Hedden, P. and A. L. Phillips, Trends Plant Sci. 5: 523-530, 2000). The identity between different groups of GA dioxygenases is approximately 20-30% within one species, such as Arabidopsis (Table 1). Within a group, however, the identity is higher, even among species. Arabidopsis GA 20-oxidases are approximately 55-70% identical to each other, and 50-60% identical to 20-oxidases of other species (Prescott, A. G. and P. John, Annu. Rev. Plant Physiol. Plant Mol. Biol. 47: 245-71, 1996). The three published Arabidopsis GA 2-oxidases are 49-68% identical to each other (Thomas, S. G. et al., Proc. Natl. Acad. Sci. USA 96: 4698-4703, 1999), and 35-65% identical to GA 2-oxidases of other species (Table 2). The various members of each dioxygenase family are differentially expressed within the plant, and may be involved in different developmental processes (Hedden, P. and A. L. Phillips, Trends Plant Sci. 5: 523-530, 2000).
[0008] Chemical modification of GA levels is common in agriculture and horticulture. Seedless grapes are often treated with GA3 to increase berry size. Conversely, many crops and ornamental plants are treated with chemicals that act to inhibit enzymes in the GA-biosynthetic pathway (Hedden, P. and A. L. Phillips, Trends Plant Sci. 5: 523-530, 2000). Height reduction in ornamentals is currently achieved in many plants, such as poinsettias and petunias, via treatment with GA-inhibiting chemicals to produce compact plants that are more desired by consumers. Height reduction in a number of crop plants has resulted in increased yields and yield stability. In fact, compact crop plants have been a cornerstone of the great enhancements in agriculture yields over the past three decades. Compact plants can be grown more densely and are more resistant to storm damage (lodging) than taller wild type versions. Compact plants are easier to harvest because they hold the seed products closer together, reducing loss during harvesting.
[0009] Many groups have manipulated GA levels by transgenetically altering the expression of genes involved in GA metabolism. Overexpression of GA 20-oxidases in Arabidopsis has yielded plants with elevated GA levels which results in plants that are taller and have lighter green leaves than wild-type plants (Huang, S. et al., Plant Physiol. 118: 773-781, 1998). Suppression of GA 20-oxidases by antisense RNA has produced Arabidopsis plants that display phenotypes similar to weak GA-deficient plants; these plants have darker green cotyledons, were about 40% shorter than wild-type plants at maturity, and flowered slightly later than wild type in short-day conditions (Coles, J. P. et al., Plant J. 17: 547-556, 1999). Overexpression of a unique pumpkin 20-oxidase, which produces an inactive GA, has produced plants with a weak GA-deficient phenotype in Solanum dulcamara. These plants are semi-dwarfs, have smaller, darker green leaves, flower earlier, and produce more fruit and seed per fruit than wild type plants (Curtis, I. S. et al., Plant J. 23: 329-338, 2000). Overexpression of a bean 2-oxidase in Arabidopsis has produced plants with a variety of phenotypes including GA-like dwarfs and semi-dwarfs (Hedden, P. and A. L. Phillips, Trends Plant Sci. 5: 523-530, 2000). The same range of phenotypes was seen when the bean 2-oxidase was overexpressed in wheat (Hedden, P. and A. L. Phillips, Trends Plant Sci. 5: 523-530, 2000). Ectopic expression of a rice 2-oxidase resulted in rice plants which were dwarfed and had darker green, shorter and wider leaf blades, a typical GA-deficient phenotype for rice (Sakamoto, T. et al., Plant Physiol. 125: 1508-1516, 2001).
[0010] Genetically altering GA-modifying enzymes has the advantage of providing a means of decreasing chemical usage in plant production, as well as decreasing energy and time expenditures in chemical applications.

BRIEF SUMMARY OF THE INVENTION

[0011] The present invention discloses the function, the cDNA sequences, and the expressed amino acid sequences of two genes, the expression of which reduced bioactive GA levels and the height of a plant. The present invention includes various nucleic acid molecules and polypeptides that are related to the two genes and useful in various applications such as detecting the genes, generating antibodies and generating dwarf plants. The present invention also includes various host cells containing the nucleic acid molecules. The present invention also includes methods of generating dwarf plants using the nucleic acid molecules and the polypeptides described above and the resulted dwarf plants themselves.
[0012] It is an object of the present invention to provide a tool to creators of new plant varieties to alter the height of a plant or the size of a specific plant organ.
[0013] It is an advantage of the present invention that the two genes are dominant with regard to the dwarf phenotype so that a dwarf transgenic plant is easy to create.
[0014] Other objects, advantages and features of the present invention will become apparent from the following specifications and claims.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

[0015] FIG. 1 shows alignment of L10 and 69 proteins.
[0016] FIG. 2 shows alignment of other GA-modifying enzymes to the L10 and 69 proteins.

DETAILED DESCRIPTION OF THE INVENTION

[0017] Set forth below are the cDNA (SEQ ID NO:3 and SEQ ID NO:5) and the deduced amino acid (SEQ ID NO:4 and SEQ ID NO:6) sequences of two plant dwarfism genes, here named L10 and 69, respectively. The names L10 and 69 are for identification purpose only and may be changed to other names (for example, GA_ox_, wherein “_” is a number) to reflect the function of these two genes when the sequences are submitted for publication. When over expressed in a plant, each of these two genes reduced the bioactive GA level and the height of the plant. Prior to the present invention, the genomic DNA sequences (SEQ ID NO:1 and SEQ ID NO:2), but not the cDNA sequences, the amino acid sequences and the function, of these two genes were known. The present invention provides plant breeders and creators a unique tool so as to sculpt the height of a plant to more closely follow the desires of the breeder.
[0018] As shown in the examples below, overexpression of either L10 or 69 cause GA-deficiency indicating they are involved in GA degradation, not biosynthesis. L10 and 69 proteins have 44% identity and 54.5% similarity to each other. Both are listed in the database as gibberellin 20-oxidase-like proteins. GA 20-oxidases, however, are involved in biosynthesis, not degradation, although there is one report of a unique pumpkin 20-oxidase whose activity results in an inactive product and causes a dwarf phenotype when overexpressed in certain species (but not in Arabidopsis) (Curtis, I. S. et al., Plant J. 23: 329-338, 2000).
[0019] By sequence analysis, L10 and 69 do not fit well into any of the three groups of dioxygenases (Tables 1 and 2). In a BLAST search, the GA 20-oxidases from a variety of species show up before any 3β-hydroxylases or 2-oxidases; however, there is only a 28-33% identity between the 20-oxidases and our novel dioxygenases. There is a 24-30% identity between the novel dioxygenases and 3β-hydroxylases or 2-oxidases (Table 1 and 2) from various species. Thus, L10 and 69 dioxygenases do not seem to be significantly more similar to 20-oxidases than to the other dioxygenases (Table 1 and FIG. 2), and their overexpression phenotypes indicate that they are not 20-oxidases or 3β-hydroxylases. 20 oxidases and 3β-hydroxylases are biosynthetic enzymes and their overexpression should therefore lead to taller plants, but overexpression of either L10 or 69 leads to dwarf plants. Thus, if the L10 and 69 dioxygenases are part of a currently recognized class, based upon the overexpression of dwarf phenotype, it is more likely that they are 2-oxidases than either 3β-hydroxylases or 20-oxidases. A complete comparison of the amino acid sequences of all cloned 2-oxidases are shown in Table 2. The unique 20-oxidase from pumpkin is also included. As can be seen in Tables 1 and 2, the L10 and 69 dioxygenases are not as similar to the 2-oxidases as the rest of the 2-oxidases are to each other, even between species. The L10 and 69 dioxygenases are no more similar to the 2-oxidases than the 2-oxidases are to the 20-oxidases or 3β-hydroxylases (Table 1 and 2). Thus, the L10 and 69 dioxygenases are either a new class of dioxygenases or a unique, more distant subgroup of an existing class of dioxygenases.
[0020] In one aspect, the present invention relates to a polypeptide including an amino acid sequence that has at least 35%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, or 99% identity to and over the entire length of that of SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:4 with conservative substitutions, or SEQ ID NO:6 with conservative substitutions. The present invention also relates to a polypeptide including a novel fragment of the amino acid sequence described above, especially a fragment that is immunogenic or has a biological activity of reducing the bioactive GA level or the height of a plant. Besides the amino acid sequence described above, the polypeptide of the present invention can include a native or non-native amino acid sequence at the N- or C-terminus or both, which will not interfere with the function of the amino acid sequence described above. The flanking native or non-native amino acid sequence can but does not have to be one that assists in purification, detection, or stabilization of the amino acid sequence described above.
[0021] As used herein, “percent identity” of the two amino acid sequences or of two nucleic acids is synonymous to “percent homology,” which is determined using the algorithm of Karlin and Altschul (Proc. Nati. Acad. Sci. USA 87:2264-2268, 1990), modified as in Karlin and Altschul (Proc. Natl. Acad. Sci. USA 90:5873-5877, 1993). Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al. (J. Mol. Biol. 215:403-410, 1990). BLAST nucleotide searches are performed with the NBLAST program, score=100, wordlength=12, to obtain nucleotide sequences homologous to a nucleic acid molecule of the invention. BLAST protein searches are performed with the XBLAST program, score=50, wordlength=3, to obtain amino acid sequences homologous to a reference polypeptide (e.g., SEQ ID NO:4 or SEQ ID NO:6). To obtain gapped alignments for comparison purposes, Gapped BLAST is utilized as described in Altschul et al. (Nucleic Acids Res. 25:3389-3402, 1997). When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) are used. The referenced programs are available on line from the National Center for Biotechnology Information. National Library of Medicine, National Institute of Health.
[0022] Also within the scope of the present invention are polypeptides that bind specifically to an antibody that binds specifically to protein L1.0 or 69.
[0023] In another aspect, the present invention relates isolated nucleic acid molecules as described below. An “isolated nucleic acid molecule” used herein is a nucleic acid the structure of which is not identical to that of any naturally occurring nucleic acid or to that of any fragment of a naturally occurring genomic nucleic acid spanning more than three separate genes. The term therefore covers, for example, (a) a DNA which has the sequence of part of a naturally occurring genomic DNA molecules but is not flanked by both of the coding sequences that flank that part of the molecule in the genome of the organism in which it naturally occurs; (b) a nucleic acid incorporated into a vector or into the genomic DNA of a prokaryote or eukaryote in a manner such that the resulting molecule is not identical to any naturally occurring vector or genomic DNA; (c) a separate molecule such as a cDNA, a genomic fragment, a fragment produced by polymerase chain reaction (PCR), or a restriction fragment; and (d) a recombinant nucleotide sequence that is part of a hybrid gene, i.e., a gene encoding a fusion protein. Specifically excluded from this definition are nucleic acids present in mixtures of (i) DNA molecules, (ii) transfected cells, and (iii) cell clones, e.g., as these occur in a DNA library such as a cDNA or genomic DNA library. An isolated nucleic acid molecule can be modified or unmodified DNA or RNA, whether fully or partially single-stranded or double-stranded or even triple-stranded. A modified nucleic acid molecule can be chemically or enzymatically induced and can include so-called non-standard bases such as inosine.
[0024] An isolated nucleic acid molecule of the present invention is one that includes a polynucleotide having an uninterrupted coding sequence that encodes a polypeptide the amino acid sequence of which is at least 35%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, or 99% identical to SEQ ID NO:4 or SEQ ID NO:6, a complement of the foregoing, or a novel fragment of any of the foregoing. A preferred nucleic acid molecule includes a polynucleotide having a sequence that is at least 35%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97% or 99% identical to SEQ ID NO:3 or SEQ ID NO:5.
[0025] The invention also includes nucleic acid molecules that hybridize under stringent hybridization conditions (as defined herein) to all or a portion of the nucleotide sequence represented by SEQ ID NO:3 or its complement, or SEQ ID NO:5 or its complement. The hybridizing portion of the hybridizing nucleic acid molecules is typically at least 15 (e.g., 20, 25, 30, or 50) nucleotides in length. The hybridizing portion of the hybridizing nucleic acid molecules is at least 80%, e.g., at least 95%, or at least 99%, identical to the sequence of a portion or all of a nucleic acid encoding a L10 or 69 polypeptide, or the sequence's complement. Hybridizing nucleic acid molecules of the type described herein can be used, for example, as a cloning probe, a primer (e.g., a PCR primer), or a diagnostic probe. Hybridization of the oligonucleotide probe to a nucleic acid sample typically is performed under stringent conditions. Nucleic acid duplex or hybrid stability is expressed as the melting temperature or Tm, which is the temperature at which a probe dissociates from a target DNA. This melting temperature is used to define the required stringency conditions. If sequences are to be identified that are related and substantially identical to the probe, rather than identical, then it is useful to first establish the lowest temperature at which only homologous hybridization occurs with a particular concentration of salt (e.g., SSC or SSPE).
[0026] Then, assuming that 1% mismatching results in a 1° C. decrease in the Tm, the temperature of the final wash in the hybridization reaction is reduced accordingly (for example, if sequences having >95% identity with the probe are sought, the final wash temperature is decreased by 5° C.). In practice, the change in Tm can be between 0.5° C. and 1.5° C. per 1% mismatch. Stringent conditions involve hybridizing at 68° C. in 5×SSC/5× Denhardt's solution/1.0% SDS, and washing in 0.2×SSC/0.1% SDS at room temperature. Moderately stringent conditions include washing in 3×SSC at 42° C. The parameters of salt concentration and temperature can be varied to achieve the optimal level of identity between the probe and the target nucleic acid. Additional guidance regarding such conditions is readily available in the art, for example, by Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, N.Y.; and Ausubel et al. (eds.), 1995, Current Protocols in Molecular Biology, (John Wiley & Sons, N.Y.) at Unit 2.10.
[0027] Isolated nucleic acid molecules of the invention can be obtained by several methods. For example, they can be isolated using procedures which are well known in the art. These include, but are not limited to: (a) hybridization of detectably labeled probes representing all or part of the L10 or 69 gene to genomic or cDNA libraries to detect similar nucleic acid sequences; (b) antibody screening of expression libraries to detect similar structural features; (c) synthesis by the polymerase chain reaction (PCR); and (d) chemical synthesis of a nucleic acid molecule. Sequences for specific coding regions of genes can also be found in GenBank, the National Institutes of Health computer database.
[0028] For the identification of isolated nucleic acid molecules using detectably labeled probes, or for the identification of polynucleotide fragments whose complements hybridize to L10 or 69, stringent hybridizing conditions described above can be used. Alternatively, higher stringency conditions can be used. Typically, lower stringency hybridization conditions permit hybridization of related but not identical L10 or 69 gene, and thereby allow identification of the L10 or 69 gene in other species.
[0029] In a related aspect, any polynucleotide sequence of the present invention, or an antisense version thereof, can be provided in a vector or genetic construct in a manner known to those skilled in the art. A polypeptide-encoding polynucleotide so provided in a vector can, but need not, be under the transcriptional control of one or more regulatory elements which can include a promoter not natively found adjacent to the polynucleotide such that the encoded polypeptide can be produced when the vector is provided in a compatible host cell or in a cell-free transcription and translation system. Such cell-based and cell-free systems are well known to the skilled artisan. Cells comprising a vector containing a polynucleotide sequence of the invention are themselves within the scope of the invention.
[0030] In another related aspect, the present invention encompass a polynucleotide having a nucleotide sequence that encodes a polypeptide the amino acid sequence of which is at least 35%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, or 99% identical to SEQ ID NO:4 or SEQ ID NO:6, operably linked to a non-native expression control sequence which can include a promoter. Such a polynucleotide of the present invention can be provided in a vector such that the encoded polypeptide can be produced when the vector is provided in a compatible host cell or in a cell-free transcription and translation system. Such cell-based and cell-free systems are well known to the skilled artisan. Cells comprising the vector are themselves within the scope of the invention.
[0031] In yet another aspect, the present invention relates to a method of reducing the height of a plant and the resulted dwarf plant. One way to reduce the height of a plant is to increase the transcription or translation rate, or the stability of the mRNA or protein products of the endogenous L10 or 69 gene. Another way to reduce the height of a plant is to make a trangenic plant to express certain isolated nucleic acid molecules of the present invention, which include for example, the L10 or 69 gene of the same or a different species (either the genomic DNA or cDNA of the L10 or 69 gene), a portion of a L10 or 69 gene the protein product of which retains the function of reducing bioactive GA level, and other nucleic acid molecules of the present invention that are effective when expressed in the transgenic plant to cause the transgenic plant to be shorter compared to a non-transgenic plant of the same genetic background.
[0032] The examples below showed that expressing the Arabidopsis L10 or 69 gene introduced into a Arabidopsis plant or the Arabidopsis L10 gene introduced into a tobacco plant reduced the height of the Arabidopsis or tobacco plant. Identical or similar techniques can be used to express a L10 or 69 gene in other plants species to reduce the height of those species. In addition, this Arabidopsis or tobacco plant system can be used to test possible L10 or 69 genes from other plant species and those nucleic acid molecules of the present invention that are effective to cause a transgenic plant to be shorter compared to a non-transgenic plant of the same genetic background.
[0033] It should be understood that techniques of plant genetic engineering have been developed to the point where it is now practical to place any genetic construct into almost any useful plant species. The process does, however, still involve some random processes, most notably that insertions of foreign DNA into the genome of plants still occurs at random sites in the plant genome. As a result, in any group of plants emerging from a plant transformation process, the results achieved for the different gene insertion events will vary, sometimes dramatically. For example, for a simple gene insertion of another copy of an endogenous plant gene, many plants produced will have a slightly higher level of activity of the endogenous protein, others will have no measurable change or even a decrease in measurable activity, while a few will have substantial increases in activity levels. However, this variation does not mean stable results cannot be achieved, since the results tend to be consistent generation-to-generation for each specific genetic insertion. Thus the high activity plants have, in effect, a high activity allele that can be transferred by normal mendelian inheritance to their progeny.
[0034] To make a transgenic plant, as is known to those of skill in the art, one needs to make a genetic construction capable of expressing an inserted protein coding sequence, whether foreign or endogenous, in a plant. One also needs a method to insert the genetic construction into the plant.
[0035] The tools and techniques for making genetic constructions that will express proteins in plants are now widely known. Any genetic construction intended to cause the synthesis in the cells of the plant of a polypeptide or protein must include a sequence of DNA known as a protein coding sequence (can be a genomic DNA or a cDNA), which specifies the sequence of the polypeptide or protein to be produced in the resultant plant. For a protein coding sequence to be expressed in a plant to produce a polypeptide or protein, it must be placed under the control of a plant expressible promoter and be followed by a plant transcriptional terminator sequence, also known as a polyadenlyation sequence. The plant expressible promoter is a promoter which will work in plants, usually either of plant origin or from a plant pathogen like a virus (e.g. Cauliflower mosaic virus) or a bacteria (e.g. Agrobacterium promoters like the nopaline synthase promoter). Plant promoters from pathogens tend to be constitutive promoters, meaning that they actually express the protein coding sequence in all of the tissues of the plant at all times. Other plant promoters are known to be tissue specific (e.g. to fruit or to flower) or developmentally specific (e.g. to stage of plant life such as emergent specific or senescent specific), while others are intended to be inducible (e.g. heat shock or metal ion induced promoters). Any of these types of promoters may by used in the practice of this invention depending on the intended affect on the transgenic plant to be produced. For example, a plant with a specific height or stature may be obtained through adjusting the expression level of a transgene by varying promoter strength. One may also use a tissue specific promoter to limit the dwarfing effect such as changing inflorescence architecture, stem elongation, or fruit development without changing any other aspect of the plant.
[0036] Several methods have been demonstrated to insert genes into plants to make them transgenic. The most widely used methods, broadly defined, are Agrobacterium-mediated transformation or accelerated particle mediated transformation. The various techniques of Agrobacterium-mediated plant transformation make use of the natural ability of the plant pathogens of the Agrobacterium genus to transfer DNA from a plasmid in the bacteria into the genome of a plant cell. Particle-mediated plant transformation techniques utilize DNA-coated small carrier particles accelerated from a device, often referred to as a gene gun, into the cells of a plant. The full implementation of either approach requires techniques to recover a fully mature, morphologically normal plant from the transformed cells. The techniques often therefore involve either selection or screening protocols to identify which plant cells were transformed and regeneration protocols to recover whole plants from the single transformed plants cells. As mentioned above, these techniques have been worked out for many plant species and many, and perhaps all, of the economically important plant species. Other techniques, such as electroporation have also been used to make transgenic plants. But fundamentally for the invention disclosed here, the particular technique of plant transformation does not matter. Once the plant has been genetically engineered, and a transgenic plant has been created, the method of transformation of the original plant becomes irrelevant. A transgene inserted into the genome of one plant is then fully inheritable by progeny plants of the original genetically engineered plant by normal rules of classical plant breeding. The term transgene is here used to apply to an inserted genetic construction carried in the cells of a target plant. Thus, the term transgenic plant, as used here, refers to a plant that carries such a transgene.
[0037] Plants in which a copy of a L10 or 69 gene is introduced may also contain a wild-type (i.e., endogenous) plant height coding region which acts to control the height of the plant. Upon introduction into the genome of a plant, the L10 or 69 gene can act to augment the activity of an endogenous height coding region to make the plant shorter. For instance, a second copy of a height coding region can be introduced into a plant to increase the amount of height reduction L 10 or 69 protein present in the plant.
[0038] The present invention also provides a genetically modified plant, characterized as having the phenotypic trait of general dwarfing of the whole plant or dwarfing of a specific plant organ. By this it is meant that the modified plants of the present invention, whether modified by incorporating a L10 or 69 gene expressing a new or additional L10 or 69 protein in the plant, demonstrate a reduced height or size in at least one tissue or organ relative to the same plant without the transgene inserted. Preferably, the dwarfing of the whole transgenic plant or a specific tissue or organ (on average) of the transgenic plant is at least about 20%, more preferably at least about 100%, most preferably at least about 200% in comparison to the same plant without the transgene. Preferably, the genetically modified plant and the same plant without the transgene are grown under the same conditions.
[0039] Plants included in the invention are any plants amenable to transformation techniques, including both monocotyledonous and dicotyledonous plants. Examples of monocotyledonous plants include, but are not limited to, vegetables such as asparagus, onions and garlic; cereals such as maize, barley, wheat, rice, sorghum, pearl millet, rye and oats; and grasses such as forage grasses and turfgrasses. Examples of dicotyledonous plants include, but are not limited to, vegetables, feed, and oil crops such as tomato, beans, soybeans, peppers, lettuce, peas, alfalfa, clover, Brassica species (e.g., cabbage, broccoli, cauliflower, brussel sprouts, rapeseed, and radish), carrot, beets, eggplant, spinach, cucumber, squash, melons, cantaloupe, sunflowers; fiber crops such as cotton; and various ornamentals such as flowers and shrubs.
[0040] In another related aspect, the isolated nucleic acid molecules of the present invention can be used to analyze and determine the pattern of L10 or 69 gene activity of a transgenic or non-transgenic plant as an aid to breeding or creating plants having desired heights.
[0041] The above disclosure generally describes the present invention. A more complete understanding can be obtained by reference to the following specific examples which are provided herein for purposes of illustration only and are not intended to limit the scope of the invention.

EXAMPLES

[0042] 1. Isolation of Mutants that Possessed Altered GA-Metabolism.
[0043] Arabidopsis was mutagenized by T-DNA derived from Agrobacterium tumefaciens to generate plants with altered phenotypes. The mutagenesis was designed to isolate plants that contained dominant phenotypes by use of a T-DNA vector that contained a transcriptional enhancer region (PSKI15 activation vector) (Weigel, D. et al., Plant Physiol. 122: 1003-1013, 2000). Plants were screened in the initial (T1) generation to identify mutant plants that displayed altered inflorescence architecture.
[0044] Two mutant plants (Line 10 (L10) and Line 69, (69)) were identified that displayed smaller and darker green leaves, delayed floral induction, and reduced primary inflorescence length (Table 3). These phenotypes are similar to loss-of-function alleles of GA biosynthetic enzymes. When GA levels were directly measured it was found that bioactive GAs in the mutants L10 and 69 were substantially lower than wild-type plants. Bioactive GA (GA4) was measured in wild-type plants at 1.84 ng/g dry weight; whereas, both L10 and 69 plants did not contain detectable levels of GA4. Additionally, other GA forms were also substantially lower in the L10 and 69 lines (Table 4). Both mutant phenotypes could be rescued by the external application of bioactive GA3, which is consistent with the notion that the phenotypes were a result of reduced levels of bioactive GAs.
[0045] Heterozygous plants of L10 and 69 were self-pollinated to create a segregating population. A 3:1 ratio of mutant to wild-type plants was observed in the segregating population of both L10 and 69 indicating that both phenotypes are dominant. There are no detectable differences between heterozygous and homozygous phenotypes for either mutant and thus each appears to behave in a fully dominant manner.
[0046] The phenotype of the mutants cosegregated with the T-DNA present in the mutants. More than 100 plants from the segregating population were assayed for both the altered GA phenotype and the presence of the T-DNA. All of the plants that displayed the GA-deficient phenotype contained the T-DNA while none of the wild-type plants contained the T-DNA. The probability of this cosegregation occurring randomly is less than 0.00001 and therefore indicated that the T-DNA caused the mutant phenotype seen in the L10 and 69 lines.
[0047] 2. Cloning of Genes that Caused the L10 and 69 Mutant Phenotypes.
[0048] Since the T-DNA cosegregated with the mutant phenotype, it was possible to sequence the genomic DNA near the T-DNA to determine where in the genome the T-DNA was located. A piece of the genomic DNA near the T-DNA from both mutants was sequenced and used to search the Arabidopsis data base (which includes sequences from many organisms) available on line from the National Center for Biotechnology Information, National Library of Medicine, National Institute of Health. The search revealed that genomic DNA sequences corresponding to predicted genes were directly adjacent to the enhancer region of the inserted T-DNA in both L10 and 69 plants. These genes were designated L10 and 69, respectively. In the Arabidopsis data base, 69 is on BAC F7J7 (accession number AL021960: Arabidopsis thaliana DNA chromosome 4, BAC clone F7J7 (ESSA project)). It is number 140 (F7J7.140) on that BAC. The nucleotide sequence is annotated as “similarity to gibberellin C-20 oxidase, Oryza sativa, PATCHX:G1854637.” The predicted protein (CAA17539.1) is annotated as “gibberellin 20-oxidase-like protein.” L10 is on BAC F8A12 (accession number AC079284: Arabidopsis thaliana chromosome 1 BAC F8A12 genomic sequence, complete sequence). It is number 18 (F8A12.18) on that BAG. The nucleotide sequence is annotated as “similar to gibberellin 20 oxidase (Triticum aestivum) GI:2222796.” The predicted protein (AAG50945.1) is annotated as “gibberellin 20-oxidase, putative.”
[0049] Based on the above information, we have determined the cDNA sequences for L10 and 69 as SEQ ID NO:3 and SEQ ID NO:5, respectively.
[0050] Reverse-transcription-based PCR was used to determine the expression levels of the L10 and 69 gene in the two mutants. Both L10 and 69 plants had substantially increased mRNA levels of their respective enzymes. This observation is consistent with the hypothesis that the phenotypes of the mutants were due to activation of gene expression caused by the enhancer region of the T-DNA.
[0051] 3. Ectopic Expression of L10 and 69 in Arabidopsis.
[0052] To test the hypothesis that the L10 and 69 phenotypes were due to the activation of the respective GA-modifying genes, L10 and 69 were constitutively overexpressed. The genomic region of the respective genes was cloned into a vector that contained a cauliflower mosaic virus 35S promoter (35S) that provides constitutive mRNA expression in most plant tissues. These new vectors that contained the 35S:L10 or 35S:69 constructs were transformed into wild-type Arabidopsis. First generation transformed plants were screened for phenotypes similar to the respective initial L10 or 69 lines. Approximately half of the transformed plants displayed phenotypes similar or identical to that of the initially isolated L10 or 69 lines, respectively. Thus, increased expression of the GA-modifying genes was sufficient to cause the alterations in plant growth and stature that were seen in the initially isolated mutant lines. This data confirmed that the activation of the GA-modifying genes near the T-DNA inserts had caused the dominant GA-deficient phenotypes. In addition to the 35S-driven genomic clones, the cDNAs for each of the L10 and 69 lines were also placed under the transcriptional control of the 35S promoter and were found to also cause a dwarf, GA-deficient-like phenotype. This indicates that the cDNAs are functional and sufficient for the purposes of altering GA metabolism to produce the aforementioned phenotypes.
[0053] 4. Ectopic Expression of L10 Functions in Tobacco to Produce GA-Deficient-Like Plants.
[0054] Introduction of the 35S:L10 or 355:69 into wild-type tobacco (Wisconsin 38) produces plants that appear to be deficient in bioactive GAs. Many phenotypic changes are similar to the phenotypic changes in Arabidopsis. For example, the leaves are smaller and darker green, plant height is reduced, and internode distance is shortened (Table 5). The 35S:L10 and 355:69 tobacco plants and the wild-type plant had similar seed yield.
[0055] 5. Sequence Alignments of L10 and 69 to GA-Modifying Enzymes.
[0056] L10 and 69 are more similar to each other than to any other protein in the Arabidopsis database. When L10 is used to BLAST search the Arabidopsis database of proteins, the closest match to L10 is 69. Likewise, when 69 is used to search the database L10 is the closest match to 69. This implies that L10 and 69 may define a group of GA-modifying enzymes that may be functionally distinct from other GA-modifying enzymes (Tables 1 and 2). An alignment of L10 to 69, depicted in FIG. 1, reveals that there is 44% identity and 54.5% similarity shared by the two proteins. In FIG. 1, lines denote identity and colons and periods denote degree of similarity.
[0057] An alignment of L10 and 69 to AtGA2ox1, AtGA2ox2, AtGA2ox3, AtGA20ox1, GA5 (a 20-oxidase), and GA4 (a 3β-hydroxylase), as depicted in FIG. 2, reveals that these enzymes contain regions of similarity (see also Table 2). In FIG. 2, amino acid residues that are identical with 69 protein are designated by a black box surrounding the amino acid residue and similarities in amino acid residues to 69 proteins are denoted by gray shading around residues. However, L10 and 69 contain unique regions that are similar to each other but show little or no relatedness to the other GA-modification enzymes. The two most prominent examples of this are the sequence from L10 at amino acid 115 through 137 and the carboxy terminus of L10 and 69 defined by the L10 protein sequence at amino acid 304 through 335 (FIGS. 1 and 2).
[0058] 
[00001] [TABLE-US-00001]
  TABLE 1
 
  Percent identity between novel dioxygenases and other known Arabidopsis dioxygenases
  (Numbers in the table are percent identity. Thick lines separate the groups of dioxygenases
  and the values under these lines illustrate the high percent of identity within each group.
  All of the dioxygenases are from Arabidopsis. At 2ox1-3 are the three cloned 2-oxidases
  (accession nos. AJ32435, AJ132436, and AJ132437). At20ox1-3 are three 20-oxidases
  (accession nos. X83379, X83380, and X83381). At 3ox1-2 are two 3β-hydroxylases
  (accession nos. L37126 and T51691)).
 
[see pdf for image]
 
[0059] 
[00002] [TABLE-US-00002]
  TABLE 2
 
  Percent identity between the L10 and 69 dioxygenases and other known GA-degrading
  enzymes (Numbers in the table are percent identity. A thick line separates the known 2-oxidases.
  L10 and 69 are our two novel dioxygenases. At 2ox1-3 are the three 2-oxidases in Arabidopsis
  (accession nos. AJ132435, AJ132436, and AJ132437). Rice 2ox is the 2-oxidase from Oryza
  sativa (Sakamota, 2001). Bean 2ox is the 2-oxidase from Phaseolus coccineus (accession no.
  AJ132438). Pea 2ox1-2 are the two 2-oxidases from Pisum sativum (accession nos. AF1009541
  and AF056935). Pumpkin 20ox is the unique 20-oxidase from Cucurbita maxima (accession no.
  AAB64345)).
 
[see pdf for image]
 
[0060] 
[00003] [TABLE-US-00003]
  TABLE 3
 
  Characterization of the Mutant Phenotypes of L10 and 69 Lines.
    Wild-         GA3-GA3-
    Type   L10   69   35S::L10   35S::69   treated L10   treated 69
   
  Flowering   8   17   15   16   15   8   8
  Time LD
  (Number of Leaves)
  Height cm   47   7.2   9.4   8.2   9.6   30   30
  Number of   41   77   84   >100   >100   65   65
  Flowering Branches
  Internode Length mm   8.9   1.8   2.3   2.4   2.6   7   7
 
[0061] 
[00004] [TABLE-US-00004]
  TABLE 4
 
  Abundance of GAs Present in Wild Type and Mutant Lines
    GAs   Ws (wild type)   69   L10
   
    Non-13-Hydroxylated:      
  GA24   51.8   0.23   0.06
  GA9   1.01   0.05   0.02
  GA4   1.84   ND   ND
    13-Hydroxylated:
  GA53   6.43   0.30   0.39
  GA44   0.79   ND   ND
  GA19   9.29   0.09   0.02
  GA20   0.19   ND   ND
  GA1   0.12   0.02   ND
   
    (All values are in ng/g dry weight. ND = not detectable).
[0062] 
[00005] [TABLE-US-00005]
  TABLE 5
 
  Phenotypic Alterations in Tobacco
  with Ectopic Expression of L10.
    Characteristic   Wild Type   35S::L10
   
    Leaf Length in cm   32   10
    Height in cm   8.5   2.5
    Internode distance in cm   0.7   0.2
   
[0063] The complete disclosures of all publications that are cited herein are hereby incorporated by reference as if individually incorporated. It is also understood that, given the limitations of the state of the art, occasional sequence errors or deletions may occur without affecting the usefulness of the data presented. Various modifications and alterations of this invention will become apparent to those skilled in the art without departing from the scope and spirit of this invention, and it should be understood that this invention is not to be unduly limited to the illustrative embodiments set forth herein, but rather is to be construed to be of spirit and scope defined by the appended claims.
(57)

Claims

1. An isolated nucleic acid molecule comprising a polynucleotide having an uninterrupted coding sequence that encodes the amino acid sequence of SEQ ID NO:6.
2. An isolated nucleic acid molecule comprising a polynucleotide having the nucleotide sequence of SEQ ID NO:5.
3. A The nucleic acid construct comprising:
a polynucleotide has having a nucleotide sequence that encodes SEQ ID NO:6, the polynucleotide being operably linked to a heterologous plant expressible promoter, wherein expression of the polynucleotide in a transgenic plant causes the plant to be shorter compared to a non-transgenic plant of the same genetic background.
4. A transgenic plant comprising in its genome the nucleic acid construct of claim 3 wherein the polynucleotide is expressed in the plant.
5. The transgenic plant of claim 4, wherein the transgenic plant is at least 20% shorter than a non-transgenic plant of the same genetic background while being grown under the same conditions.
6. A seed of the transgenic plant of claim 4 wherein the seed contains the same nucleic acid construct as the transgenic plant.
*****

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