WO2003020015A2 - Methods to produce transgenic plants resistant to osmotic stress - Google Patents

Methods to produce transgenic plants resistant to osmotic stress Download PDF

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WO2003020015A2
WO2003020015A2 PCT/US2002/027701 US0227701W WO03020015A2 WO 2003020015 A2 WO2003020015 A2 WO 2003020015A2 US 0227701 W US0227701 W US 0227701W WO 03020015 A2 WO03020015 A2 WO 03020015A2
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plant
seq
promoter
cis
transgenic
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PCT/US2002/027701
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French (fr)
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WO2003020015A3 (en
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Bruno Ruggiero
Ray A. Bressan
Paul M. Hasegawa
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Purdue Research Foundation
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Publication of WO2003020015A3 publication Critical patent/WO2003020015A3/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0069—Oxidoreductases (1.) acting on single donors with incorporation of molecular oxygen, i.e. oxygenases (1.13)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8273—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for drought, cold, salt resistance

Definitions

  • the present invention relates generally to methods of producing plants that are resistant to salt stress.
  • Salinity is a major constraint to crop productivity because it reduces yield and limits expansion of agriculture onto previously uncultivated land (Flowers and Yeo, 1995). Salinity is becoming more acute as a consequence of the intensive agricultural production that is occurring to meet the caloric and nutritional demands of the burgeoning world population. Fertilization contributes to this problem by causing added salt accumulation. It is estimated that salinity affects 6% of the land surface area (Flowers and Yeo, 1995) and, perhaps, more than 20% of the cultivated land is salt affected. Etiologies of salt stress include hyperosmolarity, ion toxicity and nutrient acquisition deficiency. The pathologies mediated by salt stress include elevated levels of reactive oxygen radicals, reduced enzyme function, photosynthesis and other metabolic processes, and membrane dysfunction (Hasegawa et al, 2000).
  • Deserts and desert-like regions occupy 1/4 to 1/3 of the earth's land mass world and are expanding.
  • Reasons for this desertification include using irrigation water with a high salt concentration, dams, irrigation and deficient draining equipment, and sea water reaching farm land, all causing salts such as NaCl, Na 2 SO , MgCl 2 , CaCl 2 to accumulate in soil.
  • salt-containing soil almost all plants have reduced growth or salt-related lesions.
  • afforestation and plant rearing have been attempted in the areas of the high-salt soil. However, few plants can grow in the high-salt soil and crop productivity in high-salt soils is markedly low.
  • salt-tolerant plants Some aspects of selection and rearing of salt-tolerant plants have been studied. For example, a salt-tolerant variety of rice is known. Furthermore, breeding salt-tolerant plants by adapting a callus of a plant to a high salt medium and reproducing the plant has been attempted. Workers have also searched for plant genes related to salt-tolerance. See, e.g., PCT Application PCT/CA99/00219.
  • Salt stress survival and adaptation are dependent on cellular ion homeostasis. Regulation of net intracellular Na + and Cl " uptake and subsequent vacuolar compartmentalization without cytotoxic ion accumulation are pivotal processes for salt tolerance (Blumwald et al, 2000; Hasegawa et al, 2000; Niu et al, 1995). Vacuolar partitioning of Na + and Cl " contributes also to maintenance of cellular water relations with organic solutes being the principal osmolytes that accumulate in the cytosol and organelles to balance intracellular osmotic status of cells in salt grown plants.
  • Intracellular compartmentation of Na + and Cl " is a salt adaptation conserved in halophytes and glycophytes (Blumwald et al, 2000; Hasegawa et al, 2000).
  • the steady-state Na + electrochemical gradients across the plasma membrane and tonoplast make it likely that efflux from the cytosol across these membranes is energy-dependent (Blumwald et al, 2000; Hasegawa et al, 2000; Niu et al, 1995).
  • Na + flux from the apoplast or vacuole into the cytosol occurs down its electrochemical gradient. Modulation of plasma membrane cation transport systems or controlled dissipation of the plasma membrane potential can reduce intracellular Na + influx.
  • Yeast Pmp3p is a 55 amino acid peptide that is responsible for attenuating hyperpolarization across the plasma membrane, which reduces influx of toxic cations, like Na + (Navarre and Goffeau, 2000). Transcription of PMP3 orthologous plant genes is induced by salt treatment (Navarre and Goffeau, 2000).
  • H + translocation across these membranes increases with salt treatment and can be attributed both to pump activation and enhanced transcription, indicating that both positive and negative control of the H + electrochemical potential may be essential features of ion homeostasis in high external Na + environments (Hasegawa et al, 2000).
  • SOSl is a 127- kDa protein with an N-terminal hydrophobic region that contains 12 predicted transmembrane spanning domains and a hydrophilic C-terminus of more than 600 amino acids. Sequence alignment analysis indicates that SOSl is most similar to the Synechocystis sp.
  • the invention provides plants that are resistant to environmental stresses such as salt.
  • the invention provides a mutant plant comprising a mutated 9-cis-epoxycarotenoid dioxygenase gene so that, as compared to a plant not comprising said mutated gene, the mutant plant exhibits increased salt tolerance or increased stress resistance.
  • the invention further provides a transgenic plant comprising a null mutation in an endogenous 9-cis-epoxycarotenoid dioxygenase gene so that, compared to a plant of the same genetic background but without the null mutation in the endogenous 9-cis-epoxycarotenoid dioxygenase gene, the transgenic plant exhibits increased salt resistance.
  • the invention also provides a transgenic plant comprising an isolated 9- cis-epoxycarotenoid dioxygenase nucleic acid having SEQ ID NO: 10, SEQ ID NO.-l l, SEQ ID NO: 12, SEQ ID NO: 14-16, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, or a complement thereof, and a promoter functional in a plant cell, wherein upone expression of the isolated nucleic acid or the complement thereof, the transgenic plant exhibits increased salt resistance relative to a plant of the same genetic background but without the isolated 9-cis-epoxycarotenoid dioxygenase nucleic acid.
  • the invention further provides a transgenic plant comprising an isolated nucleic acid that encodes an inhibitory 9-cis-epoxycarotenoid dioxygenase RNA that, when expressed from a promoter functional in a plant cell, inhibits the function of endogenous RNA encoding a 9-cis-epoxycarotenoid dioxygenase enzyme; wherein the transgenic plant exhibits increased salt resistance relative to a plant of the same genetic background but without the isolated 9-cis- epoxycarotenoid dioxygenase nucleic acid.
  • the inhibitory 9-cis- epoxycarotenoid dioxygenase RNA may be substantially complementary to the endogenous RNA encoding the 9-cis-epoxycarotenoid dioxygenase enzyme.
  • the inhibitory RNA can, for example, be substantially complementary to SEQ ID NO:l-9, SEQ ID NO:10, SEQ ID NO:ll, SEQ ID NO:12, SEQ ID NO:14- 20, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34.
  • such an inhibitory RNA hybridizes under moderately stringent hybridization conditions to the endogenous RNA encoding the 9-cis-epoxycarotenoid dioxygenase enzyme comprising SEQ ID NO:13, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID NO:33.
  • Moderately stringent hybridization conditions can include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37°C, and a wash in 0.5X to IX SSC at 55 to 60°C.
  • such an inhibitory RNA hybridizes under highly stringent hybridization conditions to the endogenous RNA encoding the 9-cis- epoxycarotenoid dioxygenase enzyme comprising SEQ ID NO: 13, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID NO:33.
  • Highly stringent conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0. IX SSC at 60 to 65°C.
  • the transgenic plant of the invention can develop in the presence of a concentration of salt that inhibits the development of the plant of the same genetic background but without the null mutation or the isolated nucleic acid.
  • the transgenic plants of the invention can develop faster than plants of a similar backround but without the null mutation or the isolated nucleic acid, even in the presence of a concentration of salt that would normally inhibit the development of the plant.
  • the transgenic plants of the invention can also develop leaves faster in the presence of a concentration of salt that inhibits the development of the plant of the same genetic background but without the null mutation or the isolated nucleic acid.
  • the transgenic plants of the invention can be dicots or monocots. Food or feed can be produced from the transgenic plant of the invention.
  • Transgenic progeny plants can be obtained from the transgenic plants of the invention. Such progeny plants have the null mutation or they have the isolated 9-cis- epoxycarotenoid dioxygenase nucleic acid, and can develop in the presence of a concentration of salt that inhibits the development of a plant not comprising said mutated gene.
  • Transgenic seeds can also be obtained from plant produced according to the invention and transgenic progeny plants can be obtained from such transgenic seeds.
  • the invention also provides a transgenic plant comprising an isolated recombinant DNA encoding a promoter functional in a plant cell that is operably linked to a DNA encoding a 9-cis-epoxycarotenoid dioxygenase or a functional subunit thereof so that RNA is expressed from the recombinant DNA in the transgenic plant.
  • a promoter can be induced by stress.
  • the 9-cis-epoxycarotenoid dioxygenase or a functional subunit thereof can also be expressed at higher levels than in a plant of the same genetic background that does not comprise the isolated recombinant DNA.
  • the recombinant DNA can encode a 9-cis-epoxycarotenoid dioxygenase-3 enzyme.
  • the 9-cis-epoxycarotenoid dioxygenase enzyme may also comprise SEQ ID NO:13, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID NO:33.
  • the invention also provides a method of increasing salt resistance in a plant comprising: (a) transforming a plant cell with an isolated nucleic acid that encodes an inhibitory 9-cis-epoxycarotenoid dioxygenase RNA that, when expressed from a promoter functional in a plant cell, inhibits the function of endogenous RNA encoding a 9-cis-epoxycarotenoid dioxygenase enzyme, to generate a transformed plant cell; and (b) regenerating the transformed plant cell into a transgenic plant that has increased resistance to salt relative to a non- transgenic plant with the same genetic background but without the isolated nucleic acid.
  • the inhibitory 9-cis-epoxycarotenoid dioxygenase RNA can be complementary to the endogenous RNA encoding the 9-cis-epoxycarotenoid dioxygenase enzyme.
  • the inhibitory RNA can be, for example, substantially complementary to SEQ ID NO: 1-9, SEQ ID NO:10, SEQ ID NO:ll, SEQ ID NO: 12, SEQ ID NO: 14-20, SEQ ID NO:26, SEQ LD NO:28, SEQ ID NO:30, SEQ ID NO:32, or SEQ ID NO:34.
  • the inhibitory RNA hybridizes under moderately stringent hybridization conditions to the endogenous RNA encoding an 9-cis-epoxycarotenoid dioxygenase enzyme comprising SEQ ID NO: 13, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID NO: 33.
  • Moderately stringent hybridization conditions comprise hybridization in 40 to 45% formamide, 1.0 M NaCl, 1 % SDS at 37°C, and a wash in 0.5X to IX SSC at 55 to 60°C.
  • such an inhibitory RNA hybridizes under highly stringent hybridization conditions to the endogenous RNA encoding an 9-cis-epoxycarotenoid dioxygenase enzyme comprising SEQ ID NO:13, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID NO:33.
  • Highly stringent conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0. IX SSC at 60 to 65°C.
  • such plants may be dicots, for example, soybean.
  • the plant can also be a monocot, for example, corn, rice, rye, oats or wheat. Food or feed can also be produced from the mutant and transgenic plants of the invention.
  • Transgenic progeny plants obtained from the transgenic plant produced by the methods of the invention are also contemplated wherein the progeny plant comprises the null mutation or the isolated 9-cis-epoxycarotenoid dioxygenase nucleic acid, and wherein the progeny plant is able to develop in the presence of a concentration of salt that inhibits the development of a plant not comprising said mutated gene.
  • the invention also provides a transgenic seed obtained from plants produced by such methods wherein the seed comprises the null mutation or the isolated 9-cis-epoxycarotenoid dioxygenase nucleic acid, and wherein the transgenic seed is able to germinate in the presence of a concentration of salt that inhibits the germination of a seed not comprising said mutated gene.
  • Transgenic progeny plants obtained from such transgenic seeds are also contemplated, wherein the progeny plant comprises the null mutation or the isolated 9-cis- epoxycarotenoid dioxygenase nucleic acid.
  • the invention further provides a method for increasing at least one of the drought, cold, salt, osmotic or pathogen tolerance of a plant comprising: (a) introducing into regenerable cells of a plant a DNA sequence encoding a 9-cis- epoxycarotenoid dioxygenase or a functional subunit thereof operably linked to a promoter functional in a plant cell to yield transformed plant cells; and (b) regenerating a plant from said transformed plant cells wherein the cells of said plant express the NCED or functional subunit thereof encoded by the DNA sequence in an amount effective to increase at least one of the drought, cold, salt, osmotic or pathogen tolerance of a plant.
  • the method can further include (c) obtaining a transgenic seed from the plant of step (b), wherein the transgenic seed comprises said DNA sequence.
  • the method can also include (d) obtaining a transgenic progeny plant from the transgenic seed of step (c) wherein the cells of the progeny plant express the 9-cis-epoxycarotenoid dioxygenase or functional subunit thereof encoded by the DNA sequence in an amount effective to increase at least one of the drought, cold, salt, osmotic or pathogen tolerance of a plant.
  • the 9-cis-epoxycarotenoid dioxygenase may be 9-cis- epoxycarotenoid dioxygenase-3.
  • the promoter can be induced by stress.
  • Such plants may have cells that express the 9-cis-epoxycarotenoid dioxygenase or functional subunit thereof encoded by the DNA sequence in an amount effective to increase at least one of the drought, cold, salt, osmotic or pathogen tolerance of a plant.
  • the invention also provides transgenic seeds obtained from such plants.
  • the invention also provides a method for increasing the salt tolerance or the stress resistance of a plant comprising: (a) altering the DNA of regenerable cells of said plant to introduce a mutation into a gene encoding a 9-cis- epoxycarotenoid dioxygenase in said plant cells so as to render the 9-cis- epoxycarotenoid dioxygenase gene product nonfunctional; and (b) regenerating a plant from said plant cells having increased salt tolerance or increased stress resistance as compared to a plant not comprising said mutated gene.
  • the method can further include (c) obtaining a seed from the plant of step (b), wherein the seed comprises said mutated gene.
  • the method can also include (d) obtaining a progeny plant from the seed of step (c) wherein the cells of the progeny plant comprise said mutated gene so that the plant exhibits at least one of increased salt tolerance or increased stress resistance as compared to a plant not comprising said mutated gene.
  • the 9-cis-epoxycarotenoid dioxygenase can be, for example, 9-cis-epoxycarotenoid dioxygenase-3. Plants obtained may exhibit at least one of increased salt tolerance or increased stress resistance as compared to a plant not comprising the mutated gene. Plants produced can be monocots or dicots. Seeds obtained from the plant are also contemplated wherein said seed comprises the mutated gene.
  • the invention further provides an isolated polynucleotide comprising a nucleotide sequence that is substantially identical to SEQ ID NO: 10 or a fragment thereof and which comprises a promoter region.
  • the invention also provides an isolated polynucleotide comprising a nucleotide sequence that is substantially complementary to SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, or a fragment thereof, wherein the isolated polynucleotide can inhibit RNA transcription from a DNA comprising SEQ ID NO: 10, SEQ ID NO:ll, SEQ ID NO:12, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34.
  • Such an isolated polynucleotide can have a nucleotide sequence that is at least 66% complementary to any one of SEQ ID NO:10, SEQ ID NO:ll, SEQ ID NO:12, SEQ ID NO:26, SEQ ID NO:34.
  • sequence comparison is made to SEQ ID NO:30.
  • Nucleic acids with such a degree of complementarity are useful for producing inhibitory RNA in plant cells.
  • an isolated NCED nucleic acid is used for over- expression of the NCED gene product.
  • the NCED gene product can have at least 66% sequence identity relative to SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31 or SEQ ID NO:33.
  • the sequence comparison is made to SEQ ID NO:29.
  • sequence complementary and identity are contemplated by the invention including, for example, at least 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% to one of the nucleic acids provided herein, e.g. SEQ ID NO:30.
  • Polypeptides contemplated for use in the invention can have similar percentages of sequence identity to one of the polypeptides provided herein, e.g. SEQ ID NO:29.
  • FIGURES Figure 1 The stol/nced3 mutation enhances germination on media supplemented with NaCl or KC1.
  • A Photographs are representative of wild type (wt) and stol/nced3 mutant plants. Seeds were placed on MS medium or MS medium supplemented with 160mM NaCl or KC1 and allowed to germinate and grow for 14 days.
  • B Percentage of germinated seeds after 14 days (significant differences at 99% confidence level). Germination was assessed on 60 seeds of wild type or stol/nced3 mutant plants distributed in three replica plates per each treatment (20 seeds per each genotype).
  • FIG. 1 Growth response of wild type and stol/nced3 plantlets at increasing NaCl concentrations.
  • A Seeds were placed in Petri plates on MS medium or MS medium supplemented with increasing concentrations of NaCl. Plant fresh weight was measured after 21 days. Values are means of 60 plants ⁇ S.E.
  • B Seeds were germinated and grown in soil at saturated atmospheric humidity (see Experimental procedures section for details) and irrigated every day with saline water with different NaCl concentrations. After 28 days, shoot fresh weight (FW) was measured. Values are means of 20 plants ⁇ S.E.
  • FIG. 3 stol/nced3 mutant plants are tolerant to KC1 and NaCl and hypersensitive to LiCl stresses.
  • A Seeds were germinated in Petri plates on standard MS medium and seven-day-old seedlings were subsequently transferred to MS medium supplemented withl60mM NaCl, KC1 or 20mM LiCl and allowed to grow for additional 20 days. Photographs are representative of wild type and stol mutant plants after 20 days from transferring onto saline medium.
  • Plant fresh weights were measured after 20 days of growth on indicated medium. Values are means of 60 plants + S.E.
  • FIG. 4 The stol/nced3 mutation inhibits growth on media supplemented with sorbitol.
  • A Seeds were germinated in Petri plates on standard MS medium and three-day-old seedlings were subsequently transferred on MS medium (not shown) or MS medium supplemented with 300 mM sorbitol and allowed to grow for additional 20 days.
  • B Root length of 14day old seedlings growing on sorbitol containing medium. Values are means of 60 plants + S.E.
  • C Fresh weight (FW) of 14day old seedlings growing on sorbitol containing medium. Values are means of 60 plants ⁇ S.E.
  • FIG. 5 stol/nced3 mutant plants are sensitive to soil desiccation.
  • A Representative photograph of wt and stol/nced3 mutant plants exposed to desiccation. Plants were grown in soil under standard irrigation regime until 4-5 fully expanded leaves were formed, at which stage irrigation was stopped. After 15 days, in coincidence with the appearance of clear symptoms of leaf desiccation, plants were re-watered and left to recover for 48 hours, at which time pictures were taken.
  • B Shoot fresh weights of desiccation stressed wild type and stol mutant plants after re- watering. Values are means of 20 plants ⁇ S.E.
  • FIG. 6 PCR analysis and genome location of T-DNA insertion in stol/nced3 mutant.
  • A Secondary TAIL-PCR product (lane 2) and shift of the tertiary PCR product (lane 3) in stol/nced.
  • B Correct genomic integration of the T-DNA insertion was verified by diagnostic PCR; lanes: 1 (marker); 2 (DNA template: wild type; primers: T-DNA LB (3') and stol/nced3 specific primer (5'); 3 (DNA template: stol; primers: T-DNA LB (3') and stol specific primer (5'); 4 (DNA template: wt; primers: stol specific primer (3') and stol specific primer (5'); 5 (DNA template: stol; primers: stol specific primer (3') and stol specific primer (5').
  • Oligonucleotide sequences are reported in Table 3.
  • C Physical map of the stol locus and insertion site of the T-DNA. Solid line represents fragment of the BAC clone MOA2.4. Black box indicates the coding region of the gene, arrow indicates the predicted transcription direction.
  • NCED3 transcript abundance is increased by NaCl treatment and is reduced in stol/nced3 mutant plants.
  • Ten ⁇ g of total RNA were isolated from 21 day old stol/nced3 mutant and wt plants that were germinated and grown on 145 NaCl, separated on a denaturing formaldehyde-agarose gel and blotted onto nylon membrane.
  • the membrane-bound RNA was hybridized with DIG-labeled DNA probe (Roche, Indianapolis, IN, USA). The probe was produced by PCR reaction using the primers listed in Table 3.
  • Figure 8 Complementation with the ST01/NCED3 gene reverts the soil desiccation sensitive phenotype of the stol/nced3 mutant.
  • A ST01/NCED3 transcript abundance detected by RT-PCR in wt, stol/nced3, line 3-14 (pBI vector control), and line 4-6 (expressing ST01/NCED3).
  • One ⁇ l of cDNA was used as template for the first PCR amplification (20 cycles).
  • B Representative photograph of line 3-14 (pBI vector control) and line 4-6 ( ⁇ I::ST01/NCED3).
  • Top panel stol/nced3 plants complemented with vector only (line 3-14) grown under standard irrigation regime (left) and exposed to desiccation (right); bottom panel: stol/nced3 plants complemented with ST01/NCED3 (line 4-6) grown under standard irrigation regime (left) and exposed to desiccation (right) showing the reverted desiccation sensitive phenotype.
  • Figure 9 ABA treatment abolishes the enhanced germination of stol/nced3 seeds on NaCl medium. Seeds of wild type and stol/nced3 mutant plants were surface sterilized and placed on MS medium supplemented with 145mM NaCl (A) or with 145mM NaCl+20 ⁇ M ABA (B). Germination on standard MS medium was also included (not shown). For each genotype (wild type and stol/nced3) the number of germinated seeds (out of 60) was assessed over 21 days and expressed as a percentage.
  • Figure 10 ABA reverts the LiCl sensitivity of stol 7nced3 seedlings to wild type. Wild type and stol seeds were surface sterilized and germinated on standard MS medium or MS supplemented with 20mM LiCl or 20mM
  • LiCl+20 ⁇ M ABA A representative photograph of 15day old seedlings (from 3 replica plates per treatment) is displayed.
  • FIG. 11 Expression of the cyclin-dependent kinase inhibitor (ICK1) gene in stol/nced3 and wild type plants.
  • Total RNA was extracted from whole seedlings that were grown for 7 days on MS medium or MS supplemented with 145mM NaCl. 20 ⁇ g of total RNA were loaded in each lane.
  • the probe was produced by PCR reaction using the primers listed in Table 3. The bottom panel shows ethidium bromide stained total RNA gel image as a loading control.
  • FIG. 12 Ethylene production of wild type and stol/nced3 seedlings. Seeds were germinated on standard solid MS medium and transferred at the cotyledon stage into 6ml plastic syringes (0.5g fresh weight per syringe) containing 3ml of standard liquid MS medium or liquid MS medium supplemented with 145mM NaCl. Seedlings were allowed to grow into the plastic syringes for 7 days. For each genotype (wt or stol/nced3) and for each treatment (plus or minus NaCl) six syringes were used. One ml of the 3ml air volume ejected from each syringe was taken for GC quantification of ethylene. Values are means of six samples ⁇ S.E.
  • FIG. 13 Ethylene-treated wild type plants mimic the stol/nced3 phenotype.
  • Top panel representative photographs of 15day old wild type and stol/nced3 seedlings germinated and grown in the presence or absence of 20ppm of C 2 H 4 on Petri plates containing standard MS medium, or MS medium supplemented with 145mM NaCl or 20mM LiCl.
  • Bottom panel number of new leaves per plant formed after 15day treatment. Values are means of 100 plants + S.E.
  • Figure 14 Transpiration of wild type and stol/nced3 mutant plants.
  • Transpiration of wild type and stol/nced3 mutant plants was measured as daily water loss over a 7day time interval. Each value represents the average daily water loss of 3 plants ⁇ S.E. (B) Daily fluctuations of rate of water loss in wild type and stol/nced3 mutant plants. The diurnal patterns displayed are representative of 3 independent experiments.
  • Figure 15 provides a nucleotide sequence comprising a NCED-3 promoter (SEQ ID NO: 10).
  • Figure 16 provides a nucleotide sequence encoding NCED-3, preprocessing (SEQ ID NO: 11).
  • Figure 17 provides a nucleotide sequence encoding NCED-3, postprocessing (SEQ ID NO: 12).
  • Figure 18 provides a polynucleotide sequence comprising a NCED-3 polypeptide (SEQ ID NO: 13).
  • the invention provides wild type 9-cis-epoxycarotenoid dioxygenase (NCED) nucleic acids and mutant 9-cis-epoxycarotenoid dioxygenase (NCED) nucleic acids that can be used to increase the salt resistance of plants.
  • NCED wild type 9-cis-epoxycarotenoid dioxygenase
  • NCED mutant 9-cis-epoxycarotenoid dioxygenase
  • NCED3 The role of the NCED3 gene in environmental stress resistance was identified through a large-scale screen of a T-DNA insertional collection of Arabidopsis thaliana C24 ecotype plants.
  • the stol mutant was more tolerant in vitro than wild type to Na + and K + in terms of germination and growth, but was hypersensitive to Li + . Post germination growth of the stol mutant on sorbitol was not improved.
  • NCED3 The involvement of the NCED3 gene was identified by locating the site of the stol mutation. A T-DNA insertion was located in the 3' end of an open reading frame on chromosome 3 that co-segregated closely with the stol phenotype. Expression of STOl gene was perturbed in the mutated plants and transcript abundance was substantially reduced.
  • supplementation of ABA to the growth medium also reverted the stol phenotype to wild type.
  • Improved growth of stol mutant plants on NaCl but not sorbitol medium was associated with a reduction of both NaCl-induced expression of the ICK1 gene and ethylene accumulation compared to wild type plants.
  • Osmotic adjustment of stol plants was substantially reduced compared to wild type plants under conditions where stol plants grew faster.
  • the stol mutation has revealed that reduced ABA can lead to more rapid growth during hyperionic stress by a signal pathway that is apparently at least partially independent of signals that mediate osmotic adjustment.
  • anti-sense RNA refers to an RNA molecule that is capable of forming a duplex with a second RNA molecule.
  • a given RNA molecule is said to be an anti-sense RNA molecule with respect to a second, complementary or partially complementary RNA molecule, i.e., the target molecule.
  • An anti-sense RNA molecule may be complementary to a translated or an untranslated region of a target RNA molecule.
  • the anti-sense RNA need not be perfectly complementary to the target RNA.
  • Anti-sense RNA may or may not be the same length of the target molecule; the anti-sense RNA molecule may be either longer or shorter than the target molecule.
  • co-suppressor RNA refers to an RNA molecule that effects suppression of expression of a target gene where the RNA is partially homologous to an RNA molecule transcribed from the target gene.
  • a co- suppressor RNA molecule is the RNA molecule that effects co-suppression as described in U.S. Pat. No. 5,231,020, Krol et al, Biotechniques 6:958-976 (1988), Mol et al., FEBS Lett. 268:427430 (1990), and Grierson, et al, Trends in Biotech. 9: 122-123 (1991) and similar publications.
  • a "co-suppressor" RNA is in the sense orientation with respect to the target gene, i.e., the opposite orientation of the anti-sense orientation.
  • the term “complementary to” is used herein to mean that the sequence of a nucleic acid strand could hybridize to all, or a portion, of a reference nucleic acid sequence.
  • the nucleotide sequence "TATAC” has 100% identity to a reference sequence 5'-TATAC-3' but is 100% complementary to a reference sequence 5 ' -GTAT A-3 ' .
  • an "exogenous” nucleic acid is an isolated nucleic acid that has been introduced into a host cell. Such an “exogenous” nucleic acid is generally not identical to any DNA sequence present in the cell in its native, untransformed state. An “endogenous” or “native” nucleic acid is naturally present in a host cell or organism.
  • inhibitory RNA refers to an RNA molecule that interferes with the expression of a target gene.
  • An “inhibitory RNA” is specific for one or more target genes.
  • An inhibitory RNA may be an anti-sense RNA with respect to an RNA molecule transcribed from the target gene.
  • the target gene inhibitory RNA may be a co-suppressor RNA with respect to an RNA molecule transcribed from the target gene.
  • inhibitory RNA encoding nucleic acid refers to a nucleic acid, e.g., DNA, RNA, and the like, capable of being transcribed, when in functional or operational combination with a promoter, so as to produce an inhibitory RNA molecule, e.g., an anti-sense RNA or a co-supressor RNA.
  • Anti-sense RNA encoding nucleic acids and co-supressor encoding nucleic acids are both embodiments of the inhibitory RNA encoding nucleic acids.
  • the inhibitory RNA transcribed from the inhibitory RNA encoding nucleic acid region of the genetic constructions of the invention is preferably perfectly complementary to the entire length of the RNA molecule or molecules for which the anti-sense RNA is specific, i.e., the target.
  • the anti-sense RNA encoding nucleic acid in the subject vectors may encode an anti-sense RNA that forms a duplex with a non-translated region of an RNA transcript such as an intron region, or 5' untranslated region, a 3' untranslated region, and the like.
  • a co-suppressor encoding nucleic acid may encode an RNA that is homologous to translated or untranslated portions of a target RNA.
  • An anti-sense RNA encoding nucleic acids may be conveniently produced by using the non-coding strand, or a portion thereof, of a DNA sequence encoding a protein of interest.
  • reduced expression is a relative term that refers to the level of expression of a given gene in a cell produced or modified by the claimed methods as compared to a comparable or corresponding unmodified cell, i.e., a cell lacking the exogenous nucleic acid, under a similar set of environmental conditions.
  • a cell modified by the subject methods i.e., a cell having "reduced expression" of the gene of interest, may express lower levels of a gene product encoded by that gene under a given set of environmental conditions, than a comparable unmodified cell under the same set of environmental conditions.
  • Nucleic acids encoding a NCED RNA or protein are "isolated” in that they were taken from their natural source and are no longer within the cell where they normally exist. Such isolated nucleic acids may have been at least partially prepared or manipulated in vitro, e.g., isolated from a cell in which they are normally found, purified, and amplified. Such isolated nucleic acids can also be "recombinant” in that they have been combined with exogenous nucleic acids.
  • a recombinant DNA can be an isolated DNA that is operably linked to an exogenous promoter, or to a promoter that is endogenous to a selected host cell.
  • a "native" gene or nucleic acid means that the gene or nucleic acid has not been changed or manipulated in vitro, i.e., it is a "wild-type” gene or nucleic acid that has not been has not been isolated, purified, amplified or mutated in vitro.
  • plastid refers to the class of plant cell organelles that includes amyloplasts, chloroplasts, chromoplasts, elaioplasts, eoplasts, etioplasts, leucoplasts, and proplastids. These organelles are self-replicating, and contain what is commonly referred to as a "plastid genome,” a circular DNA molecule that ranges in size from about 120 to about 217 kb, depending upon the plant species, and which usually contains an inverted repeat region.
  • polypeptide or "protein” means a continuous chain of amino acids that are all linked together by peptide bonds, except for the N- terminal and C-terminal amino acids that have amino and carboxylate groups, respectively, and that are not linked in peptide bonds.
  • Polypeptides and proteins can have any length and can be post-translationally modified, for example, by glycosylation or phosphorylation.
  • a plant cell, plant tissue or plant that is “resistant or tolerant to salt inhibition” is a plant cell, plant tissue, or plant that grows at least about 10% more than a corresponding wild type plant cell, plant tissue or plant in the presence of salt.
  • a plant cell, plant tissue, or plant that is “salt resistant” can grow in an amount of salt that normally inhibits growth of the untransformed plant cell, plant tissue, or plant, as determined by methodologies known to the art.
  • a homozygous backcross converted inbred plant transformed with a DNA molecule that encodes a NCED inhibitory RNA or a plant with a homozygous null mutation in the need locus is substantially salt resistant or tolerant because it grows in an amount of salt (e.g. sodium chloride or potassium chloride) that inhibits the growth of the corresponding, i.e., substantially isogenic, recurrent inbred plant.
  • salt e.g. sodium chloride or potassium chloride
  • a salt resistant plant cell, plant tissue, plant part or plant can grow in salt levels that are about 2 to 100 times, about 3 to 50 times, about 5 to 20 times or about 7 to 10 times, higher than the levels that an untransformed plant cell, plant tissue, plant part or plant can grow.
  • NCED 9-cis- epoxycarotenoid dioxygenase
  • NCED-3 9-cis-epoxycarotenoid dioxygenase-3
  • mutant alleles of various NCED genes allow plants to develop in the presence of salts such as sodium chloride or potassium chloride.
  • the open reading frame is interrupted in mutant alleles that provide this salt-resistance trait, for example, substantially no NCED mRNA is detected in plant cells having a null mutation in the NCED-3 gene.
  • Plants comprising a genome with null mutation of the NCED-3 gene also appear to germinate faster and produce leaves faster than wild type plants of a similar background but without the NCED-3 mutation.
  • over-expression of the certain NCED alleles within plants makes such plants tolerant to environmental stress.
  • plants that over-express NCED alleles like the NCED-3 allele are resistant to high salt concentrations.
  • NCED nucleic acids and polypeptides can be used in the practice of the invention to achieve stress resistant plants.
  • One of skill in the art can readily ascertain which NCED genes optimally provide resistance to environmental stress by utilizing the screening procedures provided herein along with procedures that are generally available to one of skill in the art for manipulating plants.
  • NCED alleles are present in the Arabidopsis thaliana genome at the loci identified in Table 1 A. The sequences for these genes can be found in the NCBI database at ncbi.nlm.nih.gov. A comparison of the percent identity and percent similarity to NCED3 for the other NCED genes is provided in Table IB.
  • Table 1 A Arabidopsis 9-cis-epoxycarotenoid dioxygenase genes
  • AtNCEDl At3g63520 MAA21.150 NM_116217 NP_191911.1
  • AtNCED4 At4gl9170 T18B16.140 NM_118036 NP 93652.1
  • AtNCED5a Atlg78390 F3F9.10 NM_106486 NP 77960 AtNCED5b Atlg30100 T2H7.10 NM_102749 NP_174302.1
  • AtNCED4 39% 57% AtNCED5a 66% 78%
  • the invention therefore provides wild type and mutant NCED (e.g.
  • NCED-3) nucleic acids and proteins are provided.
  • the invention provides NCED proteins, and NCED nucleic acids that encode RNAs and proteins that confer greater resistance to salt.
  • the NCED (e.g. NCED-3) nucleic acid that confers greater resistance to salt encodes an inhibitory RNA that can bind to an endogenous NCED (e.g. NCED-3) RNA and inhibit the function of that endogenous RNA.
  • the mutation that gave rise to the stol phenotype was mapped to the NCED3 gene in Arabidopsis thaliana.
  • the Arabidopsis thaliana NCED3 gene is on chromosome 4, and has an NCBI Accession Number of NM 112304 (GI: 18400395).
  • a sequence for the Arabidopsis thaliana NCED3 polypeptide is provided below (SEQ ID NO:29).
  • Such an Arabidopsis thaliana NCED3 polypeptide is encoded by a nucleic acid having NCBI Accession Number NM 112304 (GI: 18400395), with the following sequence (SEQ ID NO:30).
  • AAACCAACTC TCTCTTCTCT CTTCTCTCCT CTCTTCTACA 41 AGAAGAAAAA AAACAGAGCC TTTACACATC TCAAAATCGA
  • the invention also provides a nucleic acid that encodes a polypeptide having SEQ ID NO:13; this nucleic has SEQ ID NO:ll or SEQ ID NO:12:
  • the invention also provides a nucleic acid that encodes a related
  • the invention further provides a nucleic acid that encodes a related Arabidopsis thaliana NCED RNA and/or a related NCED polypeptide that can be used in the practice of the invention, where the nucleic acid can be found as NCBI Accession Number gi:15810432 and has the following sequence (SEQ ID NO: 15):
  • AAACCAACTC TCTCTTCTCT CTTCTCTCCT CTCTTCTACA 41 AGAAGAAAAA AAACAGAGCC TTTACACATC TCAAAATCGA
  • the invention also provides a nucleic acid that encodes a related Arabidopsis thaliana NCED RNA and/or a related NCED polypeptide, where the nucleic acid can be found as NCBI Accession Number gi:16416373 and has the following sequence (SEQ ID NO:16):
  • 3201 AACCGGTGAA TCAACTCGCC GTCCGATCAT CTCCAACGAA
  • the invention also provides a nucleic acid that encodes a related
  • Arabidopsis thaliana NCED RNA and/or a related NCED polypeptide where the nucleic acid can be found as NCBI Accession Number gi:5041970.
  • Another example of an NCED nucleic acid and polypeptide that may be used in the practice of the invention is from the Arabidopsis thaliana NCEDl gene on chromosome 3, having NCBI Accession Number NM 116217.1
  • Such an Arabidopsis thaliana NCEDl polypeptide is encoded by a nucleic acid having NCBI Accession Number NM 116217.1 (GI: 18412829), with the following sequence (SEQ ID NO:26). 1 ATGGCGGAGA AACTCAGTGA TGGCAGCAGC ATCATCTCAG
  • NCED nucleic acid or polypeptide Another example of an NCED nucleic acid or polypeptide is the
  • Arabidopsis thaliana NCED2 gene on chromosome 4 having NCBI Accession Number NM 117945 (GL18415070).
  • NCED2 polypeptide is provided below (SEQ ID NO:27).
  • Such an Arabidopsis thaliana NCED2 polypeptide is encoded by a nucleic acid having NCBI Accession Number NM 117945 (G 18415070), with the following sequence (SEQ ID NO:28).
  • the invention also provides a nucleic acid that encodes an Arabidopsis thaliana NCED promoter having SEQ ID NO : 10.
  • the invention also relates to NCED polypeptides and nucleic acids from other species that can be utilized in the invention.
  • NCED-3 nucleic acids and polypeptides from avocado can be used to generate stress resistant plants.
  • One sequence of an avocado (Persea americana) NCED-3 polypeptide is provided below (SEQ ID NO:31).
  • the invention can be practiced using NCED-3 polypeptides or nucleic acids from cowpea (Vigna unguiculata ).
  • An example of an NCED-3 polypeptide from cowpea is provided below (SEQ ID NO:33).
  • NCED-3 nucleic acid from cowpea is provided below (SEQ ID NO:34).
  • the invention also relates to sequences that are complementary to the coding strand of an NCED nucleic acid.
  • the invention relates to nucleic acids that are complementary to an RNA produced from an NCED nucleic acid, for example, a nucleic acid complementary to any of SEQ ID NO:l-9, SEQ ID NO: 10, SEQ ID NO:ll, SEQ ID NO:12, SEQ ID NO:14-20, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34.
  • Such complementary nucleic acids have utility for inhibiting the function of an endogenous NCED RNA and thereby diminishing the synthesis of a function NCED enzyme.
  • nucleic acid fragments that encompassed by the invention are not full sequences but do perform their intended function (conferring resistance environmental stresses such as salt).
  • Variants are substantially similar or substantially identical to the sequences (or the complements of the sequences) provided herein.
  • variants include those sequences that are sufficiently complementary to an endogenous NCED RNA to inhibit the function of such an endogenous NCED RNA.
  • variants include those sequences that, because of the degeneracy of the genetic code, encode the identical amino acid sequence of the reference protein.
  • Variant nucleic acids also include those nucleic acids that encode polypeptides that do not have amino acid sequences identical to that of the proteins identified herein, but which encode an active protein with conservative changes in the amino acid sequence.
  • the genetic code is "degenerate,” meaning that several trinucleotide codons can encode the same amino acid. This degeneracy is apparent from Table 2.
  • nucleic acid sequence alterations are silent, a variant nucleic acid will encode a polypeptide with the same amino acid sequence as the reference nucleic acid.
  • nucleic acid sequence of the invention also encompasses variants with degenerate codon substitutions, and complementary sequences thereof, as well as the sequence explicitly specified by a SEQ ID NO.
  • degenerate codon substitutions may be achieved by generating sequences in which the reference codon is replaced by any of the codons for the amino acid specified by the reference codon.
  • the third position of one or more selected codons can be substituted with mixed-base and/or deoxyinosine residues as disclosed by Batzer et al., Nucleic Acid Res., 19, 5081
  • variant and reference nucleic acids of the invention may differ in the encoded amino acid sequence by one or more substitutions, additions, insertions, deletions, fusions and truncations, which may be present in any combination, so long as an active protein with activity similar to the protein encoded by the reference nucleic acid is encoded by the variant nucleic acid.
  • variant nucleic acids will not encode exactly the same amino acid sequence as the reference nucleic acid, but have conservative sequence changes and an activity similar to the protein encoded by the reference nucleic acid.
  • the invention also embraces derivative nucleic acids.
  • Derivative nucleic acids can encode an inhibitory RNA that has additional ribonucleotides or an inhibitory RNA with one or more nucleotide substitutions, deletions or insertions.
  • Such a derivative nucleic acid can have an improved property, for example, greater stability, resistance to nucleases, or sequences that cause the inhibitory RNA to be transported into the cytoplasm or to be retained in the nucleus.
  • Derivative nucleic acids that encode proteins include nucleic acids with non-conservative amino acid sequences changes.
  • Such derivative nucleic acids can encode a protein with an improved property, for example, improved stability, improved longevity, or improved salt resistance activity.
  • Such derivative nucleic acids can encode a protein that is similar to the protein encoded by the reference nucleic acid, but the derivative nucleic acid will not have exactly the same amino acid sequence as the reference nucleic acid. Instead, both conservative and non-conservative amino acid changes can be present in the protein encoded by the derivative nucleic acid.
  • the encoded derivative protein still provides salt resistance when expressed in a plant cell, but such a derivative protein will provide some other benefit relative to the protein encoded by the reference nucleic acid.
  • Variant and derivative nucleic acids with silent, conservative and non- conservative changes can be defined and characterized by the degree of homology to the reference nucleic acid.
  • Preferred variant and derivative nucleic acids are "substantially homologous” or “substantially identical” to the reference nucleic acids of the invention. As recognized by one of skill in the art, such substantially homologous or substantially identical nucleic acids can hybridize under stringent conditions with the reference nucleic acids identified by SEQ ID NO herein. All of these types of substantially homologous/identical nucleic acids are encompassed by this invention.
  • nucleic acid derivatives and variants of the invention will have at least 90%, 91%, 92%, 93% or 94% sequence identity to the reference nucleotide sequence defined herein.
  • nucleic acids of the invention will have at least at least 95%, 96%, 97%, to 98% sequence identity to the reference nucleotide sequence defined herein.
  • Variant and derivative nucleic acids can be detected and isolated by standard hybridization procedures. Hybridization to detect or isolate such sequences is generally carried out under stringent conditions. "Stringent hybridization conditions” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments such as Southern and Northern hybridization are sequence dependent, and are different under different environmental parameters. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Laboratory Techniques in Biochemistry and Molecular biology- Hybridization with Nucleic Acid Probes, page 1, chapter 2 "Overview of principles of hybridization and the strategy of nucleic acid probe assays" Elsevier, New York (1993). See also, J.
  • the invention also provides methods for detection and isolation of derivative or variant nucleic acids encoding the proteins provided herein.
  • the methods involve hybridizing at least a portion of a nucleic acid comprising any one of the primers or nucleic acids provided herein to a sample nucleic acid, thereby forming a hybridization complex; and detecting the hybridization complex.
  • the presence of the complex correlates with the presence of a derivative or variant nucleic acid which can be further characterized by nucleic acid sequencing, expression of RNA and/or protein and testing to determine whether the derivative or variant retains activity.
  • the portion of a nucleic acid that is used for the inhibitory RNA or for hybridization is at least fifteen nucleotides.
  • Hybridization performed in vitro is under hybridization conditions that are sufficiently stringent to permit detection and isolation of substantially homologous nucleic acids.
  • variant nucleic acids are isolated by amplification of a selected nucleic acid sample using polymerase chain reaction and primer oligonucleotides selected from any one of the nucleic acids provided herein.
  • highly stringent hybridization and wash conditions are selected to be about 5 °C lower than the thermal melting point (T m ) for the specific double-stranded sequence at a defined ionic strength and pH.
  • T m thermal melting point
  • highly stringent hybridization and wash conditions are selected to be about 5 °C lower than the thermal melting point (T m ) for the specific double-stranded sequence at a defined ionic strength and pH.
  • T m thermal melting point
  • stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30°C for short probes (e.g., 10 to 50 nucleotides) and at least about 60°C for long probes (e.g., greater than 50 nucleotides).
  • Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
  • Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37°C, and a wash in 0.5X to IX SSC at 55 to 60°C.
  • Exemplary high stringency conditions include hybridization in 50% formamide, 1 MNaCl, 1% SDS at 37°C, and a wash in 0.1X SSC at 60 to 65°C.
  • the degree of complementarity or homology of hybrids obtained during hybridization is typically a function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution.
  • the type and length of hybridizing nucleic acids also affects whether hybridization will occur and whether any hybrids formed will be stable under a given set of hybridization and wash conditions.
  • the T m can be approximated from the equation of Meinkoth and Wahl Anal. Biochem. 138:267-284 (1984);
  • T m 81.5°C + 16.6 (log M) +0.41 (%GC) - 0.61 (% form) - 500/L
  • T m is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected for hybridization to derivative and variant nucleic acids having a T m equal to the exact complement of a particular probe, less stringent conditions are selected for hybridization to derivative and variant nucleic acids having a T m less than the exact complement of the probe.
  • T m is reduced by about 1°C for each 1% of mismatching.
  • T m , hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired sequence identity. For example, if sequences with >90% identity are sought, the T m can be decreased 10°C.
  • stringent conditions are selected to be about 5°C lower than the thermal melting point (T m ) for the specific sequence and its complement at a defined ionic strength and pH.
  • An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or Northern blot is 50% formamide with 1 mg of heparin at 42 °C, with the hybridization being carried out overnight.
  • An example of highly stringent conditions is 0.1 5 M NaCl at 72 °C for about 15 minutes.
  • An example of stringent wash conditions is a 0.2x SSC wash at 65°C for 15 minutes (see also, Sambrook, infra). Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal.
  • stringent conditions typically involve salt concentrations of less than about l.OM Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is typically at least about 30 °C.
  • Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide.
  • destabilizing agents such as formamide.
  • a signal to noise ratio of 2x (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization.
  • Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the proteins that they encode are substantially identical. This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code.
  • a reference nucleotide sequence preferably hybridizes to the reference nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO 4 , 1 mM EDTA at 50°C with washing in 2X SSC, 0.1% SDS at 50°C, more desirably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO 4 , 1 mM EDTA at 50°C with washing in IX SSC, 0.1% SDS at 50°C, more desirably still in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO 4 , 1 mM EDTA at 50°C with washing in 0.5X SSC, 0.1% SDS at 50°C, preferably in 7% sodium dodecyl sulfate
  • nucleic acids can be isolated from any number of plant or animal species and tested for variants and derivatives of the present nucleic acids by using the references and the teachings herein on the relationship between T m , mismatch, and hybridization and wash conditions. Those of ordinary skill can readily generate variants and derivatives of the present nucleic acids.
  • Computer analyses can also be utilized for comparison of sequences to determine sequence identity. Such analyses include, but are not limited to: CLUSTAL in the PC/Gene program (available from fritelligenetics, Mountain View, California); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Version 8 (available from Genetics Computer Group (GCG), 575 Science Drive, Madison, Wisconsin, USA). Alignments using these programs can be performed using the default parameters.
  • the CLUSTAL program is well described by Higgins et al. Gene 73:237 244 (1988); Higgins et al. CABIOS 5:151-153 (1989); Corpet et al. Nucleic Acids Res.
  • PSI-BLAST in BLAST 2.0
  • PSI-BLAST can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al., supra.
  • the default parameters of the respective programs e.g. BLASTN for nucleotide sequences, BLASTX for proteins
  • the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA, 89, 10915 (1989)). See the website at ncbi.nlm.nih.gov. Alignment may also be performed manually by inspection.
  • comparison of nucleotide sequences for determination of percent sequence identity to the nucleic acid sequences disclosed herein is preferably made using the BlastN program (version 1.4.7 or later) with its default parameters or any equivalent program.
  • equivalent program is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by the preferred program.
  • the expression of a target gene can be reduced through inhibitory RNA interactions with target mRNA.
  • Such regulation of expression in plant cells is achieved by integrating into the plant cell host a nucleic acid sequence in which the transcribed nucleic acid sequences are at least partially complementary to a nucleic acid sequence that is already transcribed by the host.
  • the exogenous nucleic acid is under the transcriptional control of a transcriptional initiation region recognized by the plant cell host. Transcription of the exogenous nucleic acid may produce multiple copies of an antisense RNA that is complementary to an endogenous RNA of the host cell. This antisense mRNA reduces the functioning of the naturally existing RNA.
  • Inhibitory RNA can be produced in the nucleus so as to and operate to inhibit the function of endogenous RNA within the nucleus. Moreover, inhibitory RNA can also be produced in the cytoplasm. Cytoplasmic expression of inhibitory RNA (specific for target genes) has some advantages over nuclear expression, for example, the ability to use high level expression vectors that are not suitable for nuclear expression. The use of such vectors is particularly advantageous in plants, because vectors capable of systemically infecting plants may be used to produce the inhibitory RNA.
  • the invention described herein has many aspects.
  • These aspects include novel genetic constructions for the expression of target gene inhibitory RNA in the cytoplasm of eukaryotic cells, cells transfected with these genetic constructions, multicellular organisms comprising the transfected cells, and methods for reducing the expression of selected genes in a cell by transforming a cell with a genetic construction of the invention.
  • compositions are therefore provided herein for modulating RNA utilization, particularly modulation of amino acid biosynthesis in a plant host cell.
  • the compositions involve transcription constructs having transcriptional initiation and termination regions separated by a sequence that is complementary to a sequence present in an endogenous RNA, particularly messenger RNA.
  • a sequence is a 9-cis-epoxycarotenoid dioxygenase (NCED) inhibitory RNA encoding nucleic acid.
  • NCED 9-cis-epoxycarotenoid dioxygenase
  • an NCED inhibitory RNA encoding nucleic acid reduces the production of the 9-cis-epoxycarotenoid dioxygenase protein and lower its effective activity.
  • the sequence of the NCED inhibitory RNA encoding nucleic acid that is complementary to a sequence of the endogenous messenger RNA is usually at least about 17 nucleotides, at least about 20 nucleotides, or at least about 25 nucleotides.
  • the upper limit on the length is not critical but generally the NCED inhibitory RNA encoding nucleic acid is smaller than about 7000 nucleotides, about 5000 nucleotides, or about 2000 nucleotides.
  • Convenient lengths for the NCED inhibitory RNA encoding nucleic acid are about 17 to about 200 nucleotides, about 20 to about 100 nucleotides, or about 25 to about 50 nucleotides.
  • the sequence may be complementary to any sequence of the endogenous NCED messenger RNA, that is, it may be proximal to the 5'-terminus or capping site, downstream from the capping site, between the capping site and the initiation codon and may cover all or only a portion of the non-coding region, may bridge the non-coding and coding region, be complementary to all or part of the coding region, complementary to the 3 '-terminus of the coding region, or complementary to the 3 '-untranslated region of the mRNA.
  • the particular site(s) to which the anti-sense sequence binds and the length of the anti-sense sequence will vary depending upon the degree of inhibition desired, the uniqueness of the sequence, the stability of the anti-sense sequence, or the like. Therefore, to some degree, these factors will be determined empirically based on the experience observed with a particular anti-sense sequence, such as the phenotype of resulting transgenic plants.
  • the sequence may be a single sequence or a repetitive sequence having two or more repetitive sequences in tandem, where the single sequence may bind to a plurality of messenger RNAs.
  • heteroduplexing may be employed, where the same sequence may provide for inhibition of a plurality of messenger RNAs by having regions complementary to different messenger RNAs.
  • the antisense sequence may be complementary to a unique sequence or a repeated sequence, so as to enhance the probability of binding.
  • the antisense sequence may be involved with the binding of a unique sequence, a single unit of a repetitive sequence or of a plurality of units of a repetitive sequence.
  • the antisense sequence may result in the modulation of expression of a single gene or a plurality of genes.
  • the transcriptional construct will be comprised of, in the direction of transcription, a transcriptional initiation region, the sequence coding for the antisense RNA on the sense strand, and a transcriptional termination region.
  • the transcriptional initiation region may provide for constitutive expression or regulated expression.
  • the transcriptional initiation regions comprise a promoter region in functional combination with an inhibitory RNA encoding nucleic acid.
  • the promoter region is selected so as to be capable of driving the transcription of a polynucleotide sequence in a host cell of interest. A large number of promoters are available which are functional in plants.
  • the promoter driving transcription of the inhibitory RNA is selected so as to achieve a level of transcriptional activity sufficient to attain the desired degree of expression of the target gene inhibitory RNA of interest.
  • the promoter may be native or heterologous to the cell selected for genetic modification.
  • the promoter may also be native or heterologous to the expression vector, i.e., the portion of the vector other than the promoter and the inhibitory RNA encoding region.
  • the promoter may be inducible or constitutive. Strong promoters can be used to drive transcription of the inhibitory RNA encoding nucleic acid when the target RNA is highly expressed. These promoters may be obtained from Ti- or Ri-plasmids, from plant cells, plant viruses or other hosts where the promoters are found to be functional in plants.
  • An RNA virus subgenomic promoter can be used as a promoter region. RNA virus subgenomic promoters are described, among other places in Dawson and Lehto, Advances in Virus Research, 38:307- 342, and in PCT published application WO 93/03161.
  • Illustrative promoters also include the octopine synthetase promoter, the nopaline synthase promoter, the manopine synthetase promoter, etc., as illustrative of promoters of bacterial origin functional in plants.
  • Viral promoters include the cauliflower mosaic virus full length (35S) and region VI promoters, etc.
  • Endogenous plant promoters include the ribulose-l,6-biphosphate (RUBP) carboxylase small subunit (ssu), the beta-conglycinin promoter, the phaseolin promoter, the ADH promoter, heat-shock promoters, tissue specific promoters, e.g., promoters associated with fruit ripening, etc.
  • the transcriptional initiation region may be a naturally-occurring region, a RNA polymerase binding region freed of the regulatory region, or a combination of an RNA polymerase binding region from one gene and regulatory region from a different gene.
  • the regulatory region may be responsive to a physical stimulus, such as heat, with heat shock genes, light, as with the RUBP carboxylase SSU, or the like.
  • the regulatory region may be sensitive to differentiation signals, such as the ⁇ -conglycinin gene, the phaseolin gene, or the like.
  • a third type of regulatory region is responsive to metabolites.
  • the time and level of expression of the antisense RNA can have a definite effect on the phenotype produced. Thus the promoters chosen will determine the effect of the antisense RNA.
  • any convenient termination region may be employed, conveniently the termination region of the RNA polymerase binding region, or a different termination region.
  • Various termination regions are available and the choice is primarily one of convenience, where prior constructions or DNA sequences may be available.
  • the opine termination regions may be employed, or termination regions from endogenous genes, such as the genes which have been described previously.
  • the various fragments may be joined by linkers, adapters, or the like, or directly where convenient restriction sites are available.
  • the DNA sequences, particularly bound to a replication system may be joined stepwise, where markers present on the replication system may be employed for selection.
  • the expression cassettes and vectors containing NCED inhibitory RNA encoding nucleic acid constructs of the invention may be introduced into the host cell in a variety of ways.
  • Agrobacterium tumefaciens with protoplasts, injured leaves, or other explant tissues.
  • Other techniques which may find use include electroporation with protoplasts, liposome fusion, microinjection, microprojectile bombardment, or the like. Other methods are described in more detail below.
  • the particular method for transforming the plant cells is not critical to this invention.
  • Tobamoviruses whose genomes consist of one plus-sense RNA strand of approximately 6.4 kb, replicate solely in the cytoplasm, and can be used as episomal RNA vectors to generate inhibitory RNA within the cytoplasm of plant cells.
  • Hybrid tobacco mosaic (TMV)/odontoglosum ringspot viruses (ORSN) have been used previously to express heterologous enzymes in transfected plants (Donson, et al., Proc. ⁇ atl. Acad. Sci. USA 88:7204 (1991) and Kumagai, et al., Proc. ⁇ atl. Acad. Sci.
  • R ⁇ A plant virus vectors are positive strand single-stranded R ⁇ A viruses.
  • R ⁇ A plant virus vectors may be conveniently manipulated and introduced into cells in a DNA form instead of working directly with RNA vectors.
  • Viral vector derived from tobamoviruses are preferred for some embodiments.
  • Descriptions of suitable plant virus vectors that may be modified so as to contain an inhibitory RNA encoding region in functional combination with a promoter, as well as how to make and use such vectors, can be found in, among other places, PCT publication number WO 93/03161, Kumagai et al., Proc. Natl. Acad. Sci. USA 90:427-430 (1993).
  • the genetic constructions for cytoplasmic expression of the NCED inhibitory RNA are capable of replication or maintenance, at least transiently, in the cytoplasm of plant cells of interest.
  • Many vectors capable of replication (or stable maintenance) in different types of eukaryotic cells are known.
  • vectors for use in plant cells include vectors derived from cauliflower mosaic virus, tobacco mosaic virus, tomato mosaic virus, and the like. Information describing plant cell vectors and their use in plant cells can be found, among other places, in PCT published application WO 93/03161, and Donson, et al., Proc. Natl. Acad. Sci. USA 88:7204-7208 (1991).
  • the invention also provides methods of reducing the expression of a gene or genes of interest in a eukaryotic cell.
  • the subject invention also provides methods of producing a eukaryotic cell having reduced expression of a gene of interest and eukaryotic cells that have reduced expression of a gene of interest, as produced by the methods of the invention.
  • Reduction of gene expression is achieved by introducing one or more of the vectors of the invention into a eukaryotic cell.
  • the vector used to transform the cell of interest comprises an inhibitory RNA encoding polynucleotide that encodes an inhibitory RNA specific for the gene for which reduced expression is sought.
  • the method of reducing expression of the gene of interest comprises the step of introducing the subject genetic vector into a host cell that is capable of expressing the gene of interest under certain environmental conditions.
  • the vector may be introduced into a cell of interest by any of a variety of well known transformation methods. Such methods include: infection, transfection, electroporation, ballistic projectile transformation, conjugation, and the like.
  • the inventive aspect of the subject methods is not dependent upon the particular means by which the inhibitory RNA encoding vector is introduced into the cell of interest.
  • the particular methods of introducing the vector into a cell of interest is, in part, dependent upon the particular cell for modification and the precise type of vector selected.
  • nucleic acids of the invention can be placed within an expression cassette.
  • Nucleic acids encoding an inhibitory NCED RNA or a NCED protein can be placed in an expression cassette.
  • Such an expression cassette includes regulatory elements that are needed for transcription and/or expression of an
  • the expression cassettes of the invention contain at least a promoter capable of expressing RNA in a plant cell and a terminator.
  • expression cassettes can also contain enhancers, infrons, untranslated leader sequences, cloning sites, elements of the Gateway recombination system, matrix attachment regions for silencing the effects of chromosomal control elements, and other elements known to one of skill in the art.
  • Expression cassettes have promoters that can regulate gene expression. Promoter regions are typically found in the flanking DNA sequence upstream from coding regions in both prokaryotic and eukaryotic cells. A promoter sequence provides for regulation of transcription of the downstream gene sequence and typically includes from about 50 to about 2,000 nucleotide base pairs. Promoter sequences also contain regulatory sequences such as enhancer sequences that can influence the level of gene expression. Many isolated promoter sequences can provide for gene expression of heterologous genes, that is, a gene different from the native or homologous gene.
  • Promoter sequences can be strong or weak or inducible.
  • a strong promoter provides for a high level of gene expression, whereas a weak promoter provides for a very low level of gene expression.
  • An inducible promoter is a promoter that can be turned on and off so that the encoded RNA is transcribed in response to an exogenously added agent or in response to an environmental or developmental stimulus. Promoters can also provide for tissue specific or developmental regulation.
  • An isolated promoter sequence that is a strong promoter for heterologous genes is advantageous because it provides for a sufficient level of gene expression to allow for easy detection and selection of transformed cells and provides for a high level of gene expression when desired.
  • Preferred promoters will generally include, but are not limited to, bacterial, bacteriophage or plant promoters.
  • Useful promoters include the CaMV 35S promoter (Odell et al., Nature. 313. 810 (1985)), the CaMV 19S (Lawton et al., Plant Mol. Biol.. 9, 3 IF (1987)), nos (Ebert et al., PNAS USA. 84, 5745 (1987)), Adh (Walker et al., PNAS USA. 84, 6624 (1987)), sucrose synthase (Yang et al., PNAS USA. 87, 4144 (1990)), tubulin, napin, actin (Wang et al, Mol. Cell.
  • promoters include the tomato E8, patatin, ubiquitin, mannopine synthase (mas), soybean seed protein glycinin (Gyl), soybean vegetative storage protein (vsp), bacteriophage SP6, T3, and T7 promoters.
  • Other promoters useful in the practice of the invention that are known to those of skill in the art are also contemplated by the invention.
  • An inducible promoter can be turned on or off by an exogenously added agent so that expression of operably linked nucleic acids is also turned on or off.
  • a bacterial promoter such as the P tac promoter can be induced to varying levels of gene expression depending on the level of isothiopropylgalactoside added to the transformed bacterial cells.
  • tissue-specific promoters including but not limited to, root-cell promoters (Conkling et al., Plant Physiol.. 93, 1203 (1990)), and tissue-specific enhancers (Fromm et al., The Plant Cell. I, 977 (1989)) are also contemplated to be particularly useful, as are inducible promoters such as ABA-inducible and turgor-inducible promoters, and the like.
  • Placing a nucleic acid under the regulatory control of a promoter or a regulatory element means positioning the nucleic acid such that the expression of the nucleic acid is controlled by these sequences.
  • promoters are found positioned 5' (upstream) to the nucleic acid that that they control.
  • the promoter is preferably positioned upstream to the nucleic acid and at a distance from the transcription start site of the nucleic acid that the distance between the promoter and the transcription star site approximates the distance observed in the natural setting. As is known in the art, some variation in this distance can be tolerated without loss of promoter function.
  • a regulatory element with respect to a heterologous nucleic acid placed under its control is the natural position of the regulatory element relative to the structural gene it naturally regulates. Again, as is known in the art, some variation in this distance can be accommodated.
  • Promoter function during expression of a heterologous nucleic acid under its regulatory control can be tested at the transcriptional stage using reverse transcription/PCR methods and or DNA-RNA hybridization assays ("Northern" blots). Promoter function at the translational stage can be tested by using specific functional assays for the protein synthesized (for example, by enzymatic activity or by immunoassay of the protein).
  • transcription enhancers or duplications of enhancers can be used to increase expression from a particular promoter.
  • enhancers include, but are not limited to, elements from the CaMV 35S promoter and octopine synthase genes (Last et al., U.S. Patent No. 5,290,924, issued March 1, 1994).
  • vectors for use in accordance with the present invention may be constructed to include the octopine synthase gene (ocs) enhancer element. This element was first identified as a 16 bp palindromic enhancer from the octopine synthase (ocs) gene of Agrobacterium (Ellis et al., EMBO J..
  • leader sequences can also be employed with the nucleic acids of the invention.
  • Preferred leader sequences include those that direct optimum expression of the attached gene, for example, consensus leader sequences that can increase or maintain mRNA stability and prevent inappropriate initiation of translation (Joshi, Nucl. Acid Res., 15, 6643 (1987)). Sequences that are derived from genes that are highly expressed in dicots, such as those in soybeans, and monocots, such as those in corn, are preferred. Those of skill in the art can readily identify and incorporate such sequences into the present vectors.
  • the promoter is a ubiquitin regulatory system described, for example, in U.S. Patent 6,054,574, which in addition to a promoter, has an intron sequence before the initiation codon.
  • a ubiquitin regulatory system is approximately 2 kb and includes nucleic acids sequences that are 5' to the translation start site of the maize ubiquitin gene.
  • the ubiquitin regulatory system has sequences that direct initiation of transcription, regulation of transcription, control of expression level, induction of stress genes and enhancement of expression in response to stress.
  • Expression cassettes of the invention also include a sequence near the 3' end of the cassette that acts as a signal to terminate transcription from a heterologous nucleic acid and that directs polyadenylation of the resultant mRNA.
  • Some 3' elements that can act as termination signals include those from the nopaline synthase gene of Agrobacterium tumefaciens (Bevan et al., Nucl. Acid Res., 11, 369 (1983)), the terminator for the T7 transcript from the octopine synthase gene of Agrobacterium tumefaciens, the 3' end of the protease inhibitor I or II genes from potato or tomato, the vegetative storage protein (vsp), and the geminiviral short intergenic (sir) termination sequences.
  • Other 3' elements known to those of skill in the art also can be used in the vectors of the invention. Regulatory elements such as Adh intron 1 (Callis et al., Genes Develop..
  • sucrose synthase intron Vasil et al., Plant Phvsiol.. 91, 5175 (1989)
  • TMV omega element Gallie et al., The Plant Cell. 1, 301 (1989)
  • These 3' nontranslated regulatory sequences can be obtained as described in An, Methods in Enzymology, 153, 292 (1987) or are already present in plasmids available from commercial sources such as Clontech, Palo Alto, California.
  • the 3' nontranslated regulatory sequences can be operably linked to the 3 'terminus of any heterologous nucleic acid to be expressed by the expression cassettes contained within the present vectors.
  • Other such regulatory elements useful in the practice of the invention are known to those of skill in the art and can also be placed in the vectors of the invention.
  • expression cassettes may be constructed and employed to target the heterologous gene product to a desired intracellular compartment within a plant cell or to direct the heterologous gene product to the extracellular environment. This will generally be achieved by joining a DNA sequence encoding a transit or signal peptide sequence to the coding sequence of a particular gene. The resultant transit, or signal, peptide will transport the protein to a particular intracellular, or extracellular destination, respectively, and will then be post-translationally removed. Transit or signal peptides act by facilitating the transport of proteins through intracellular membranes, e.g., vacuole, vesicle, plastid and mitochondrial membranes, whereas signal peptides direct proteins through the extracellular membrane. By facilitating transport of the protein into compartments inside or outside the cell, these sequences may increase the accumulation of gene product.
  • Vectors that are used for expression of a protein of the invention can be optimized for protein expression in plants by having one or more codons of selcted coding regions degenerate to corresponding codons that are preferably translated by the translation machinery of the plant species in which the vector is used.
  • Selectable marker genes or reporter genes can also be linked to the nucleic acids of the invention, for example, by placing such genes within a vector that contains the nucleic acid of the invention. When expressed, such selectable markers or reporter genes can impart a distinct phenotype to a host cell and thus allow that host cell to be distinguished from cells that do not have the marker or reporter gene.
  • Some selectable marker genes confer a trait which one can 'select' for by chemical means, for example, through the use of a selectable agent such as a herbicide, antibiotic, or the like. Reporter genes confer a trait that one can identify through observing, testing, or 'screening' for the trait. Other examples of suitable marker genes are known to the art and can be employed in the practice of the invention.
  • selectable marker or reporter genes include genes which encode a "secretable marker” whose secretion can be detected as a means of identifying or selecting for transformed cells. Examples include markers that encode a secretable antigen that can be identified by antibody interaction, or a secretable enzyme that can be detected by its catalytic activity.
  • Secretable proteins fall into a number of classes, including small, diffusible proteins detectable, e.g., by ELISA; and proteins that are inserted or trapped in the cell wall (e.g., proteins that include a leader sequence such as that found in the expression unit of extensin or tobacco PR-S).
  • the selectable or reporter marker can encode a protein that becomes sequestered in the cell wall, and that includes a unique epitope that is considered to be advantageous.
  • a secreted antigen marker would ideally employ an epitope sequence that would provide low background in plant tissue, a promoter-leader sequence that would impart efficient expression and targeting across the plasma membrane, and would produce protein that is bound in the cell wall and yet accessible to antibodies.
  • a normally secreted wall protein modified to include a unique epitope would satisfy all such requirements.
  • a protein suitable for modification in this manner is extensin, or hydroxyproline rich glycoprotein (HPRG). The use of the maize HPRG (Steifel et al., The Plant Cell.
  • Possible selectable markers for use in connection with the present invention include, but are not limited to, a neo gene (Potrykus et al., Mol. Gen. Genet., 199, 183 (1985)) which codes for kanamycin resistance and can be selected for using kanamycin, G418, and the like; a bar gene which codes for bialaphos resistance; a gene which encodes an altered EPSP synthase protein (Hinchee et al., Biotech., 6, 915 (1988)) thus conferring glyphosate resistance; a nitrilase gene such as bxn from Klebsiella ozaenae which confers resistance to bromoxynil (Stalker et al., Science, 242, 419 (1988)); a mutant acetolactate synthase gene (ALS) which confers resistance to imidazolinone, sulfonylurea or other ALS-inhibiting chemicals (European Patent Application 154,204,
  • a dalapon dehalogenase gene that confers resistance to the herbicide dalapon; or a mutated anthranilate synthase gene that confers resistance to 5- methyl tryptophan.
  • CTP chloroplast transit peptide
  • Selectable markers can also be, for example, luciferase, glucuronosidase (GUS), or green fluorescent protein (GFP).
  • a selectable marker gene capable of being used in systems to select transformants is the gene set that encodes the enzyme phosphinothricin acetyltransferase, such as the bar gene from Streptomyces hygros copious or the pat gene from Streptomyces viridochromogenes (U.S. Pat. No. 5,550,318, which is incorporated by reference herein).
  • the enzyme phosphinothricin acetyl transferase (PAT) inactivates the active ingredient in the herbicide bialaphos, phosphinothricin (PPT). PPT inhibits glutamine synthetase, (Murakami et al., Mol. Gen.
  • GUS glucuronidase or uidA gene
  • R-locus gene which encodes a product that regulates the production of anthocyanin pigments (red color) in plant tissues (Dellaporta et al, in Chromosome Structure and Function. pp. 263-282 (1988)); a lactamase gene (Sutcliffe, PNAS USA.
  • 129, 2703 (1983)) which encodes an enzyme capable of oxidizing tyrosine to DOPA and dopaquinone which in turn condenses to form the easily detectable compound melanin; a galactosidase gene, which encodes an enzyme for which there are chromogenic substrates; a luciferase (lux or luc) gene (Ow et al, Science, 234, 856 (1986)), which allows for bioluminescence detection; or even an aequorin gene (Prasher et al, Biochem. Biophys. Res. Comm.. 126.
  • lux gene in transformed cells may be detected using, for example, X-ray film, scintillation counting, fluorescent spectrophotometry, low- light video cameras, photon-counting cameras, or multiwell luminometry. It is also envisioned that a such a detectable marker may be used for populational screening for bioluminescence, such as on tissue culture plates, or even for whole plant screening.
  • nucleic acids, expression cassettes and/or vectors of the invention are introduced into prokaryotic or eukaryotic host cells by available methods.
  • Methods of transformation include, but are not limited to, the syringe infiltration method, the vacuum infiltration method (Bechtold et al, C.R. Acad. Sci. Paris, 316:1194-1199 (1993)), the microprojectile bombardment of immature embryos (U.S. Pat. No. 5,990,390) or Type II embryogenic callus cells as described by W.J. Gordon-Kamm et al (Plant Cell 2, 603 (1990)), M.E. Fromm et al (Bio/Technology. 8, 833 (1990)) and D.A. Walters et al. (Plant Molecular Biology, 18.
  • Host cells containing the nucleic acids or vectors of the invention can be selected or isolated using the selectable markers or reporter genes described herein. Host cells are cultured using available tissue culture and conditions optimized to allow growth and accumulation of host cells containing the nucleic acids or vectors of the invention.
  • Nucleic acids of the invention can be introduced into plant cells or plants by the methods described above under the section entitled Host Cells.
  • the infiltration method is preferred, for example, as described by Bechtold et al, (1993); see also U.S. Patent 6,291,742.
  • intact plants are immersed in a suspension of nucleic acid, vector, or bacteria containing the nucleic acid or vector, then transferred to a vacuum chamber and placed under vacuum until the plant tissues appear uniformly water-soaked. Plants are then grown under standard conditions.
  • Transiently transformed plants have some advantageous properties. For example, expression at discrete time periods in a plant's life cycle may be desirable and higher levels of expression can often be obtained when a protein is transiently expressed. Moreover, plants that do not stably transmit a genetic trait encoded in the vectors of the invention are not capable of dispersing that trait to related plants. Accordingly, other plants will not be inadvertently altered by the genetic trait. Moreover, the public may exhibit less concern that the environment will be adversely affected by genetically engineered organisms than if the plant were stably transformed and capable of transmitting the genetic trait to other plants.
  • the invention provides a method of transiently expressing a nucleic acid (e.g. an inhibitory NCED RNA) or a NCED protein of the invention in a plant that includes contacting a plant with a vector or nucleic acid of the invention, replicating the vector or nucleic acid within the plant and expressing a protein encoded by the nucleic acid or the vector.
  • a nucleic acid may present in an expression cassette and/or within the vector.
  • This method involves amplifying, i.e., increasing the copy number, of a nucleic acids or vectors of the invention, thereby permitting expression of an encoded protein over basal levels obtained in the absence of amplification.
  • the nucleic acid or vector is provided in the plant but is not stably integrated into the germ line of the plant, and the method involves replicating the nucleic acid or vector within the plant and expressing an encoded protein.
  • a nucleic acid may be present in an expression cassette and/or within a vector.
  • the invention also provides a method of amplifying a nucleic acid of the invention that involves replicating a nucleic acid or vector of the invention within a host cell.
  • the host cell can be any host cell, for example, any of those described herein, as well as any organism or plant contemplated herein.
  • Nucleic acids of the invention can be introduced into plant cells or plants by the methods described above under the section entitled Host Cells.
  • the infiltration method can also be used for stable transformation of whole plants, plant calli or plant cuttings by exposing the plants, calli and cuttings to the present vectors, and identifying transformants.
  • Transformed embryogenic calli, meristemate tissue, embryos, leaf discs and the like can be used to generate transgenic plants that exhibit stable inheritance of the nucleic acids of the invention.
  • Plant cell lines having the nucleic acids of the invention are put through a plant regeneration protocol to obtain mature plants and seeds expressing the traits by methods well known in the art (for example, see U.S. Pat. Nos.
  • the plant regeneration protocol allows the development of somatic embryos and the subsequent growth of roots and shoots.
  • regenerated plants can be assayed for the selectable markers and/or reporter genes described herein, in various portions of the plant relative to regenerated, non-transformed plants.
  • Transgenic plants and seeds can be generated from transformed cells and tissues having the present nucleic acids by using standard methods.
  • Mature plants can be obtained from cell lines that contain the present vectors. If possible, the regenerated plants are self-pollinated. In addition, pollen obtained from the regenerated plants is crossed to seed grown plants of agronomically important inbred lines. In some cases, pollen from plants of these inbred lines is used to pollinate regenerated plants.
  • the nucleic acids and vectors of the invention are genetically traced by evaluating the segregation of the selectable marker or reporter gene in first and later generation progeny. The heritability and expression in plants of traits selected in tissue culture are of particular importance if the traits are to be commercially useful.
  • the commercial value of the plants of the invention can be optimized by providing different combinations of hybrids.
  • the farmer typically grows more than one kind of hybrid based on such differences as maturity, standability or other agronomic traits. Additionally, hybrids adapted to one part of the country are not adapted to another part because of differences in such traits as maturity, disease, and insect resistance. Because of this, it is preferable to breed the nucleic acids into a large number of parental lines so that many hybrid combinations can be produced.
  • a conversion process, known as backcrossing is carried out by crossing the original producing line to normal elite lines and then crossing the progeny back to the normal parent. The progeny from this cross will segregate such that some plants carry the gene responsible for production whereas some do not.
  • Plants carrying such genes will be crossed again to the normal parent resulting in progeny that segregate for production and normal production once more. This is repeated until the original normal parent has been converted to an producing line, yet possesses all other important attributes as originally found in the normal parent.
  • a separate backcrossing program is implemented for every elite line that is to be converted to production line capable of expressing the heterologous nucleic acids in the expression cassettes of the invention.
  • Producer lines and hybrids are produced which are true to type of the original normal lines and hybrids. This requires evaluation under a range of environmental conditions where the lines or hybrids will generally be grown commercially. Parental lines of hybrids that perform satisfactorily are increased and used for hybrid production using standard hybrid seed production practices.
  • Transgenic plants may find use in the commercial manufacture of proteins or other molecules, where the molecule of interest is extracted or purified from plant parts, seeds, and the like. Cells or tissue from the plants may also be cultured, grown in vitro, or fermented to manufacture such molecules.
  • transgenic plants may also be used in commercial breeding programs, or may be crossed or bred to plants of related crop species. Improvements encoded by the recombinant DNA may be transferred, e.g., from cells of one species to cells of other species, e.g., by protoplast fusion.
  • the invention also provides for a method of stably expressing a protein of the invention in a plant, which includes, contacting the plant cell with a nucleic acid or vector of the invention that has an associated selectable marker gene, under conditions effective to infect or transfect the plant cell.
  • the nucleic acid of the invention can be provided with an expression cassette as described herein.
  • a promoter within the expression cassette can be any of the promoters provided herein, for example, a constitutive promoter, an inducible promoter, a tissue-specific promoter or a fruit ripening-dependent promoter. Such promoters can provide expression of an encoded protein at a desired time, or at a desired developmental stage, or in a desired tissue.
  • the invention also provides for a method of stably expressing an inhibitory RNA or a NCED protein of the invention in a plant, which includes, contacting the plant cell with a nucleic acid encoding the an inhibitory RNA or a NCED protein of the invention, under conditions effective to transfer and integrate the nucleic acid into the nuclear genome of the cell.
  • a plant may be generated from the plant cell using available methods, including those described herein.
  • the plant or the plant cell may be exposed to a chemical or developmental agent, which induces expression of the inhibitory RNA or protein in the cell.
  • the nucleic acid may be present in a vector that can also include a selectable marker gene. When using such a vector with Agrobacterium tumefaciens, the vector can have an Agrobacterium tumefaciens origin of replication.
  • Plants Plants for use with the NCED nucleic acids and polypeptides of the invention include dicots and monocots, including but not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B.
  • juncea particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatus), cassava (Manihot esculent
  • genus Lemna L. aequinoctialis, L. disperma, L. ecuadoriensis, L. gibba, L. japonica, L. minor, L. miniscula, L. obscura, L. perpusilla, L. tenera, L. trisulca, L. turionifera, L. valdiviana
  • genus Spirodela S. intermedia, S. polyrrhiza, S. punctata
  • genus Woffia Wa. angusta, Wa. arrhiza, Wa. australina, Wa. borealis, Wa. brasiliensis, Wa. columbiana, Wa.
  • Lemnaceae Any other genera or species of Lemnaceae, if they exist, are also aspects of the present invention. Lemna gibba, Lemna minor, and Lemna miniscula are preferred, with Lemna minor and Lemna miniscula being most preferred.
  • Lemna species can be classified using the taxonomic scheme described by Landolt, Biosystematic Investigation on the Family of Duckweeds: The family of Lemnaceae - A Monograph Study. Geobatanischen Institut ETH, founded Rubel, Zurich (1986)); vegetables including tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo).
  • tomatoes Loxicon esculentum
  • lettuce e.g., Lactuca sativa
  • green beans Phaseeolus vulgaris
  • lima beans Phaseeolus limensis
  • peas Lathyrus spp.
  • Ornamentals include azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum.
  • Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata), Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga canadensis); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and balsam fir (Abies balsamea); and cedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis); and leguminous plants.
  • pines such as loblolly pine (Pinus taeda
  • Leguminous plants include beans and peas.
  • Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc.
  • Legumes include, but are not limited to, Arachis, e.g., peanuts, Vicia, e.g., crown vetch, hairy vetch, adzuki bean, mung bean, and chickpea, Lupinus, e.g., lupine, trifolium, Phaseolus, e.g., common bean and lima bean, Pisum, e.g., field bean, Melilotus, e.g., clover, Medicago, e.g., alfalfa, Lotus, e.g., trefoil, lens, e.g., lentil, and false indigo.
  • Arachis e.g., peanuts
  • Vicia e.g., crown vetch, hairy vetch, adzuki bean, mung bean, and chickpea
  • Lupinus e.g., lupine, trifolium
  • Phaseolus e.g., common bean and lim
  • nucleic acids and proteins of the invention include Acacia, aneth, artichoke, arugula, blackberry, canola, cilantro, Clementines, escarole, eucalyptus, fennel, grapefruit, honey dew, jicama, kiwifruit, lemon, lime, mushroom, nut, okra, orange, parsley, persimmon, plantain, pomegranate, poplar, radiata pine, radicchio, Southern pine, sweetgum, tangerine, triticale, vine, yams, apple, pear, quince, cherry, apricot, melon, hemp, buckwheat, grape, raspberry, chenopodium, blueberry, nectarine, peach, plum, strawberry, watermelon, eggplant, pepper, cauliflower, Brassica, e.g., broccoli, cabbage, brussel sprouts, onion, carrot, leek, beet, broad bean, celery
  • the NCED3 gene encodes the 9-cis-epoxycarotenoid cleavage enzyme that is thought to catalyze a rate-limiting reaction in ABA biosynthesis (luchi et al, 2001).
  • the gene encoding this enzyme is induced by osmotic stress in Arabidopsis and several other species and, according to the invention, this NCED3 gene plays a key role in ABA-mediated responses to osmotic stress such as increased seed dormancy, reduced seedling growth, stomatal behavior, increased osmotic adjustment and transition to flowering (Leon-Kloosterziel et al, 1996 ).
  • Arabidopsis there is a small family of at least seven NCED genes, luchi et al.
  • NCED3 and to a small extent NCED9 genes in Arabidopsis are desiccation-induced but other members of the NCED gene family are not.
  • Ablation of the ABA response in plants with a mutated nced3 gene leads to many changes in gene expression. Prior to the invention, however, only a few changes in such expressionhave been examined.
  • Anti-sense expression of the NCED 3 gene leads to suppression of desiccation induction of the RD29B gene but not the RAB18 or KIN1 genes.
  • the transcript of the ABA-induced ICK1 gene also fails to accumulate in NaCl- treated stol/nced3 plants.
  • the affects of the nced3 mutation on other gene expression and physiological responses may depend on the specific effects of this mutation on tissue and cell-specific perturbations in ABA content.
  • Disruption of the NCED3 gene has revealed that in Arabidopsis this leads to a syndrome of phenotypic changes that indicates that there may be a number of ABA-associated responses to stress that are not always necessarily coupled in previously assumed ways. For instance, it has been generally believed that when plants are exposed to decreased water potential, cell growth ceases or slows due to inadequate solute potential needed to compensate for the water potential imbalance with the environment (Morgan et al, 1984; Bressan et al., 1990).
  • This invention identifies the stol/nced3 mutant of Arabidopsis as a mutant that exhibits enhanced germination, and increased root and shoot growth at low water potentials, ( Figures 1, 2 and 3) indicates that ABA increase during osmotic stress in wild type plants reduces growth.
  • ABA increase during osmotic stress in wild type plants reduces growth.
  • osmotic stress-induced growth inhibition caused by salt is largely dependent on ABA, and ablation of the stress-induced increase in ABA accumulation in stol/nced3 mutant plants allows faster growth.
  • non-ionic osmotic stress mediated by sorbitol can apparently inhibit growth by an ABA-independent pathway, since stol/nced3 plants exhibit osmotic-stress induced growth reduction without the normal increased ABA accumulation associated with osmotic stress (Figure 4).
  • increased ABA appears to be required for growth maintenance during nonionic osmotic stress as reported previously (Sharp, 2002). This strongly implies that plants are able to sense ionic and non-ionic osmotic stresses differently.
  • This invention has identified the specific characteristics of the stol/nced3 mutant that influence ABA in directly controlling stress-induced growth and development. These effects include ABA effects on stomatal function and indicate that the diminished capacity of stol/nced3 plants to accumulate ABA at low water potentials dramatically alters stomatal behavior (Figure 14). Other studies on stomatal have not explored the relationship between these alterations in ABA physiology and the diurnal cycle of stomatal movements that is largely controlled by light and CO levels (Hedrich et al, 2001). Most studies have employed epidermal peels (Raschke et al, 1979) which are, of course, disconnected from mesophyl, root and other tissues.
  • This Example illustrates the isolation and characterization of a stol (for salt tolerant) mutation that lead to the identification of the nced3 gene as an important regulator of tolerance to environmental stress. As shown herein both mutation and over-expression of the nced3 gene can lead to tolerance by plants to environmental stress.
  • RD29A::LUC reporter gene (Ishitani et ⁇ /.,1997) was provided by Professor J.K. Zhu, University of Arizona.
  • a T-DNA population was obtained after Agrobacterium tumefaciens floral transformation with GV3101 (pMP90RK) carrying the binary vector pSK1015 and selection based on Liberty (bialaphos) (30 mg/1) resistance (Koiwa et al. , 2002).
  • Herbicide resistant plants were combined into 10 plant pools and T seeds were collected for screening. Plants from T 2 seeds were grown either in a controlled environment room with 16 hr of light at 22° C and 8 hr in darkness at 18° C or in a greenhouse.
  • the screening was performed in vitro for the ability of the seeds to germinate in a media containing 145 mM NaCl Seeds were surface sterilized (2% sodium hypocloride for 15 min.), sowed onto medium containing Murashige and Skoog (MS) basal salt mixture, 2% sucrose, 145 mM NaCl, solidified with 1% agar (pH 5.7). After sowing the seeds were stratified for 2 to 4 days at 4°C. For the mutant characterization in vitro, MS either contained no supplement or was supplemented with 100, 130, 145, 150, 200, 250 mM NaCl ⁇ ABA, 20 mM
  • LiCl ⁇ ABA LiCl ⁇ ABA, or 160 mM KC1.
  • seeds were plated onto medium containing 1/4X MS salt, 30 ⁇ g/ml hygromicin B, 100 ⁇ g/ml tiamine and 1% agar.
  • ⁇ t-C24-(RD29::LUC) wild type (wt) and t-C24-(RD29::LUC) stol (stol) mutant seeds were sterilized and sowed on Petri plates containing either basic MS agar medium or MS supplemented with 100, 130, 150, 160, 200, 250 mM NaCl, 160mM KCl or 20 mM LiCl, stratified at 4 °C for 4 days and transferred in a growth chamber with 16 h of light at 22°C and 8 h of darkness at 18°C. Fourteen days after sowing, the number of germinated seeds was assessed. After 7 additional days of growth on saline media plant fresh weight was measured.
  • Wild type and stol mutant plants were germinated in vitro on MS medium. Seven-day old seedlings were transferred onto MS medium or MS medium supplemented with 160mM NaCl, 160mM KCl or 20mM LiCl After 20 days from transferring the plants, they were collected for fresh weight measurements.
  • (stol) mutant seeds were sterilized and sowed on Petri plates containing either basic MS agar medium or MS supplemented with 300 mM sorbitol, stratified at 4 °C for 4 days and transferred in a growth chamber with 16 h of light at 22°C and 8 h of darkness at 18°C. Twenty one days after sowing, the number of germinated seeds was assessed. Wild type and stol mutant plants were germinated in vitro on MS medium, 3day old seedlings were transferred onto MS medium or MS medium supplemented with 300mM sorbitol. After 14 days from transferring the plants, they were collected for fresh weight and roots length measurements.
  • Seeds of wild type and stol mutant plants were directly sowed in turface (MPN Bancroft, Bag Inc., Louisiana, USA). Fifty uniform plants from the wild type and stol/nced3 populations were selected and grown in the greenhouse using a standard irrigation regime. After 15 days, when plantlets had reached the stage of 5-6 fully expanded leaves, irrigation was stopped for half of the plants (25 for each genotype), whereas the other half was grown under standard irrigation regime as a control. After 15 days, water stressed plants were re- watered and for 2 additional days were allowed to recover before measuring plant fresh weight. To assess salt stress tolerance in soil under saturated atmospheric humidity, Arabidopsis seeds were directly sowed in turface and allowed to grow for one week under non-saline irrigation.
  • Genomic sequence flanking the T-D ⁇ A insertion was determined by using Thermal Asymmetric Interlaced-PCR (TAIL-PCR) procedure of Liu et al.
  • TAIL-PCR Thermal Asymmetric Interlaced-PCR
  • Primers 1, 2, 3, 4, 5 were used for the TAIL-PCR analysis.
  • Primers 3, 6 and 7 were used for the identification of the TD ⁇ A genotype.
  • Primers 6 and 7 were used for the detection of ⁇ CED-4 gene.
  • Primers 8 and 9 were used to synthesize the probe for the Northern blot hybridization.
  • RNA for RT-PCR was extracted as described.
  • First strand cDNA was synthesized using the Superscript II kit (Gibco BRL, Rockville, MD, USA).
  • First-strand cDNA of total RNA (4ug) from shoots of three- week old plants was used for PCR amplification.
  • PCR was carried out using ExTaq DNA polymerase (TaKaRa, Shiga, Japan) and gene-specific primers for stol/nced3 as described in Table 3.
  • Stable F3 stol mutant plants were backcrossed with the parental C24 wild type plants and co-segregation for the stol salt tolerance (germination assay) and herbicide resistance phenotypes was determined in FI and F2 generations.
  • Three separate fragments of 2.2, 0.8, and 2.3 kbp, respectively were amplified from the BAC clone MOA2.4 and sub-cloned into pBluescript.
  • the resulting 4.5 kbp DNA fragment was digested with Smal(5') and Kpnl(3') and ligated into the pBIB vector (Higromycin + ).
  • the plasmid was transferred into Agrobacterium strain GV3101.
  • the Agrobacterium transformed colonies were selected with 50mg/l kanamicin (binary vector marker), 30mg/l rifampicin (agro strain marker) and 30mg/l gentamycin (Ti-plasmid marker).
  • Single transformed colonies were isolated and grown in liquid medium, confirmed for their insert size by PCR, and stored frozen at -80°C.
  • a 5 ⁇ l aliquot from the -80°C stock was used to inoculate 250ml of Yeast Extract Phosphate (YEP) medium (DIFCO, Becton Dickinson & Co., Sparks, MD, USA) plus appropriate antibiotics and incubated on a shaker in the dark at 28°C and allow to grow to an OD 60 oof >1.5 to 2.0 (16-20 hr). The bacteria were then centrifuged for 10 min.
  • YEP Yeast Extract Phosphate
  • ABA was extracted as described by Xiong et al. (2001) from 3week old wild type and stol/nced3 plants grown in Petri plates on standard MS or MS supplemented with 145 mM sorbitol. ABA was quantified using an immunoassay ELISA kit according to the manufacturer's instructions (Phytodetek ABA, AGDIA, Elkhart, IN, USA). Osmotic potential measurements
  • the sap osmotic potential of wild type and stol/nced3 plants was measured after germination and growth on NaCl- and sorbitol- containing media. Fifteen days after germination, plantlets were collected, frozen in liquid nitrogen, and centrifuged for 20 min. at 4000 rpm in microcentrifuge tubes. Further separation of the cellular fluid from plant debris was obtained by centrifugation at 10000 rpm for 10 min. and osmotic potential was measured using lO ⁇ l samples with a Wescor 5500 vapor pressure osmometer (Wescor Inc. Logan, Utah, USA). The same procedure was followed for plants sown and grown for 7 days on basic MS medium and then transferred and grown for an additional 15 days on NaCl or sorbitol media before measuring the osmotic potential.
  • Wild type and stol/nced3 mutant seeds were sterilized and sown in vitro on MS medium or MS medium supplemented with 160mM NaCl ⁇ 20 ⁇ M ABA, stratified at 4°C for 4 days and placed in a growth chamber with 16 hr of light at 22° C and 8 hr of darkness at 18° C. The number of germinated seeds was determined periodically over a 21 day time interval.
  • Wild type and stol/nced3 mutant plants were germinated in vitro on MS medium. Seven-day old seedlings were transferred onto MS medium or MS medium supplemented with 20mM LiCl ⁇ 20 ⁇ M ABA. Seedlings were allowed to grow for additional 7 days before visual assessment of LiCl sensitivity.
  • Ethylene production in wild type and stol/nced3 mutant plants was assayed on 7day old seedlings germinated on basic MS medium and then transferred in liquid medium. Seedlings were allowed to grow for 7 days in 3 ml of a 6 ml plastic syringe filled with liquid MS or MS supplemented with 160mM NaCl. Ethylene accumulated during this time in the remaining 3ml volume of the syringe and was collected by injecting the non-liquid volume (air) of the syringe in sealed vials. The ethylene concentration was subsequently quantified using standard GC analysis and normalized per 0.5 g of plant FW.
  • Table 4 illustrates the genetic analysis performed on plants bearing the mutant nced-4 allele.
  • nced-4 mutation isolated is a recessive mutation in a single nuclear gene.
  • the ratio of salt tolerance to salt sensitivity is 1:3.
  • the salt resistance phenotype of mutant nced-4 plants also cosegregates with the bialaphos resistance phenotype.
  • hi F2 progeny the ratio of bialaphos resistance to salt sensitivity is 3:1.
  • stol seedlings were allowed to first germinate on non-saline media and then transferred (at the stage of fully expanded cotyledons) to hyperosmotic media to examine their growth response independent of germination.
  • stol plantlets were able to withstand the abrupt hyperosmotic stress and grow until flowering (data not shown), whereas wild type seedlings became chlorotic upon exposure to high salinity and they never reached flowering (Figure 3).
  • NCED3 (9-cis- epoxicarotenoid dioxygenase) gene in stol mutants
  • STOl /NCED 3 transcript is expressed in both leaf and root (not shown) tissue of unstressed wild type plants and its level is increased moderately upon 145 mM NaCl treatment ( Figure 7) as previously reported (luchi et al, 2001).
  • the ST01/NCED3 transcript abundance was substantially reduced in unstressed stol /need plants compared to wild type plants, possibly due to instability of the transcript (3').
  • Upon 145 mM NaCl treatment there was an increase of the ST01/NCED3 transcript abundance in the mutant plants, but the level remained well below that observed in stressed wild type plants (Figure 7). Consistent with the fact that the ST01/NCED3 gene encodes for a key enzyme in ABA biosynthesis, the level of this hormone was significantly affected in stol/nced3 plants (Table 5).
  • Table 5 ABA Content in Wild Type and stol Plants (ng/g fresh weight)
  • Values are the mean values of three plants + S.E.
  • a 4.5 kb Smal(5yKpnl(3') genomic fragment, including the full length ST01/NCED3 gene and its promoter was cloned from wild type C24 plants and introduced via agrobacterium transformation (pBIB vector) into stol/ncedS mutant plants.
  • pBIB vector agrobacterium transformation
  • Phenotypic and molecular evaluation of line 4-6 revealed that expression of the wild type ST01/NCED3 gene in mutant plants (Figure 8 A) eliminated their enhanced ability to germinate on salt (data not shown) and hypersensitivity to desiccation (Figure 8B).
  • Pharmacological complementation of stol Vnced3 plants by addition of ABA to the medium also reverted both their enhanced germination on NaCl medium ( Figure 9) and growth sensitivity in LiCl ( Figure 10).
  • Enhanced growth of stol Mced3 plants on hyperosmotic medium is associated with blockage of ABA-mediated growth inhibition independent of the degree of osmotic adjustment
  • osmotic potentials in the absence or presence of stress were measured.
  • cellular saps from stol/nced3 plants had less negative osmotic potential under stress compared to wild type plants (Table 6).
  • Table 6 Osmotic Potential (MPa) a
  • Nalues are means of 3 seedling preparations ⁇ S.E.
  • b Nalues refer to seeds germinated and grown on non-saline (control), ⁇ aCl or sorbitol media.
  • c Nalues refer to seeds germinated on non-saline medium and subsequently transferred and grown on non-saline, ⁇ aCl or sorbitol media (see Experimental procedure for details).
  • Table 7 illustrates that over-expression of NCED-3 leads to increased plant survival under stressful conditions such as high salt or low water conditions.
  • NCED3 gene in Arabidopsis was achieved in another experiment that employed the cauliflower mosaic virus promoter ( 35 S), or the superpromoter (Super) in an (OCS) 3 Mas-bar cassette (see Narasilhulu et al, 1996 Early transcription of Agrobacterium T-DNA genes in tobacco and maize. Plant Cell 8:873-886). Plants were watered normally in 2" pots containing soil for two weeks (6 leaf stage) after which water was withheld for 12 days. Plants were then rewatered and scored as either surviving or not, two weeks following rewatering.
  • 35 S cauliflower mosaic virus promoter
  • Super superpromoter
  • Table 8 illustrates that the abundance of NCED3 transcripts (relative to C24rd29 control plants receiving vectors only) correlates with the percent survival of plant under such dessicating conditions. NCED3 transcripts were detected using the primers for Northern probes that are listed in Table 3.
  • yeast HAL1 gene improves salt tolerance of transgenic tomato. Plant Physiol. 123, 393-402.
  • Narasimhan, MX. Hasegawa, P.M., Joly, R.J. and Bressan, R.A.
  • AtHKTl is a salt tolerance determinant that controls Na + entry into plant roots.
  • Arabidopsis aldehyde oxidase 3 (AAO3) gene product catalyzes the final step in abscisic acid biosynthesis in leaves. Proc. Natl. Acad. Sci. USA.
  • ICK1 a cyclin-dependent protein kinase inhibitor from Arabidopsis thaliana interacts with both Cdc2a and CycD3, and its expression is induced by abscisic acid.
  • Plant J. 15, 501-510. Wang, H., Zhou, Y., Gilmer, S., Whitwill, S. and Fowke, L.C. (2000)
  • LOS5/ABA3 locus encodes a molybdenum cofactor sulfurase and modulates cold stress- and osmotic stress-responsive gene expression.

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Abstract

The invention provides transgenic plants that are resistant to environmental stress that utilize 9-cis-epoxycarotenoid dioxygenase nucleic acids and polypeptides. The invention also provides methods of producing plants that are resistant to environmental stress.

Description

METHODS TO PRODUCE TRANSGENIC PLANTS RESISTANT TO OSMOTIC STRESS
FIELD OF THE INVENTION
The present invention relates generally to methods of producing plants that are resistant to salt stress.
BACKGROUND OF THE INVENTION
Salinity is a major constraint to crop productivity because it reduces yield and limits expansion of agriculture onto previously uncultivated land (Flowers and Yeo, 1995). Salinity is becoming more acute as a consequence of the intensive agricultural production that is occurring to meet the caloric and nutritional demands of the burgeoning world population. Fertilization contributes to this problem by causing added salt accumulation. It is estimated that salinity affects 6% of the land surface area (Flowers and Yeo, 1995) and, perhaps, more than 20% of the cultivated land is salt affected. Etiologies of salt stress include hyperosmolarity, ion toxicity and nutrient acquisition deficiency. The pathologies mediated by salt stress include elevated levels of reactive oxygen radicals, reduced enzyme function, photosynthesis and other metabolic processes, and membrane dysfunction (Hasegawa et al, 2000).
Deserts and desert-like regions occupy 1/4 to 1/3 of the earth's land mass world and are expanding. Reasons for this desertification include using irrigation water with a high salt concentration, dams, irrigation and deficient draining equipment, and sea water reaching farm land, all causing salts such as NaCl, Na2SO , MgCl2, CaCl2 to accumulate in soil. In such salt-containing soil, almost all plants have reduced growth or salt-related lesions. To check enlargement of the deserts, afforestation and plant rearing have been attempted in the areas of the high-salt soil. However, few plants can grow in the high-salt soil and crop productivity in high-salt soils is markedly low. Hence, only a small proportion of high-salt lands are used as farmland. hi the Middle East, salt water processed into fresh water is used for agricultural irrigation. However, a great deal of energy is expended for processing of salt water into fresh water and the environment is negatively impacted. Obtaining large quantities of irrigation water with a low salt concentration at low cost has been very difficult. Reliable methods for obtaining salt-resistant plants would reduce the need for such low salt irrigation water.
Some aspects of selection and rearing of salt-tolerant plants have been studied. For example, a salt-tolerant variety of rice is known. Furthermore, breeding salt-tolerant plants by adapting a callus of a plant to a high salt medium and reproducing the plant has been attempted. Workers have also searched for plant genes related to salt-tolerance. See, e.g., PCT Application PCT/CA99/00219.
Salt stress survival and adaptation (resumption of growth after stress exposure) are dependent on cellular ion homeostasis. Regulation of net intracellular Na+ and Cl" uptake and subsequent vacuolar compartmentalization without cytotoxic ion accumulation are pivotal processes for salt tolerance (Blumwald et al, 2000; Hasegawa et al, 2000; Niu et al, 1995). Vacuolar partitioning of Na+ and Cl" contributes also to maintenance of cellular water relations with organic solutes being the principal osmolytes that accumulate in the cytosol and organelles to balance intracellular osmotic status of cells in salt grown plants. Many unicellular organisms can exclude effectively toxic ions from the extracellular milieu and adjust their water relations by the synthesis or accumulation of compatible osmolytes (Rhodes and Hanson, 1993). Cellular ion exclusion is not an adaptation of higher plants presumably because cell enlargement is a part of development whereby cells increase their volume as much as 100-fold after division (Lyndon 1990). Such massive cell enlargement is mediated primarily by expansion of the vacuole. Intracellular uptake of Na+ and Cl" by cells of plants growing in saline soils or solutions presumably is a more energetically efficient mode of osmotic adjustment compared to biosynthesis of organic solutes. Intracellular compartmentation of Na+ and Cl" is a salt adaptation conserved in halophytes and glycophytes (Blumwald et al, 2000; Hasegawa et al, 2000). The steady-state Na+ electrochemical gradients across the plasma membrane and tonoplast make it likely that efflux from the cytosol across these membranes is energy-dependent (Blumwald et al, 2000; Hasegawa et al, 2000; Niu et al, 1995). Conversely, Na+ flux from the apoplast or vacuole into the cytosol occurs down its electrochemical gradient. Modulation of plasma membrane cation transport systems or controlled dissipation of the plasma membrane potential can reduce intracellular Na+ influx. Yeast Pmp3p is a 55 amino acid peptide that is responsible for attenuating hyperpolarization across the plasma membrane, which reduces influx of toxic cations, like Na+ (Navarre and Goffeau, 2000). Transcription of PMP3 orthologous plant genes is induced by salt treatment (Navarre and Goffeau, 2000).
Energy-dependent transport of solutes across plant cell membranes, with some exceptions for Ca2+, is coupled to the proton (H") electrochemical potential established by H+ translocating pumps (Blumwald et al, 2000; Hasegawa et al, 2000). Therefore Na+ efflux from the cytosol relies on H+ gradients. H+ translocation across these membranes increases with salt treatment and can be attributed both to pump activation and enhanced transcription, indicating that both positive and negative control of the H+ electrochemical potential may be essential features of ion homeostasis in high external Na+ environments (Hasegawa et al, 2000). Data from physiological experiments using isolated vesicles implicated plasma membrane and tonoplast transporters that couple the downhill transport of H+s to the cytosol with energy-dependent Na+ efflux from the cytosol. Both plasma membrane and tonoplast Na+ H+ antiporter activities increase in response to salt treatment, at least in halophytic species (Blumwald et al, 2000).
The Na+ hypersensitive Arabidopsis mutant sosl is defective for a putative plasma membrane Na+/H+ antiporter (Shi et al, 2000). SOSl is a 127- kDa protein with an N-terminal hydrophobic region that contains 12 predicted transmembrane spanning domains and a hydrophilic C-terminus of more than 600 amino acids. Sequence alignment analysis indicates that SOSl is most similar to the Synechocystis sp. and Pseudomonas aeruginosa Na+/H+ antiporters SynNhaP and NhaP, respectively, within the transmembrane region (Hamada et al, 2001; Utsugi et al, 1998) and can be categorized phylogenetically together with Saccharomyces cerevisiae NHA1 and Schizosaccharomyces pombe SOD2 (Hahnenberger et al, 1996; Jia et al, 1992; Nass et al, 1997).
However, while some mechanisms and genes relating to salt-tolerance have been identified, generally, plant salt-tolerance has not been achieved. Therefore, effective methods for developing improved plant salt-tolerance are needed. Moreover, effective methods for generating salt-tolerant plants would reduce the amount of water needed for agricultural irrigation. Such methods would therefore help prevent the desertification of arable land and would allow crop production in high-salt soil.
SUMMARY OF THE INVENTION The invention provides plants that are resistant to environmental stresses such as salt. In one embodiment, the invention provides a mutant plant comprising a mutated 9-cis-epoxycarotenoid dioxygenase gene so that, as compared to a plant not comprising said mutated gene, the mutant plant exhibits increased salt tolerance or increased stress resistance. In another embodiment, the invention further provides a transgenic plant comprising a null mutation in an endogenous 9-cis-epoxycarotenoid dioxygenase gene so that, compared to a plant of the same genetic background but without the null mutation in the endogenous 9-cis-epoxycarotenoid dioxygenase gene, the transgenic plant exhibits increased salt resistance.
The invention also provides a transgenic plant comprising an isolated 9- cis-epoxycarotenoid dioxygenase nucleic acid having SEQ ID NO: 10, SEQ ID NO.-l l, SEQ ID NO: 12, SEQ ID NO: 14-16, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, or a complement thereof, and a promoter functional in a plant cell, wherein upone expression of the isolated nucleic acid or the complement thereof, the transgenic plant exhibits increased salt resistance relative to a plant of the same genetic background but without the isolated 9-cis-epoxycarotenoid dioxygenase nucleic acid. The invention further provides a transgenic plant comprising an isolated nucleic acid that encodes an inhibitory 9-cis-epoxycarotenoid dioxygenase RNA that, when expressed from a promoter functional in a plant cell, inhibits the function of endogenous RNA encoding a 9-cis-epoxycarotenoid dioxygenase enzyme; wherein the transgenic plant exhibits increased salt resistance relative to a plant of the same genetic background but without the isolated 9-cis- epoxycarotenoid dioxygenase nucleic acid. The inhibitory 9-cis- epoxycarotenoid dioxygenase RNA may be substantially complementary to the endogenous RNA encoding the 9-cis-epoxycarotenoid dioxygenase enzyme. The inhibitory RNA can, for example, be substantially complementary to SEQ ID NO:l-9, SEQ ID NO:10, SEQ ID NO:ll, SEQ ID NO:12, SEQ ID NO:14- 20, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34. In some embodiments, such an inhibitory RNA hybridizes under moderately stringent hybridization conditions to the endogenous RNA encoding the 9-cis-epoxycarotenoid dioxygenase enzyme comprising SEQ ID NO:13, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID NO:33. Moderately stringent hybridization conditions can include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37°C, and a wash in 0.5X to IX SSC at 55 to 60°C. In other embodiments, such an inhibitory RNA hybridizes under highly stringent hybridization conditions to the endogenous RNA encoding the 9-cis- epoxycarotenoid dioxygenase enzyme comprising SEQ ID NO: 13, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID NO:33. Highly stringent conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0. IX SSC at 60 to 65°C.
The transgenic plant of the invention can develop in the presence of a concentration of salt that inhibits the development of the plant of the same genetic background but without the null mutation or the isolated nucleic acid. The transgenic plants of the invention can develop faster than plants of a similar backround but without the null mutation or the isolated nucleic acid, even in the presence of a concentration of salt that would normally inhibit the development of the plant. The transgenic plants of the invention can also develop leaves faster in the presence of a concentration of salt that inhibits the development of the plant of the same genetic background but without the null mutation or the isolated nucleic acid.
The transgenic plants of the invention can be dicots or monocots. Food or feed can be produced from the transgenic plant of the invention. Transgenic progeny plants can be obtained from the transgenic plants of the invention. Such progeny plants have the null mutation or they have the isolated 9-cis- epoxycarotenoid dioxygenase nucleic acid, and can develop in the presence of a concentration of salt that inhibits the development of a plant not comprising said mutated gene. Transgenic seeds can also be obtained from plant produced according to the invention and transgenic progeny plants can be obtained from such transgenic seeds.
The invention also provides a transgenic plant comprising an isolated recombinant DNA encoding a promoter functional in a plant cell that is operably linked to a DNA encoding a 9-cis-epoxycarotenoid dioxygenase or a functional subunit thereof so that RNA is expressed from the recombinant DNA in the transgenic plant. Such expression increases at least one of the drought, cold, salt, osmotic or pathogen tolerance of the transgenic plant. Such a promoter can be induced by stress. The 9-cis-epoxycarotenoid dioxygenase or a functional subunit thereof can also be expressed at higher levels than in a plant of the same genetic background that does not comprise the isolated recombinant DNA. The recombinant DNA can encode a 9-cis-epoxycarotenoid dioxygenase-3 enzyme. The 9-cis-epoxycarotenoid dioxygenase enzyme may also comprise SEQ ID NO:13, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID NO:33. The invention also provides a method of increasing salt resistance in a plant comprising: (a) transforming a plant cell with an isolated nucleic acid that encodes an inhibitory 9-cis-epoxycarotenoid dioxygenase RNA that, when expressed from a promoter functional in a plant cell, inhibits the function of endogenous RNA encoding a 9-cis-epoxycarotenoid dioxygenase enzyme, to generate a transformed plant cell; and (b) regenerating the transformed plant cell into a transgenic plant that has increased resistance to salt relative to a non- transgenic plant with the same genetic background but without the isolated nucleic acid.
The inhibitory 9-cis-epoxycarotenoid dioxygenase RNA can be complementary to the endogenous RNA encoding the 9-cis-epoxycarotenoid dioxygenase enzyme. The inhibitory RNA can be, for example, substantially complementary to SEQ ID NO: 1-9, SEQ ID NO:10, SEQ ID NO:ll, SEQ ID NO: 12, SEQ ID NO: 14-20, SEQ ID NO:26, SEQ LD NO:28, SEQ ID NO:30, SEQ ID NO:32, or SEQ ID NO:34. In some embodiments, the inhibitory RNA hybridizes under moderately stringent hybridization conditions to the endogenous RNA encoding an 9-cis-epoxycarotenoid dioxygenase enzyme comprising SEQ ID NO: 13, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID NO: 33. Moderately stringent hybridization conditions comprise hybridization in 40 to 45% formamide, 1.0 M NaCl, 1 % SDS at 37°C, and a wash in 0.5X to IX SSC at 55 to 60°C. In other embodiments, such an inhibitory RNA hybridizes under highly stringent hybridization conditions to the endogenous RNA encoding an 9-cis-epoxycarotenoid dioxygenase enzyme comprising SEQ ID NO:13, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID NO:33. Highly stringent conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0. IX SSC at 60 to 65°C.
The promoter functional in a plant cell cam be a viral coat protein promoter, a tissue-specific promoter, a ubiquitin promoter, a CaMV 35S promoter, a CaMV 19S promoter, a nos promoter, an Adh promoter, a sucrose synthase promoter, a tubulin promoter, a napin promoter, an actin promoter, a cab promoter, a PEPCase promoter, a 7S-alpha'-conglycinin promoter, an R gene complex promoter, a tomato E8 promoter, a patatin promoter, a mannopine synthase promoter, a soybean seed protein glycinin promoter, a soybean vegetative storage protein promoter, a bacteriophage SP6 promoter, a bacteriophage T3 promoter, a bacteriophage T7 promoter, a Ptac promoter, a root-cell promoter, an ABA-inducible promoter or a turgor-inducible promoter. Examples of plants that can be produced or manipulated by the methods of the invention include alfalfa, avocado, Brassica campestris, canola, cantaloupe, cotton, cowpea, cranberry, cucumber, eucalyptus, fescue, flax, gladiolus, lettuce, liliacea, maize, mellon, millet, muskmelon, oat, oil palm, olive, papaya, peanut, perennial ryegrass, potato, rapeseed, rice, rye, safflower, sorghum, soybean, sugarbeet, sugarcane, sunflower, tritordeum, turfgrass, or wheat. Hence, such plants may be dicots, for example, soybean. The plant can also be a monocot, for example, corn, rice, rye, oats or wheat. Food or feed can also be produced from the mutant and transgenic plants of the invention.
Transgenic progeny plants obtained from the transgenic plant produced by the methods of the invention are also contemplated wherein the progeny plant comprises the null mutation or the isolated 9-cis-epoxycarotenoid dioxygenase nucleic acid, and wherein the progeny plant is able to develop in the presence of a concentration of salt that inhibits the development of a plant not comprising said mutated gene. The invention also provides a transgenic seed obtained from plants produced by such methods wherein the seed comprises the null mutation or the isolated 9-cis-epoxycarotenoid dioxygenase nucleic acid, and wherein the transgenic seed is able to germinate in the presence of a concentration of salt that inhibits the germination of a seed not comprising said mutated gene. Transgenic progeny plants obtained from such transgenic seeds are also contemplated, wherein the progeny plant comprises the null mutation or the isolated 9-cis- epoxycarotenoid dioxygenase nucleic acid.
The invention further provides a method for increasing at least one of the drought, cold, salt, osmotic or pathogen tolerance of a plant comprising: (a) introducing into regenerable cells of a plant a DNA sequence encoding a 9-cis- epoxycarotenoid dioxygenase or a functional subunit thereof operably linked to a promoter functional in a plant cell to yield transformed plant cells; and (b) regenerating a plant from said transformed plant cells wherein the cells of said plant express the NCED or functional subunit thereof encoded by the DNA sequence in an amount effective to increase at least one of the drought, cold, salt, osmotic or pathogen tolerance of a plant. The method can further include (c) obtaining a transgenic seed from the plant of step (b), wherein the transgenic seed comprises said DNA sequence. The method can also include (d) obtaining a transgenic progeny plant from the transgenic seed of step (c) wherein the cells of the progeny plant express the 9-cis-epoxycarotenoid dioxygenase or functional subunit thereof encoded by the DNA sequence in an amount effective to increase at least one of the drought, cold, salt, osmotic or pathogen tolerance of a plant. The 9-cis-epoxycarotenoid dioxygenase may be 9-cis- epoxycarotenoid dioxygenase-3. The promoter can be induced by stress. Such plants may have cells that express the 9-cis-epoxycarotenoid dioxygenase or functional subunit thereof encoded by the DNA sequence in an amount effective to increase at least one of the drought, cold, salt, osmotic or pathogen tolerance of a plant. The invention also provides transgenic seeds obtained from such plants. The invention also provides a method for increasing the salt tolerance or the stress resistance of a plant comprising: (a) altering the DNA of regenerable cells of said plant to introduce a mutation into a gene encoding a 9-cis- epoxycarotenoid dioxygenase in said plant cells so as to render the 9-cis- epoxycarotenoid dioxygenase gene product nonfunctional; and (b) regenerating a plant from said plant cells having increased salt tolerance or increased stress resistance as compared to a plant not comprising said mutated gene. The method can further include (c) obtaining a seed from the plant of step (b), wherein the seed comprises said mutated gene. The method can also include (d) obtaining a progeny plant from the seed of step (c) wherein the cells of the progeny plant comprise said mutated gene so that the plant exhibits at least one of increased salt tolerance or increased stress resistance as compared to a plant not comprising said mutated gene. The 9-cis-epoxycarotenoid dioxygenase can be, for example, 9-cis-epoxycarotenoid dioxygenase-3. Plants obtained may exhibit at least one of increased salt tolerance or increased stress resistance as compared to a plant not comprising the mutated gene. Plants produced can be monocots or dicots. Seeds obtained from the plant are also contemplated wherein said seed comprises the mutated gene.
The invention further provides an isolated polynucleotide comprising a nucleotide sequence that is substantially identical to SEQ ID NO: 10 or a fragment thereof and which comprises a promoter region.
The invention also provides an isolated polynucleotide comprising a nucleotide sequence that is substantially complementary to SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, or a fragment thereof, wherein the isolated polynucleotide can inhibit RNA transcription from a DNA comprising SEQ ID NO: 10, SEQ ID NO:ll, SEQ ID NO:12, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34. Such an isolated polynucleotide can have a nucleotide sequence that is at least 66% complementary to any one of SEQ ID NO:10, SEQ ID NO:ll, SEQ ID NO:12, SEQ ID NO:26, SEQ ID
NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34. In some embodiments the sequence comparison is made to SEQ ID NO:30. Nucleic acids with such a degree of complementarity are useful for producing inhibitory RNA in plant cells.
In other embodiments, an isolated NCED nucleic acid is used for over- expression of the NCED gene product. In such cases, the NCED gene product can have at least 66% sequence identity relative to SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31 or SEQ ID NO:33. In some embodiments the sequence comparison is made to SEQ ID NO:29. Such gene products and the nucleic acids encoding such gene products are useful for generating plants resistant to osmotic stress. Other degrees of sequence complementary and identity are contemplated by the invention including, for example, at least 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% to one of the nucleic acids provided herein, e.g. SEQ ID NO:30. Polypeptides contemplated for use in the invention can have similar percentages of sequence identity to one of the polypeptides provided herein, e.g. SEQ ID NO:29.
DESCRIPTION OF THE FIGURES Figure 1. The stol/nced3 mutation enhances germination on media supplemented with NaCl or KC1. (A) Photographs are representative of wild type (wt) and stol/nced3 mutant plants. Seeds were placed on MS medium or MS medium supplemented with 160mM NaCl or KC1 and allowed to germinate and grow for 14 days. (B) Percentage of germinated seeds after 14 days (significant differences at 99% confidence level). Germination was assessed on 60 seeds of wild type or stol/nced3 mutant plants distributed in three replica plates per each treatment (20 seeds per each genotype).
Figure 2. Growth response of wild type and stol/nced3 plantlets at increasing NaCl concentrations. (A) Seeds were placed in Petri plates on MS medium or MS medium supplemented with increasing concentrations of NaCl. Plant fresh weight was measured after 21 days. Values are means of 60 plants ± S.E. (B) Seeds were germinated and grown in soil at saturated atmospheric humidity (see Experimental procedures section for details) and irrigated every day with saline water with different NaCl concentrations. After 28 days, shoot fresh weight (FW) was measured. Values are means of 20 plants ± S.E.
Figure 3. stol/nced3 mutant plants are tolerant to KC1 and NaCl and hypersensitive to LiCl stresses. (A) Seeds were germinated in Petri plates on standard MS medium and seven-day-old seedlings were subsequently transferred to MS medium supplemented withl60mM NaCl, KC1 or 20mM LiCl and allowed to grow for additional 20 days. Photographs are representative of wild type and stol mutant plants after 20 days from transferring onto saline medium. (B) Plant fresh weights were measured after 20 days of growth on indicated medium. Values are means of 60 plants + S.E.
Figure 4. The stol/nced3 mutation inhibits growth on media supplemented with sorbitol. (A) Seeds were germinated in Petri plates on standard MS medium and three-day-old seedlings were subsequently transferred on MS medium (not shown) or MS medium supplemented with 300 mM sorbitol and allowed to grow for additional 20 days. (B) Root length of 14day old seedlings growing on sorbitol containing medium. Values are means of 60 plants + S.E. (C) Fresh weight (FW) of 14day old seedlings growing on sorbitol containing medium. Values are means of 60 plants ± S.E. (D) Percentage of germinated wild type and stol/nced3 seeds on MS medium supplemented with 300 mM sorbitol over a 21 day time period. Germination was assessed on 60 seeds of wild type and stol/nced3 plants distributed on three replica plates (20 seeds per each genotype).
Figure 5. stol/nced3 mutant plants are sensitive to soil desiccation. (A) Representative photograph of wt and stol/nced3 mutant plants exposed to desiccation. Plants were grown in soil under standard irrigation regime until 4-5 fully expanded leaves were formed, at which stage irrigation was stopped. After 15 days, in coincidence with the appearance of clear symptoms of leaf desiccation, plants were re-watered and left to recover for 48 hours, at which time pictures were taken. (B) Shoot fresh weights of desiccation stressed wild type and stol mutant plants after re- watering. Values are means of 20 plants ± S.E.
Figure 6. PCR analysis and genome location of T-DNA insertion in stol/nced3 mutant. (A) Secondary TAIL-PCR product (lane 2) and shift of the tertiary PCR product (lane 3) in stol/nced. (B) Correct genomic integration of the T-DNA insertion was verified by diagnostic PCR; lanes: 1 (marker); 2 (DNA template: wild type; primers: T-DNA LB (3') and stol/nced3 specific primer (5'); 3 (DNA template: stol; primers: T-DNA LB (3') and stol specific primer (5'); 4 (DNA template: wt; primers: stol specific primer (3') and stol specific primer (5'); 5 (DNA template: stol; primers: stol specific primer (3') and stol specific primer (5'). Oligonucleotide sequences are reported in Table 3. (C) Physical map of the stol locus and insertion site of the T-DNA. Solid line represents fragment of the BAC clone MOA2.4. Black box indicates the coding region of the gene, arrow indicates the predicted transcription direction.
Figure 7. NCED3 transcript abundance is increased by NaCl treatment and is reduced in stol/nced3 mutant plants. Ten μg of total RNA were isolated from 21 day old stol/nced3 mutant and wt plants that were germinated and grown on 145 NaCl, separated on a denaturing formaldehyde-agarose gel and blotted onto nylon membrane. The membrane-bound RNA was hybridized with DIG-labeled DNA probe (Roche, Indianapolis, IN, USA). The probe was produced by PCR reaction using the primers listed in Table 3.
Figure 8. Complementation with the ST01/NCED3 gene reverts the soil desiccation sensitive phenotype of the stol/nced3 mutant. (A) ST01/NCED3 transcript abundance detected by RT-PCR in wt, stol/nced3, line 3-14 (pBI vector control), and line 4-6 (expressing ST01/NCED3). One μl of cDNA was used as template for the first PCR amplification (20 cycles). (B) Representative photograph of line 3-14 (pBI vector control) and line 4-6 (ρ I::ST01/NCED3). Top panel: stol/nced3 plants complemented with vector only (line 3-14) grown under standard irrigation regime (left) and exposed to desiccation (right); bottom panel: stol/nced3 plants complemented with ST01/NCED3 (line 4-6) grown under standard irrigation regime (left) and exposed to desiccation (right) showing the reverted desiccation sensitive phenotype.
Figure 9. ABA treatment abolishes the enhanced germination of stol/nced3 seeds on NaCl medium. Seeds of wild type and stol/nced3 mutant plants were surface sterilized and placed on MS medium supplemented with 145mM NaCl (A) or with 145mM NaCl+20 μM ABA (B). Germination on standard MS medium was also included (not shown). For each genotype (wild type and stol/nced3) the number of germinated seeds (out of 60) was assessed over 21 days and expressed as a percentage.
Figure 10. ABA reverts the LiCl sensitivity of stol 7nced3 seedlings to wild type. Wild type and stol seeds were surface sterilized and germinated on standard MS medium or MS supplemented with 20mM LiCl or 20mM
LiCl+20μM ABA. A representative photograph of 15day old seedlings (from 3 replica plates per treatment) is displayed.
Figure 11. Expression of the cyclin-dependent kinase inhibitor (ICK1) gene in stol/nced3 and wild type plants. Total RNA was extracted from whole seedlings that were grown for 7 days on MS medium or MS supplemented with 145mM NaCl. 20 μg of total RNA were loaded in each lane. The probe was produced by PCR reaction using the primers listed in Table 3. The bottom panel shows ethidium bromide stained total RNA gel image as a loading control.
Figure 12. Ethylene production of wild type and stol/nced3 seedlings. Seeds were germinated on standard solid MS medium and transferred at the cotyledon stage into 6ml plastic syringes (0.5g fresh weight per syringe) containing 3ml of standard liquid MS medium or liquid MS medium supplemented with 145mM NaCl. Seedlings were allowed to grow into the plastic syringes for 7 days. For each genotype (wt or stol/nced3) and for each treatment (plus or minus NaCl) six syringes were used. One ml of the 3ml air volume ejected from each syringe was taken for GC quantification of ethylene. Values are means of six samples ± S.E.
Figure 13. Ethylene-treated wild type plants mimic the stol/nced3 phenotype. Top panel: representative photographs of 15day old wild type and stol/nced3 seedlings germinated and grown in the presence or absence of 20ppm of C2H4 on Petri plates containing standard MS medium, or MS medium supplemented with 145mM NaCl or 20mM LiCl. Bottom panel: number of new leaves per plant formed after 15day treatment. Values are means of 100 plants + S.E. Figure 14. Transpiration of wild type and stol/nced3 mutant plants. (A)
Transpiration of wild type and stol/nced3 mutant plants was measured as daily water loss over a 7day time interval. Each value represents the average daily water loss of 3 plants ± S.E. (B) Daily fluctuations of rate of water loss in wild type and stol/nced3 mutant plants. The diurnal patterns displayed are representative of 3 independent experiments.
Figure 15 provides a nucleotide sequence comprising a NCED-3 promoter (SEQ ID NO: 10). Figure 16 provides a nucleotide sequence encoding NCED-3, preprocessing (SEQ ID NO: 11).
Figure 17 provides a nucleotide sequence encoding NCED-3, postprocessing (SEQ ID NO: 12).
Figure 18 provides a polynucleotide sequence comprising a NCED-3 polypeptide (SEQ ID NO: 13).
DETAILED DESCRIPTION OF THE INVENTION
The invention provides wild type 9-cis-epoxycarotenoid dioxygenase (NCED) nucleic acids and mutant 9-cis-epoxycarotenoid dioxygenase (NCED) nucleic acids that can be used to increase the salt resistance of plants.
The role of the NCED3 gene in environmental stress resistance was identified through a large-scale screen of a T-DNA insertional collection of Arabidopsis thaliana C24 ecotype plants. A mutant named stol for salt tolerant, was identified that exhibited enhanced germination on both ionic (NaCl) and non-ionic (sorbitol) hyperosmotic medium. The stol mutant was more tolerant in vitro than wild type to Na+ and K+ in terms of germination and growth, but was hypersensitive to Li+. Post germination growth of the stol mutant on sorbitol was not improved.
The involvement of the NCED3 gene was identified by locating the site of the stol mutation. A T-DNA insertion was located in the 3' end of an open reading frame on chromosome 3 that co-segregated closely with the stol phenotype. Expression of STOl gene was perturbed in the mutated plants and transcript abundance was substantially reduced. Analysis of the amino acid sequence of the disrupted gene revealed that STOl encoded a 9-cis- epoxicarotenoid dioxygenase [similar to 9-cis-epoxicarotenoid dioxygenase GB:AAF26356 (Phaseoulus vulgaris) and to NCED3 (Arabidopsis thaliana GB:AB020817)], a key enzyme in the ABA biosynthetic pathway. Consistent with this finding, stol plants were unable to accumulate ABA following a hyperosmotic stress, although their basal ABA level was not altered. Complementation of the stol mutant plant with the native gene from the wild type genome restored the wild type phenotype. Furthermore, supplementation of ABA to the growth medium also reverted the stol phenotype to wild type. Improved growth of stol mutant plants on NaCl but not sorbitol medium was associated with a reduction of both NaCl-induced expression of the ICK1 gene and ethylene accumulation compared to wild type plants. Osmotic adjustment of stol plants was substantially reduced compared to wild type plants under conditions where stol plants grew faster. The stol mutation has revealed that reduced ABA can lead to more rapid growth during hyperionic stress by a signal pathway that is apparently at least partially independent of signals that mediate osmotic adjustment.
Definitions The term "anti-sense RNA" as used herein, refers to an RNA molecule that is capable of forming a duplex with a second RNA molecule. Thus a given RNA molecule is said to be an anti-sense RNA molecule with respect to a second, complementary or partially complementary RNA molecule, i.e., the target molecule. An anti-sense RNA molecule may be complementary to a translated or an untranslated region of a target RNA molecule. The anti-sense RNA need not be perfectly complementary to the target RNA. Anti-sense RNA may or may not be the same length of the target molecule; the anti-sense RNA molecule may be either longer or shorter than the target molecule.
The term "co-suppressor RNA" refers to an RNA molecule that effects suppression of expression of a target gene where the RNA is partially homologous to an RNA molecule transcribed from the target gene. A co- suppressor RNA molecule is the RNA molecule that effects co-suppression as described in U.S. Pat. No. 5,231,020, Krol et al, Biotechniques 6:958-976 (1988), Mol et al., FEBS Lett. 268:427430 (1990), and Grierson, et al, Trends in Biotech. 9: 122-123 (1991) and similar publications. A "co-suppressor" RNA is in the sense orientation with respect to the target gene, i.e., the opposite orientation of the anti-sense orientation. The term "complementary to" is used herein to mean that the sequence of a nucleic acid strand could hybridize to all, or a portion, of a reference nucleic acid sequence. For illustration, the nucleotide sequence "TATAC" has 100% identity to a reference sequence 5'-TATAC-3' but is 100% complementary to a reference sequence 5 ' -GTAT A-3 ' .
The term "corresponds to" is used herein to mean that a polynucleotide or nucleic acid is at least partially identical (not necessarily strictly evolutionarily related) to all or a portion of a reference polynucleotide or nucleic acid sequence. As used herein, an "exogenous" nucleic acid is an isolated nucleic acid that has been introduced into a host cell. Such an "exogenous" nucleic acid is generally not identical to any DNA sequence present in the cell in its native, untransformed state. An "endogenous" or "native" nucleic acid is naturally present in a host cell or organism.
The term "inhibitory RNA", as used herein, refers to an RNA molecule that interferes with the expression of a target gene. An "inhibitory RNA" is specific for one or more target genes. An inhibitory RNA may be an anti-sense RNA with respect to an RNA molecule transcribed from the target gene. Alternatively, the target gene inhibitory RNA may be a co-suppressor RNA with respect to an RNA molecule transcribed from the target gene. The term "inhibitory RNA encoding nucleic acid" as used herein, refers to a nucleic acid, e.g., DNA, RNA, and the like, capable of being transcribed, when in functional or operational combination with a promoter, so as to produce an inhibitory RNA molecule, e.g., an anti-sense RNA or a co-supressor RNA. Anti-sense RNA encoding nucleic acids and co-supressor encoding nucleic acids are both embodiments of the inhibitory RNA encoding nucleic acids. When the inhibitory RNA is an anti-sense RNA, the inhibitory RNA transcribed from the inhibitory RNA encoding nucleic acid region of the genetic constructions of the invention is preferably perfectly complementary to the entire length of the RNA molecule or molecules for which the anti-sense RNA is specific, i.e., the target. The anti-sense RNA encoding nucleic acid in the subject vectors may encode an anti-sense RNA that forms a duplex with a non-translated region of an RNA transcript such as an intron region, or 5' untranslated region, a 3' untranslated region, and the like. Similarly, a co-suppressor encoding nucleic acid may encode an RNA that is homologous to translated or untranslated portions of a target RNA. An anti-sense RNA encoding nucleic acids may be conveniently produced by using the non-coding strand, or a portion thereof, of a DNA sequence encoding a protein of interest. The term "reduced expression," as used herein, is a relative term that refers to the level of expression of a given gene in a cell produced or modified by the claimed methods as compared to a comparable or corresponding unmodified cell, i.e., a cell lacking the exogenous nucleic acid, under a similar set of environmental conditions. Thus, a cell modified by the subject methods, i.e., a cell having "reduced expression" of the gene of interest, may express lower levels of a gene product encoded by that gene under a given set of environmental conditions, than a comparable unmodified cell under the same set of environmental conditions.
Nucleic acids encoding a NCED RNA or protein are "isolated" in that they were taken from their natural source and are no longer within the cell where they normally exist. Such isolated nucleic acids may have been at least partially prepared or manipulated in vitro, e.g., isolated from a cell in which they are normally found, purified, and amplified. Such isolated nucleic acids can also be "recombinant" in that they have been combined with exogenous nucleic acids. For example, a recombinant DNA can be an isolated DNA that is operably linked to an exogenous promoter, or to a promoter that is endogenous to a selected host cell.
As used herein, a "native" gene or nucleic acid means that the gene or nucleic acid has not been changed or manipulated in vitro, i.e., it is a "wild-type" gene or nucleic acid that has not been has not been isolated, purified, amplified or mutated in vitro.
The term "plastid" refers to the class of plant cell organelles that includes amyloplasts, chloroplasts, chromoplasts, elaioplasts, eoplasts, etioplasts, leucoplasts, and proplastids. These organelles are self-replicating, and contain what is commonly referred to as a "plastid genome," a circular DNA molecule that ranges in size from about 120 to about 217 kb, depending upon the plant species, and which usually contains an inverted repeat region. As used herein, "polypeptide" or "protein" means a continuous chain of amino acids that are all linked together by peptide bonds, except for the N- terminal and C-terminal amino acids that have amino and carboxylate groups, respectively, and that are not linked in peptide bonds. Polypeptides and proteins can have any length and can be post-translationally modified, for example, by glycosylation or phosphorylation.
As used herein, a plant cell, plant tissue or plant that is "resistant or tolerant to salt inhibition" is a plant cell, plant tissue, or plant that grows at least about 10% more than a corresponding wild type plant cell, plant tissue or plant in the presence of salt. In general, a plant cell, plant tissue, or plant that is "salt resistant" can grow in an amount of salt that normally inhibits growth of the untransformed plant cell, plant tissue, or plant, as determined by methodologies known to the art. For example, a homozygous backcross converted inbred plant transformed with a DNA molecule that encodes a NCED inhibitory RNA or a plant with a homozygous null mutation in the need locus is substantially salt resistant or tolerant because it grows in an amount of salt (e.g. sodium chloride or potassium chloride) that inhibits the growth of the corresponding, i.e., substantially isogenic, recurrent inbred plant.
In some embodiments, a salt resistant plant cell, plant tissue, plant part or plant can grow in salt levels that are about 2 to 100 times, about 3 to 50 times, about 5 to 20 times or about 7 to 10 times, higher than the levels that an untransformed plant cell, plant tissue, plant part or plant can grow.
Nucleic Acids and Proteins of the Invention The invention provides mutant and recombinant forms of 9-cis- epoxycarotenoid dioxygenase (NCED), particularly 9-cis-epoxycarotenoid dioxygenase-3 (NCED-3), that are useful for increasing the resistance of plants to environmental stresses relative to plants having the same genetic background but without the mutant or recombinant NCED nucleic acid. According to the invention, mutant alleles of various NCED genes allow plants to develop in the presence of salts such as sodium chloride or potassium chloride. In some embodiments, the open reading frame is interrupted in mutant alleles that provide this salt-resistance trait, for example, substantially no NCED mRNA is detected in plant cells having a null mutation in the NCED-3 gene. Plants comprising a genome with null mutation of the NCED-3 gene also appear to germinate faster and produce leaves faster than wild type plants of a similar background but without the NCED-3 mutation. Also according to the invention, over-expression of the certain NCED alleles within plants makes such plants tolerant to environmental stress. In particular, plants that over-express NCED alleles like the NCED-3 allele are resistant to high salt concentrations.
Many NCED nucleic acids and polypeptides can be used in the practice of the invention to achieve stress resistant plants. One of skill in the art can readily ascertain which NCED genes optimally provide resistance to environmental stress by utilizing the screening procedures provided herein along with procedures that are generally available to one of skill in the art for manipulating plants. For example, several NCED alleles are present in the Arabidopsis thaliana genome at the loci identified in Table 1 A. The sequences for these genes can be found in the NCBI database at ncbi.nlm.nih.gov. A comparison of the percent identity and percent similarity to NCED3 for the other NCED genes is provided in Table IB. Table 1 A: Arabidopsis 9-cis-epoxycarotenoid dioxygenase genes
Gene AGI ID BAC location Accession No. Accession No. for annotation for Protein
AtNCEDl At3g63520 MAA21.150 NM_116217 NP_191911.1
AINCED2 At4gl8350 F28J12.10 NM_117945 NP 93569.1
AtNCEDS At3gl4440 MOA2.4 NM_112304 NP_188062.1
AtNCED4 At4gl9170 T18B16.140 NM_118036 NP 93652.1
AtNCED5a Atlg78390 F3F9.10 NM_106486 NP 77960 AtNCED5b Atlg30100 T2H7.10 NM_102749 NP_174302.1
AtNCED6 At3g24220 MUJ8.12 NM 113327 NP 189064.1 Table IB: Sequence Identity/Similarity Comparisons
Protein name Identity Similarity
AtNCEDl 36% 54%
AtNCED2 70% 83%
AtNCED3 100% 100%
AtNCED4 39% 57% AtNCED5a 66% 78%
AtNCED5b 68% 80%
AtNCED6 54% 71%
The invention therefore provides wild type and mutant NCED (e.g.
NCED-3) nucleic acids and proteins. In particular, the invention provides NCED proteins, and NCED nucleic acids that encode RNAs and proteins that confer greater resistance to salt. In one embodiment, the NCED (e.g. NCED-3) nucleic acid that confers greater resistance to salt encodes an inhibitory RNA that can bind to an endogenous NCED (e.g. NCED-3) RNA and inhibit the function of that endogenous RNA.
The mutation that gave rise to the stol phenotype was mapped to the NCED3 gene in Arabidopsis thaliana. The Arabidopsis thaliana NCED3 gene is on chromosome 4, and has an NCBI Accession Number of NM 112304 (GI: 18400395). A sequence for the Arabidopsis thaliana NCED3 polypeptide is provided below (SEQ ID NO:29).
1 MASFTATAAV SGRWLGGNHT QPP SSSQSS DLSYCSSLPM
41 ASRVTRKL V SSALHTPPAL HFPKQSSNSP AIWKPKAKE
81 SNTKQMNLFQ RAAAAALDAA EGFLVSHEKL HPLPKTADPS 121 VQIAGNFAPV NEQPVRRNLP WGKLPDSIK GVYVRNGA P
161 LHEPVTGHHF FDGDGMVHAV KFEHGSASYA CRFTQTNRFV
201 QERQLGRPVF PKAIGELHGH TGIARLMLFY ARAAAGIVDP
241 AHGTGVANAG LVYFNGRLLA MSEDDLPYQV QITPNGDLKT
281 VGRFDFDGQL ESTMIAHPKV DPESGELFAL SYDWSKPYL 321 KYFRFSPDGT KSPDVEIQLD QPTMMHDFAI TENFVWPDQ
361 QWFKLPEMI RGGSPWYDK NKVARFGILD KYAEDSSNIK
401 WIDAPDCFCF HL NAWEEPE TDEWVIGSC MTPPDSIFNE
441 SDENLKSVLS EIRLNLKTGE STRRPIISNE DQQVNLEAGM 481 VNRNMLGRKT KFAYLALAEP PKVSGFAKV DLTTGEVKKH
521 LYGDNRYGGE PLFLPGEGGE EDEGYILCFV HDEKTWKSEL
561 QIVNAVSLEV EATVKLPSRV PYGFHGTFIG ADDLAKQW
Such an Arabidopsis thaliana NCED3 polypeptide is encoded by a nucleic acid having NCBI Accession Number NM 112304 (GI: 18400395), with the following sequence (SEQ ID NO:30).
1 AAACCAACTC TCTCTTCTCT CTTCTCTCCT CTCTTCTACA 41 AGAAGAAAAA AAACAGAGCC TTTACACATC TCAAAATCGA
81 ACTTACTTTA ACCACCAAAT ACTGATTGAA CACACTTGAA
121 AAATGGCTTC TTTCACGGCA ACGGCTGCGG TTTCTGGGAG
161 ATGGCTTGGT GGCAATCATA CTCAGCCGCC ATTATCGTCT
201 TCTCAAAGCT CCGACTTGAG TTATTGTAGC TCCTTACCTA 241 TGGCCAGTCG TGTCACACGT AAGCTCAATG TTTCATCTGC
281 GCTTCACACT CCTCCAGCTC TTCATTTCCC TAAGCAATCA 321 TCAAACTCTC CCGCCATTGT TGTTAAGCCC AAAGCCAAAG
361 AATCCAACAC TAAACAGATG AATTTGTTCC AGAGAGCGGC
401 GGCGGCAGCG TTGGACGCGG CGGAGGGTTT CCTTGTCAGC 441 CACGAGAAGC TACACCCGCT TCCTAAAACG GCTGATCCTA
481 GTGTTCAGAT CGCCGGAAAT TTTGCTCCGG TGAATGAACA
521 GCCCGTCCGG CGTAATCTTC CGGTGGTCGG AAAACTTCCC
561 GATTCCATCA AAGGAGTGTA TGTGCGCAAC GGAGCTAACC
601 CACTTCACGA GCCGGTGACA GGTCACCACT TCTTCGACGG 641 AGACGGTATG GTTCACGCCG TCAAATTCGA ACACGGTTCA
681 GCTAGCTACG CTTGCCGGTT TACTCAGACT AACCGGTTTG
721 TTCAGGAACG TCAATTGGGT CGACCGGTTT TCCCCAAAGC
761 CATCGGTGAG CTTCACGGCC ACACCGGTAT TGCCCGACTC
801 ATGCTATTCT ACGCCAGAGC TGCAGCCGGT ATAGTCGACC 841 CGGCACACGG AACCGGTGTA GCTAACGCCG GTTTGGTCTA
881 TTTCAATGGC CGGTTATTGG CTATGTCGGA GGATGATTTA
921 CCTTACCAAG TTCAGATCAC TCCCAATGGA GATTTAAAAA
961 CCGTTGGTCG GTTCGATTTT GATGGACAAT TAGAATCCAC
1001 AATGATTGCC CACCCGAAAG TCGACCCGGA ATCCGGTGAA 1041 CTCTTCGCTT TAAGCTACGA CGTCGTTTCA AAGCCTTACC 1081 TAAAATACTT CCGATTCTCA CCGGACGGAA CTAAATCACC 1121 GGACGTCGAG ATTCAGCTTG ATCAGCCAAC GATGATGCAC 1161 GATTTCGCGA TTACAGAGAA CTTCGTCGTC GTACCTGACC 1201 AGCAAGTCGT TTTCAAGCTG CCGGAGATGA TCCGCGGTGG 1241 GTCTCCGGTG GTTTACGACA AGAACAAGGT CGCAAGATTC 1281 GGGATTTTAG ACAAATACGC CGAAGATTCA TCGAACATTA 1321 AGTGGATTGA TGCTCCAGAT TGCTTCTGCT TCCATCTCTG 1361 GAACGCTTGG GAAGAGCCAG AAACAGATGA AGTCGTCGTG 1401 ATAGGGTCCT GTATGACTCC ACCAGACTCA ATTTTCAACG 1441 AGTCTGACGA GAATCTCAAG AGTGTCCTGT CTGAAATCCG 1481 CCTGAATCTC AAAACCGGTG AATCAACTCG CCGTCCGATC 1521 ATCTCCAACG AAGATCAACA AGTCAACCTC GAAGCAGGGA 1561 TGGTCAACAG AAACATGCTC GGCCGTAAAA CCAAATTCGC 1601 TTACTTGGCT TTAGCCGAGC CGTGGCCTAA AGTCTCAGGA 16 1 TTCGCTAAAG TTGATCTCAC TACTGGAGAA GTTAAGAAAC 1681 ATCTTTACGG CGATAACCGT TACGGAGGAG AGCCTCTGTT 1721 TCTCCCCGGA GAAGGAGGAG AGGAAGACGA AGGATACATC 1761 CTCTGTTTCG TTCACGACGA GAAGACATGG AAATCGGAGT 1801 TACAGATAGT TAACGCCGTT AGCTTAGAGG TTGAAGCAAC 18 1 GGTTAAACTT CCGTCAAGGG TTCCGTACGG ATTTCACGGT 1881 ACATTCATCG GAGCCGATGA TTTGGCGAAG CAGGTCGTGT 1921 GAGTTCTTAT GTGTAAATAC GCACAAAATA CATATACGTG 1961 ATGAAGAAGC TTCTAGAAGG AAAAGAGAGA GCGAGATTTA 2001 CCAGTGGGAT GCTCTGCATA TACGTCCCCG GAATCTGCTC 2041 CTCTGTTTTT TTTTTTTTGC TCTGTTTCTT GTTTGTTGTT 2081 TCTTTTGGGG TGCGGTTTGC TAGTTCCCTT TTTTTTGGGG 2121 TCAATCTAGA AATCTGAAAG ATTTTGAGGG ACCAGCTTGT 2161 AGCTTTTGGG CTGTAGGGTA GCCTAGCCGT TCGAGCTCAG 2201 CTGGTTTCTG TTATTCTTTC ACTTATTGTT CATCGTAATG 2241 AGAAGTATAT AAAATATTAA ACAACAAAGA TATGTTTGTA 2281 TATGTGCATG AATTAAGGAA CATTTTTTTT CCAA The invention may also be practiced with an NCED polypeptide with the following sequence (SEQ ID NO: 13):
1 MASFTATAAV SGRW GGNHT QPPLSSSQSS DLSYCSSLPM
41 ASRVTRKLNV SSALHTPPAL HFPKQSSNSP AIWKPKAKE 81 SNTKQMNLFQ RAAAAALDAA EGFLVSHEKL HPLPKTADPS
121 VQIAGNFAPV NEQPVRRNLP WGKLPDSIK GVYVRNGA P
161 LHEPVTGHHF FDGDGMVHAV KFEHGSASYA CRFTQTNRFV
201 QERQLGRPVF PKAIGELHGH TGIARLMLFY ARAAAGIVDP 241 AHGTGVANAG LVYFNGRLLA MSEDDLPYQV QITPNGDLKT 281 VGRFDFDGQL ESTMIAHPKV DPESGE FAL SYDWSKPYL 321 KYFRFSPDGT KSPDVEIQLD QPTMMHDFAI TENFVWPDQ
361 QWFKLPEMI RGGSPWYDK NKVARFGILD KYAEDSSNIK 401 WIDAPDCFCF HLW AWEEPE TDEVWIGSC MTPPDSIFNE 441 SDENLKSVLS EIRLNLKTGE STRRPIISNE DQQVNLEAGM 481 VNRNMLGRKT KFAYLALAEP WPKVSGFAKV DLTTGEVKKH 521 LYGDNRYGGE PLFLPGEGGE EDEGYILCFV HDEKTWKSEL 561 QIVNAVSLEV EATVKLPSRV PYGFHGTFIG ADDLAKQW
The invention also provides a nucleic acid that encodes a polypeptide having SEQ ID NO:13; this nucleic has SEQ ID NO:ll or SEQ ID NO:12:
The invention also provides a nucleic acid that encodes a related
Arabidopsis thaliana NCED RNA and/or a related NCED polypeptide that can be used in the practice of the invention, where the nucleic acid can be found as
NCBI Accession Number gi: 18400395, and has the following sequence (SEQ ID NO: 14):
1 AAACCAACTC TCTCTTCTCT CTTCTCTCCT CTCTTCTACA
41 AGAAGAAAAA AAACAGAGCC TTTACACATC TCAAAATCGA
81 ACTTACTTTA ACCACCAAAT ACTGATTGAA CACACTTGAA
121 AAATGGCTTC TTTCACGGCA ACGGCTGCGG TTTCTGGGAG 161 ATGGCTTGGT GGCAATCATA CTCAGCCGCC ATTATCGTCT
201 TCTCAAAGCT CCGACTTGAG TTATTGTAGC TCCTTACCTA
241 TGGCCAGTCG TGTCACACGT AAGCTCAATG TTTCATCTGC
281 GCTTCACACT CCTCCAGCTC TTCATTTCCC TAAGCAATCA
321 TCAAACTCTC CCGCCATTGT TGTTAAGCCC AAAGCCAAAG 361 AATCCAACAC TAAACAGATG AATTTGTTCC AGAGAGCGGC
401 GGCGGCAGCG TTGGACGCGG CGGAGGGTTT CCTTGTCAGC 441 CACGAGAAGC TACACCCGCT TCCTAAAACG GCTGATCCTA 481 GTGTTCAGAT CGCCGGAAAT TTTGCTCCGG TGAATGAACA 521 GCCCGTCCGG CGTAATCTTC CGGTGGTCGG AAAACTTCCC
561 GATTCCATCA AAGGAGTGTA TGTGCGCAAC GGAGCTAACC
601 CACTTCACGA GCCGGTGACA GGTCACCACT TCTTCGACGG
641 AGACGGTATG GTTCACGCCG TCAAATTCGA ACACGGTTCA
681 GCTAGCTACG CTTGCCGGTT TACTCAGACT AACCGGTTTG 721 TTCAGGAACG TCAATTGGGT CGACCGGTTT TCCCCAAAGC
761 CATCGGTGAG CTTCACGGCC ACACCGGTAT TGCCCGACTC
801 ATGCTATTCT ACGCCAGAGC TGCAGCCGGT ATAGTCGACC
841 CGGCACACGG AACCGGTGTA GCTAACGCCG GTTTGGTCTA
881 TTTCAATGGC CGGTTATTGG CTATGTCGGA GGATGATTTA 921 CCTTACCAAG TTCAGATCAC TCCCAATGGA GATTTAAAAA
961 CCGTTGGTCG GTTCGATTTT GATGGACAAT TAGAATCCAC
1001 AATGATTGCC CACCCGAAAG TCGACCCGGA ATCCGGTGAA
1041 CTCTTCGCTT TAAGCTACGA CGTCGTTTCA AAGCCTTACC
1081 TAAAATACTT CCGATTCTCA CCGGACGGAA CTAAATCACC 1121 GGACGTCGAG ATTCAGCTTG ATCAGCCAAC GATGATGCAC
1161 GATTTCGCGA TTACAGAGAA CTTCGTCGTC GTACCTGACC
1201 AGCAAGTCGT TTTCAAGCTG CCGGAGATGA TCCGCGGTGG 1241 GTCTCCGGTG GTTTACGACA AGAACAAGGT CGCAAGATTC 1281 GGGATTTTAG ACAAATACGC CGAAGATTCA TCGAACATTA 1321 AGTGGATTGA TGCTCCAGAT TGCTTCTGCT TCCATCTCTG
1361 GAACGCTTGG GAAGAGCCAG AAACAGATGA AGTCGTCGTG
1401 ATAGGGTCCT GTATGACTCC ACCAGACTCA ATTTTCAACG 1441 AGTCTGACGA GAATCTCAAG AGTGTCCTGT CTGAAATCCG 1481 CCTGAATCTC AAAACCGGTG AATCAACTCG CCGTCCGATC 1521 ATCTCCAACG AAGATCAACA AGTCAACCTC GAAGCAGGGA 1561 TGGTCAACAG AAACATGCTC GGCCGTAAAA CCAAATTCGC 1601 TTACTTGGCT TTAGCCGAGC CGTGGCCTAA AGTCTCAGGA 1641 TTCGCTAAAG TTGATCTCAC TACTGGAGAA GTTAAGAAAC 1681 ATCTTTACGG CGATAACCGT TACGGAGGAG AGCCTCTGTT 1721 TCTCCCCGGA GAAGGAGGAG AGGAAGACGA AGGATACATC 1761 CTCTGTTTCG TTCACGACGA GAAGACATGG AAATCGGAGT 1801 TACAGATAGT TAACGCCGTT AGCTTAGAGG TTGAAGCAAC 1841 GGTTAAACTT CCGTCAAGGG TTCCGTACGG ATTTCACGGT 1881 ACATTCATCG GAGCCGATGA TTTGGCGAAG CAGGTCGTGT 1921 GAGTTCTTAT GTGTAAATAC GCACAAAATA CATATACGTG 1961 ATGAAGAAGC TTCTAGAAGG AAAAGAGAGA GCGAGATTTA 2001 CCAGTGGGAT GCTCTGCATA TACGTCCCCG GAATCTGCTC 2041 CTCTGTTTTT TTTTTTTTGC TCTGTTTCTT GTTTGTTGTT 2081 TCTTTTGGGG TGCGGTTTGC TAGTTCCCTT TTTTTTGGGG 2121 TCAATCTAGA AATCTGAAAG ATTTTGAGGG ACCAGCTTGT 2161 AGCTTTTGGG CTGTAGGGTA GCCTAGCCGT TCGAGCTCAG 2201 CTGGTTTCTG TTATTCTTTC ACTTATTGTT CATCGTAATG 2241 AGAAGTATAT AAAATATTAA ACAACAAAGA TATGTTTGTA 2281 TATGTGCATG AATTAAGGAA CATTTTTTTT CCAA
The invention further provides a nucleic acid that encodes a related Arabidopsis thaliana NCED RNA and/or a related NCED polypeptide that can be used in the practice of the invention, where the nucleic acid can be found as NCBI Accession Number gi:15810432 and has the following sequence (SEQ ID NO: 15):
1 AAACCAACTC TCTCTTCTCT CTTCTCTCCT CTCTTCTACA 41 AGAAGAAAAA AAACAGAGCC TTTACACATC TCAAAATCGA
81 ACTTACTTTA ACCACCAAAT ACTGATTGAA CACACTTGAA
121 AAATGGCTTC TTTCACGGCA ACGGCTGCGG TTTCTGGGAG
161 ATGGCTTGGT GGCAATCATA CTCAGCCGCC ATTATCGTCT
201 TCTCAAAGCT CCGACTTGAG TTATTGTAGC TCCTTACCTA 241 TGGCCAGTCG TGTCACACGT AAGCTCAATG TTTCATCTGC
281 GCTTCACACT CCTCCAGCTC TTCATTTCCC TAAGCAATCA 321 TCAAACTCTC CCGCCATTGT TGTTAAGCCC AAAGCCAAAG
361 AATCCAACAC TAAACAGATG AATTTGTTCC AGAGAGCGGC 401 GGCGGCAGCG TTGGACGCGG CGGAGGGTTT CCTTGTCAGC 441 CACGAGAAGC TACACCCGCT TCCTAAAACG GCTGATCCTA
481 GTGTTCAGAT CGCCGGAAAT TTTGCTCCGG TGAATGAACA
521 GCCCGTCCGG CGTAATCTTC CGGTGGTCGG AAAACTTCCC
561 GATTCCATCA AAGGAGTGTA TGTGCGCAAC GGAGCTAACC 601 CACTTCACGA GCCGGTGACA GGTCACCACT TCTTCGACGG
641 AGACGGTATG GTTCACGCCG TCAAATTCGA ACACGGTTCA
681 GCTAGCTACG CTTGCCGGTT TACTCAGACT AACCGGTTTG
721 TTCAGGAACG TCAATTGGGT CGACCGGTTT TCCCCAAAGC
761 CATCGGTGAG CTTCACGGCC ACACCGGTAT TGCCCGACTC 801 ATGCTATTCT ACGCCAGAGC TGCAGCCGGT ATAGTCGACC
841 CGGCACACGG AACCGGTGTA GCTAACGCCG GTTTGGTCTA
881 TTTCAATGGC CGGTTATTGG CTATGTCGGA GGATGATTTA
921 CCTTACCAAG TTCAGATCAC TCCCAATGGA GATTTAAAAA
961 CCGTTGGTCG GTTCGATTTT GATGGACAAT TAGAATCCAC 1001 AATGATTGCC CACCCGAAAG TCGACCCGGA ATCCGGTGAA
1041 CTCTTCGCTT TAAGCTACGA CGTCGTTTCA AAGCCTTACC
1081 TAAAATACTT CCGATTCTCA CCGGACGGAA CTAAATCACC
1121 GGACGTCGAG ATTCAGCTTG ATCAGCCAAC GATGATGCAC
1161 GATTTCGCGA TTACAGAGAA CTTCGTCGTC GTACCTGACC 1201 AGCAAGTCGT TTTCAAGCTG CCGGAGATGA TCCTCGGTGG
1241 GTCTCCGGTG GTTTACGACA AGAACAAGGT CGCAAGATTC
1281 GGGATTTTAG ACAAATACGC CGAAGATTCA TCGAACATTA
1321 AGTGGATTGA TGCTCCAGAT TGCTTCTGCT TCCATCTCTG
1361 GAACGCTTGG GAAGAGCCAG AAACAGATGA AGTCGTCGTG 1401 ATAGGGTCCT GTATGACTCC ACCAGACTCA ATTTTCAACG
1441 AGTCTGACGA GAATCTCAAG AGTGTCCTGT CTGAAATCCG
1481 CCTGAATCTC AAAACCGGTG AATCAACTCG CCGTCCGATC
1521 ATCTCCAACG AAGATCAACA AGTCAACCTC GAAGCAGGGA
1561 TGGTCAACAG AAACATGCTC GGCCGTAAAA CCAAATTCGC 1601 TTACTTGGCT TTAGCCGAGC CGTGGCCTAA AGTCTCAGGA
1641 TTCGCTAAAG TTGATCTCAC TACTGGAGAA GTTAAGAAAC
1681 ATCTTTACGG CGATAACCGT TACGGAGGAG AGCCTCTGTT
1721 TCTCCCCGGA GAAGGAGGAG AGGAAGACGA AGGATACATC
1761 CTCTGTTTCG TTCACGACGA GAAGACATGG AAATCGGAGT 1801 TACAGATAGT TAACGCCGTT AGCTTAGAGG TTGAAGCAAC 1841 GGTTAAACTT CCGTCAAGGG TTCCGTACGG ATTTCACGGT 1881 ACATTCATCG GAGCCGATGA TTTGGCGAAG CAGGTCGTGT 1921 GAGTTCTTAT GTGTAAATAC GCACAAAATA CATATACGTG 1961 ATGAAGAAGC TTCTAGAAGG AAAAGAGAGA GCGAGATTTA 2001 CCAGTGGGAT GCTCTGCATA TACGTCCCCG GAATCTGCTC 2041 CTCTGTTTTT TTTTTTTTTG CTCTGTTTCT TGTTTGTTGT 2081 TTCTTTTGGG GTGCGGTTTG CTAGTTCCCT TTTTTTTGGG 2121 GTCAATCTAG AAATCTGAAA GATTTTGAGG GACCAGCTTG 2161 TAGCTTTTGG GCTGTAGGGT AGCCTAGCCG TTCGAGCTCA 2201 GCTGGTTTCT GTTATTCTTT CACTTATTGT TCATCGTAAT 2241 GAGAAGTATA TAAAATATTA AACAACAAAG ATATGTTTGT 2281 ATATGTGCAT GAATTAAGGA ACATTTTTTT TTCCGAAAAA 2321 AAAAAAAAAA A
The invention also provides a nucleic acid that encodes a related Arabidopsis thaliana NCED RNA and/or a related NCED polypeptide, where the nucleic acid can be found as NCBI Accession Number gi:16416373 and has the following sequence (SEQ ID NO:16):
1 GTCGACTCTA GGCCTCACTG GCCTAATACG ACTCACTATA
41 GGGAGCTCGA GGATCAATAG AAAAATTAAC CTATTGTGCT
81 TATACTTTTA CAATTATCAT ATTCCACGTA AATCATAAAT
121 TCAAAGCTTT GCATGGTGAC ATAAACAACA TATTTTGAAA 161 ACAAATACAT ATCCAAAAGT GACGATGATT TAAAAATTAT
201 GTCGGTAATT GAGTATTTGT TGCCAACAAG TATTTGAGTA
241 AGTTAATATA AACGTAAATG TAAGAATAAT CCGATAACAA
281 AAGTATAAAA CATAAATGTA AGAATCCCTG TTGAGAGTGT
321 TGTCCAAATA GAAAAAGGAG TGGTCGAACA TCTCTATAGA 361 TCTCGTCAAC TAAAATCCAA GTGAAAAAAC ATTATCACCA
401 GACAATTCAA AGTTAATATC TTAGAGTAGA GAGCGCACGT
441 TAATGATGTA ACACACCGAC TTTTGTAGAT AAATTGCGTG
481 CGTAGGGTAT TAGTGTTCAA TTAAGGATTT TGTTCACTTC
521 TTCAAGTTAT GAATATTTTT GGGAAACTGG TTTCTAGGAT 561 AATAGACAAC TGAAAGAGGT ACTACTATTT AGTGTTCAAT
601 GTTTTGTTTA ATTCAGGTAT ATATTGACAC AGGCACAAGT
641 ATTTCGTATG GTTAATTGCG TTAGCTATTT CAGACTTATT
681 AAATTACATA ATGATTAGAT GAGATCGCGA AGTATTAGAG 721 TTCTTGCGTC CGAATAATTG ATAGATTCTA TACCCTAAAA
761 AAAAGGTCGG AGATCACCCT CTAAATTATA AGTATAACAT
801 AAATCTAATT GTACGGACAT AAACTCATGA CTCAAGCAAT
841 AGGACAAGCC AAAAAAAATT CCAATTATTG TGTTACTCTA
881 TTCTTCTAAA TTTGAACACT AATAGACTAT GACATATGAG 921 TATATAATGT GAAGTCTTAA GATATTTTCA TGTGGGAGAT
961 GAATAGGCCA AGTTGGAGTC TGCAAACAAG AAGCTCTTGA
1001 GCCACGACAT AAGCCAAGTT GATGACCGTA ATTAATGAAA
1041 CTAAATGTGT GTGGTTATAT ATTAGGGACC CATGGCCATA
1081 TACACAATTT TTGTTTCTGT CGATAGCATG CGTTTATATA 1121 TATTTCTAAA AAAACTAACA TATTTACTGG ATTTGAGTTC
1161 GAATATTGAC ACTAATATAA ACTACGTACC AAACTACATA
1201 TGTTTATCTA TATTTGATTG ATCGAAGAAT TCTGAACTGT
1241 TTTAGAAAAT TTCAATACAC TTAACTTCAT CTTACAACGG
1281 TAAAAGAAAT CACCACTAGA CAAACAATGC CTCATAATGT 1321 CTCGAACCCT CAAACTCAAG AGTATACATT TTACTAGATT
1361 AGAGAATTTG ATATCCTCAA GTTGCCAAAG AATTGGAAGC
1401 TTTTGTTACC AAACTTAGAA ACAGAAGAAG CCACAAAAAA 1441 AGACAAAGGG AGTTAAAGAT TGAAGTGATG CATTTGTCTA 1481 AGTGTGAAAG GTCTCAAGTC TCAACTTTGA ACCATAATAA 1521 CATTACTCAC ACTCCCTTTT TTTTTCTTTT TTTTTCCCAA
1561 AGTACCCTTT TTAATTCCCT CTATAACCCA CTCACTCCAT
1601 TCCCTCTTTC TGTCACTGAT TCAACACGTG GCCACACTGA
1641 TGGGATCCAC CTTTCCTCTT ACCCACCTCC CGGTTTATAT
1681 AAACCCTTCA CAACACTTCA TCGCTCTCAA ACCAACTCTC 1721 TCTTCTCTCT TCTCTCCTCT CTTCTACAAG AAGAAAAAAA
1761 ACAGAGCCTT TACACATCTC AAAATCGAAC TTACTTTAAC
1801 CACCAAATAC TGATTGAACA CACTTGAAAA ATGGCTTCTT
1841 TCACGGCAAC GGCTGCGGTT TCTGGGAGAT GGCTTGGTGG
1881 CAATCATACT CAGCCGCCAT TATCGTCTTC TCAAAGCTCC 1921 GACTTGAGTT ATTGTAGCTC CTTACCTATG GCCAGTCGTG
1961 TCACACGTAA GCTCAATGTT TCATCTGCGC TTCACACTCC
2001 TCCAGCTCTT CATTTCCCTA AGCAATCATC AAACTCTCCC
2041 GCCATTGTTG TTAAGCCCAA AGCCAAAGAA TCCAACACTA 2081 AACAGATGAA TTTGTTCCAG AGAGCGGCGG CGGCAGCGTT
2121 GGACGCGGCG GAGGGTTTCC TTGTCAGCCA CGAGAAGCTA
2161 CACCCGCTTC CTAAAACGGC TGATCCTAGT GTTCAGATCG
2201 CCGGAAATTT TGCTCCGGTG AATGAACAGC CCGTCCGGCG 2241 TAATCTTCCG GTGGTCGGAA AACTTCCCGA TTCCATCAAA 2281 GGAGTGTATG TGCGCAACGG AGCTAACCCA CTTCACGAGC
2321 CGGTGACAGG TCACCACTTC TTCGACGGAG ACGGTATGGT
2361 TCACGCCGTC AAATTCGAAC ACGGTTCAGC TAGCTACGCT
2401 TGCCGGTTTA CTCAGACTAA CCGGTTTGTT CAGGAACGTC 2441 AATTGGGTCG ACCGGTTTTC CCCAAAGCCA TCGGTGAGCT 2481 TCACGGCCAC ACCGGTATTG CCCGACTCAT GCTATTCTAC
2521 GCCAGAGCTG CAGCCGGTAT AGTCGACCCG GCACACGGAA
2561 CCGGTGTAGC TAACGCCGGT TTGGTCTATT TCAATGGCCG
2601 GTTATTGGCT ATGTCGGAGG ATGATTTACC TTACCAAGTT
2641 CAGATCACTC CCAATGGAGA TTTAAAAACC GTTGGTCGGT 2681 TCGATTTTGA TGGACAATTA GAATCCACAA TGATTGCCCA
2721 CCCGAAAGTC GACCCGGAAT CCGGTGAACT CTTCGCTTTA
2761 AGCTACGACG TCGTTTCAAA GCCTTACCTA AAATACTTCC
2801 GATTCTCACC GGACGGAACT AAATCACCGG ACGTCGAGAT
2841 TCAGCTTGAT CAGCCAACGA TGATGCACGA TTTCGCGATT 2881 ACAGAGAACT TCGTCGTCGT ACCTGACCAG CAAGTCGTTT
2921 TCAAGCTGCC GGAGATGATC CGCGGTGGGT CTCCGGTGGT
2961 TTACGACAAG AACAAGGTCG CAAGATTCGG GATTTTAGAC
3001 AAATACGCCG AAGATTCATC GAACATTAAG TGGATTGATG 3041 CTCCAGATTG CTTCTGCTTC CATCTCTGGA ACGCTTGGGA 3081 AGAGCCAGAA ACAGATGAAG TCGTCGTGAT AGGGTCCTGT
3121 ATGACTCCAC CAGACTCAAT TTTCAACGAG TCTGACGAGA
3161 ATCTCAAGAG TGTCCTGTCT GAAATCCGCC TGAATCTCAA
3201 AACCGGTGAA TCAACTCGCC GTCCGATCAT CTCCAACGAA
3241 GATCAACAAG TCAACCTCGA AGCAGGGATG GTCAACAGAA 3281 ACATGCTCGG CCGTAAAACC AAATTCGCTT ACTTGGCTTT 3321 AGCCGAGCCG TGGCCTAAAG TCTCAGGATT CGCTAAAGTT
3361 GATCTCACTA CTGGAGAAGT TAAGAAACAT CTTTACGGCG 3401 ATAACCGTTA CGGAGGAGAG CCTCTGTTTC TCCCCGGAGA 3441 AGGAGGAGAG GAAGACGAAG GATACATCCT CTGTTTCGTT
3481 CACGACGAGA AGACATGGAA ATCGGAGTTA CAGATAGTTA 3521 ACGCCGTTAG CTTAGAGGTT GAAGCAACGG TTAAACTTCC 3561 GTCAAGGGTT CCGTACGGAT TTCACGGTAC ATTCATCGGA 3601 GCCGATGATT TGGCGAAGCA GGTCGTGTGA GTTCTTATGT 3641 GTAAATACGC ACAAAATACA TATACGTGAT GAAGAAGCTT
3681 CTAGAAGGAA AAGAGAGAGC GAGATTTACC AGTGGGATGC
3721 TCTGCATATA CGTCCCCGGA ATCTGCTCCT CTGTTTTTTT
3761 TTTTTTGCTC TGTTTCTTGT TTGTTGTTTC TTTTGGGGTG
3801 CGGTTTGCTA GTTCCCTTTT TTTTGGGGTC AATCTAGAAA 3841 TCTGAAAGAT TTTGGGATCC GCGGCCGCC
The invention also provides a nucleic acid that encodes a related
Arabidopsis thaliana NCED RNA and/or a related NCED polypeptide, where the nucleic acid can be found as NCBI Accession Number gi:5041970. Another example of an NCED nucleic acid and polypeptide that may be used in the practice of the invention is from the Arabidopsis thaliana NCEDl gene on chromosome 3, having NCBI Accession Number NM 116217.1
(GI: 18412829). A sequence for the Arabidopsis thaliana NCEDl polypeptide is provided for illustration below (SEQ ID NO:25).
1 MAEKLSDGSS IISVHPRPSK GFSSKLLDLL ERLWKLMHD
41 ASLPLHYLSG NFAPIRDETP PVKDLPVHGF LPECLNGEFV
81 RVGPNPKFDA VAGYHWFDGD GMIHGVRIKD GKATYVSRYV
121 KTSRLKQEEF FGAAKFMKIG DLKGFFGLLM VNVQQLRTKL 161 KILDNTYGNG TANTALVYHH GKLLALQEAD KPYVIKVLED
201 GDLQTLGIID YDKRLTHSFT AHPKVDPVTG EMFTFGYSHT
241 PPYLTYRVIS KDGIMHDPVP ITISEPIMMH DFAITETYAI
281 FMDLPMHFRP KEMVKEKKMI YSFDPTKKAR FGVLPRYAKD
321 ELMIRWFELP NCFIFHNANA WEEEDEWLI TCRLENPDLD 361 MVSGKVKEKL ENFGNELYEM RFNMKTGSAS QKKLSASAVD 401 FPRINECYTG KKQRYVYGTI LDSIAKVTGI IKFDLHAEAE 441 TGKRMLEVGG NIKGIYDLGE GRYGSEAIYV PRETAEEDDG 481 YLIFFVHDEN TGKSCVTVID AKTMSAEPVA WELPHRVPY 521 GFHALFVTEE QLQEQTLI
Such an Arabidopsis thaliana NCEDl polypeptide is encoded by a nucleic acid having NCBI Accession Number NM 116217.1 (GI: 18412829), with the following sequence (SEQ ID NO:26). 1 ATGGCGGAGA AACTCAGTGA TGGCAGCAGC ATCATCTCAG
41 TCCATCCTAG ACCCTCCAAG GGTTTCTCCT CGAAGCTTCT
81 CGATCTTCTC GAGAGACTTG TTGTCAAGCT CATGCACGAT
121 GCTTCTCTCC CTCTCCACTA CCTCTCAGGC AACTTCGCTC
161 CCATCCGTGA TGAAACTCCT CCCGTCAAGG ATCTCCCCGT 201 CCATGGATTT CTTCCCGAAT GCTTGAATGG TGAATTTGTG
241 AGGGTTGGTC CAAACCCCAA GTTTGATGCT GTCGCTGGAT
281 ATCACTGGTT TGATGGAGAT GGGATGATTC ATGGGGTACG 321 CATCAAAGAT GGGAAAGCTA CTTATGTTTC TCGATATGTT
361 AAGACATCAC GTCTTAAGCA GGAAGAGTTC TTCGGAGCTG 401 CCAAATTCAT GAAGATTGGT GACCTTAAGG GGTTTTTCGG
441 ATTGCTAATG GTCAATGTCC AACAGCTGAG AACGAAGCTC 481 AAAATATTGG ACAACACTTA TGGAAATGGA ACTGCCAATA 521 CAGCACTCGT ATATCACCAT GGAAAACTTC TAGCATTACA 561 GGAGGCAGAT AAGCCGTACG TCATCAAAGT TTTGGAAGAT 601 GGAGACCTGC AAACTCTTGG TATAATAGAT TATGACAAGA 641 GATTGACCCA CTCCTTCACT GCTCACCCAA AAGTTGACCC 681 GGTTACGGGT GAAATGTTTA CATTCGGCTA TTCGCATACG 721 CCACCTTATC TCACATACAG AGTTATCTCG AAAGATGGCA 761 TTATGCATGA CCCAGTCCCA ATTACTATAT CAGAGCCTAT 801 CATGATGCAT GATTTTGCTA TTACTGAGAC TTATGCAATC 841 TTCATGGATC TTCCTATGCA CTTCAGGCCA AAGGAAATGG 881 TGAAAGAGAA GAAAATGATA TACTCATTTG ATCCCACAAA 921 AAAGGCTCGT TTTGGTGTTC TTCCACGCTA TGCCAAGGAT 961 GAACTTATGA TTAGATGGTT TGAGCTTCCC AACTGCTTTA 1001 TTTTCCACAA CGCCAATGCT TGGGAAGAAG AGGATGAAGT 1041 CGTCCTCATC ACTTGTCGTC TTGAGAATCC AGATCTTGAC 1081 ATGGTCAGTG GGAAAGTGAA AGAAAAACTC GAAAATTTTG 1121 GCAACGAACT GTACGAAATG AGATTCAACA TGAAAACGGG 1161 CTCAGCTTCT CAAAAAAAAC TATCCGCATC TGCGGTTGAT 1201 TTCCCCAGAA TCAATGAGTG CTACACCGGA AAGAAACAGA 1241 GATACGTATA TGGAACAATT CTGGACAGTA TCGCAAAGGT 1281 TACCGGAATC ATCAAGTTTG ATCTGCATGC AGAAGCTGAG 1321 ACAGGGAAAA GAATGCTGGA AGTAGGAGGT AATATCAAAG 1361 GAATATATGA CCTGGGAGAA GGCAGATATG GTTCAGAGGC 1401 TATCTATGTT CCGCGTGAGA CAGCAGAAGA AGACGACGGT 1441 TACTTGATAT TCTTTGTTCA TGATGAAAAC ACAGGGAAAT 1481 CATGCGTGAC TGTGATAGAC GCAAAAACAA TGTCGGCTGA 1521 ACCGGTGGCA GTGGTGGAGC TGCCGCACAG GGTCCCATAT 1561 GGCTTCCATG CCTTGTTTGT TACAGAGGAA CAACTCCAGG 1601 AACAAACTCT TATATAA
Another example of an NCED nucleic acid or polypeptide is the
Arabidopsis thaliana NCED2 gene on chromosome 4, having NCBI Accession Number NM 117945 (GL18415070). A sequence for the Arabidopsis thaliana
NCED2 polypeptide is provided below (SEQ ID NO:27).
1 MVSLLTMPMS GGIKT PQAQ IDLGFRPIKR QPKVIKCTVQ
41 IDVTELTKKR QLFTPRTTAT PPQHNPLRLN IFQKAAAIAI
81 DAAERALISH EQDSPLPKTA DPRVQIAGNY SPVPESSVRR 121 NLTVEGTIPD CIDGVYIRNG ANPMFEPTAG HHLFDGDGMV
161 HAVKITNGSA SYACRFTKTE RLVQEKRLGR PVFPKAIGEL
201 HGHSGIARLM LFYARGLCGL INNQNGVGVA NAGLVYFNNR
241 LLAMSEDDLP YQLKITQTGD LQTVGRYDFD GQLKSAMIAH
281 PKLDPVTKEL HALSYDWKK PYLKYFRFSP DGVKSPELEI 321 PLETPTMIHD FAITENFWI PDQQWFKLG EMISGKSPW
361 FDGEKVSRLG IMPKDATEAS QII VNSPET FCFHLWNA E
401 SPETEEIWI GSCMSPADSI FNERDESLRS VLSEIRINLR
441 TRKTTRRSLL VNEDVNLEIG MVNRNRLGRK TRFAFLAIAY
481 PWPKVSGFAK VDLCTGEMKK YIYGGEKYGG EPFFLPGNSG 521 NGEENEDDGY IFCHVHDEET KTSELQIINA VNLKLEATIK 561 LPSRVPYGFH GTFVDSNELV DQL
Such an Arabidopsis thaliana NCED2 polypeptide is encoded by a nucleic acid having NCBI Accession Number NM 117945 (G 18415070), with the following sequence (SEQ ID NO:28).
1 ATGGTTTCTC TTCTTACAAT GCCGATGAGT GGTGGTATTA
41 AAACATGGCC TCAAGCCCAA ATTGATTTGG GTTTTAGGCC 81 CATTAAAAGA CAACCGAAGG TTATTAAATG CACGGTGCAG
121 ATCGACGTAA CGGAATTAAC CAAAAAACGC CAATTATTTA
161 CACCCAGAAC CACCGCTACT CCGCCGCAGC ATAATCCTCT
201 CCGGCTAAAC ATCTTCCAGA AAGCGGCGGC GATTGCGATC 241 GACGCGGCTG AGCGTGCATT AATCTCACAC GAGCAAGATT 281 CTCCACTTCC CAAAACCGCT GATCCACGTG TTCAGATTGC
321 CGGGAATTAT TCCCCGGTAC CGGAATCTTC CGTCCGGCGA
361 AACCTCACCG TCGAAGGAAC AATCCCTGAC TGCATTGACG 401 GTGTTTATAT CCGTAACGGC GCGAATCCGA TGTTTGAGCC 441 AACAGCTGGG CACCATTTAT TCGACGGAGA CGGAATGGTT 481 CACGCAGTTA AAATAACCAA CGGTTCAGCT AGCTACGCAT 521 GCCGGTTTAC AAAAACCGAG AGATTGGTTC AGGAAAAACG 561 ATTGGGTCGA CCAGTTTTCC CGAAAGCAAT CGGCGAGCTT 601 CACGGTCACT CGGGAATCGC ACGTTTGATG CTGTTTTACG 641 CACGTGGGCT TTGTGGTCTG ATCAACAACC AAAACGGCGT 681 CGGAGTAGCA AACGCCGGTT TGGTTTACTT TAATAACCGG 721 CTTTTAGCTA TGTCAGAAGA CGATTTACCG TACCAATTAA 761 AAATTACTCA AACCGGCGAT CTCCAAACCG TTGGACGTTA 801 CGATTTCGAC GGTCAGTTAA AATCCGCAAT GATAGCTCAC 841 CCGAAACTGG ACCCGGTTAC GAAGGAGCTT CACGCGTTAA 881 GCTACGACGT CGTTAAGAAA CCTTACCTGA AATACTTCAG
921 ATTCTCGCCA GACGGCGTTA AATCGCCGGA ATTGGAGATC
961 CCGCTCGAAA CTCCGACGAT GATTCACGAT TTCGCTATAA
1001 CGGAGAATTT TGTGGTGATT CCTGATCAAC AAGTCGTGTT
1041 CAAGCTCGGC GAGATGATTT CCGGTAAATC TCCGGTTGTT 1081 TTCGACGGAG AAAAGGTTTC CCGATTGGGG ATAATGCCCA 1121 AGGACGCGAC AGAAGCTTCT CAGATAATCT GGGTGAACTC 1161 TCCGGAGACG TTCTGTTTTC ATCTCTGGAA TGCATGGGAA 1201 TCGCCGGAGA CGGAGGAGAT TGTGGTGATC GGATCGTGTA 1241 TGTCGCCGGC GGATTCAATC TTCAACGAGA GAGACGAGAG
1281 CTTGAGAAGC GTTTTGTCGG AGATCAGGAT AAACCTCAGA 1321 ACACGTAAAA CCACGCGTCG TTCGTTGTTG GTTAACGAGG
1361 ATGTAAATTT AGAGATTGGT ATGGTTAACC GGAACCGGTT
1401 AGGAAGAAAA ACCCGGTTCG CGTTTTTGGC TATTGCTTAT 1441 CCTTGGCCAA AAGTTTCCGG TTTCGCTAAG GTCGATCTTT
1481 GCACCGGTGA GATGAAAAAA TATATTTACG GCGGTGAGAA 1521 ATATGGCGGC GAACCGTTTT TCTTGCCCGG CAACTCCGGT 1561 AACGGCGAAG AAAATGAAGA TGACGGTTAT ATATTTTGTC 1601 ACGTTCATGA CGAAGAAACA AAGACATCAG AGCTTCAGAT 1641 TATTAACGCT GTTAATTTAA AGCTTGAAGC TACGATTAAA 1681 CTACCGTCTA GAGTACCGTA TGGGTTTCAT GGCACATTTG 1721 TGGATTCGAA TGAACTCGTT GATCAATTAT AA
The invention also provides a nucleic acid that encodes an Arabidopsis thaliana NCED promoter having SEQ ID NO : 10.
The invention also relates to NCED polypeptides and nucleic acids from other species that can be utilized in the invention. For example, NCED-3 nucleic acids and polypeptides from avocado can be used to generate stress resistant plants. One sequence of an avocado (Persea americana) NCED-3 polypeptide is provided below (SEQ ID NO:31).
1 MSMATPTTTC GAGDLLQNPK LLPISKNLSR PKNFIMLKHN
41 TPLIQCCSHS PSSSSAAVLH LPPKQPTKSK PSIKKGEKSS
81 TLTPSIEKNP GSHQVKTDQS GPNRVGPN N IFQRTAAFAL
121 DAIEEKLIAR VLERRHPLPK TADPEVQIAG NFAPVAEHPV 161 QHGIPVAGRI PRCLDGVYVR NGANPLFEPI AGHHFFDGDG
201 MIHAVRFRNG SASYSCRYTE TRRLVQERQL SRPIFPKAIG
241 ELHGHSGIAR LLLFYTRGLF GLVNADEGMG VANAGLVYFN
281 RRLLAMSEDD LPYHVRITPS GDLKTVGRHD FDNQLRSSMI
321 AHPKLDPESG ELFSLSYDVA RKPYLKYFHF APDGWKSPDV 361 EIPLDRPTMI HDFAITENFV VIPDQQWFK LEEMIRGGSP
401 WYDKNKTSR FGILPKYAPD ASEMIWVDAP DCFCFHL NA 441 WEEPESGEW WGSCMTPPD SIFNENEESL KSILTEIRLN 481 TRTGESTRRT IIDPQKPLNL EAGMVNRNRL GRKTRFAYLA 521 IAEPWPKVSG IAKVDLGTGE VNRFVYGERQ FGGEPYFIPR 561 EPSTSGREDD GYWSFMHDE KTSRSELLIL NAMNMRLEAS 601 VMLPSRVPYG FHGTFISSRD LAKQA
One sequence of an avocado (Persea americana) NCED-3 nucleic acid is provided below (SEQ ID NO:32).
1 CTGAGAGAGA CAGCTCTTCA AATCCAATAC TCTTCGATAC
41 TCTTATGTCA ATGGCTACTC CTACTACTAC TTGTGGGGCA
81 GGTGATCTAC TTCAAAATCC CAAATTGCTC CCCATTTCAA 121 AGAATCTCAG CCGTCCAAAA AACTTCATCA TGCTAAAACA
161 CAACACCCCA TTAATTCAGT GCTGCTCACA TTCTCCTTCT
201 TCTTCTTCTG CTGCTGTCCT TCATCTACCA CCAAAGCAGC 241 CGACAAAATC CAAACCGTCC ATCAAGAAAG GAGAGAAATC 281 GTCGACTCTC ACTCCATCGA TAGAGAAGAA TCCTGGCAGC 321 CATCAAGTGA AAACAGATCA ATCGGGTCCG AACCGGGTCG
361 GACCCAACTG GAACATTTTT CAACGGACTG CTGCCTTCGC
401 CTTGGACGCG ATCGAGGAGA AACTCATTGC TCGGGTGCTC 441 GAGCGCCGCC ACCCGCTTCC AAAGACCGCG GACCCGGAGG 481 TTCAGATTGC CGGAAATTTT GCACCGGTCG CCGAGCATCC 521 TGTACAGCAC GGCATCCCCG TCGCCGGAAG AATTCCTCGC 561 TGTCTCGACG GCGTCTACGT CCGCAACGGT GCCAACCCCT 601 TGTTCGAGCC GATCGCCGGC CACCATTTCT TCGATGGAGA 641 CGGGATGATC CACGCCGTCC GGTTCCGAAA TGGGTCCGCG 681 AGTTACTCTT GCAGGTACAC CGAGACTCGG AGGCTGGTGC 721 AGGAGCGCCA GCTCAGCCGG CCGATTTTTC CGAAGGCTAT 761 CGGCGAGCTG CACGGCCACT CTGGCATCGC CCGCCTCCTT 801 CTCTTCTATA CAAGAGGGCT GTTTGGGCTG GTGAACGCCG 841 ACGAGGGAAT GGGAGTAGCC AACGCCGGTT TGGTCTACTT 881 CAATCGCCGC CTCCTCGCTA TGTCTGAGGA TGACCTCCCC 921 TACCACGTCC GCATCACCCC GTCCGGCGAC CTGAAGACCG
961 TCGGACGACA CGACTTCGAC AACCAGCTCC GCTCCTCCAT
1001 GATCGCCCAC CCCAAGCTCG ACCCAGAATC GGGCGAGCTC
1041 TTCTCCCTCA GCTACGACGT CGCCCGAAAG CCTTATCTGA 1081 AATACTTCCA CTTCGCCCCC GACGGCTGGA AGTCGCCGGA
1121 CGTCGAGATC CCCCTCGACA GGCCGACCAT GATCCACGAC
1161 TTCGCCATTA CCGAAAACTT CGTCGTGATT CCCGACCAAC
1201 AGGTGGTCTT CAAGCTAGAA GAGATGATAA GAGGGGGCTC 1241 TCCGGTCGTC TACGACAAGA ACAAGACCTC CCGATTCGGA 1281 ATTCTCCCGA AATACGCCCC CGACGCGTCG GAAATGATAT 1321 GGGTCGACGC CCCGGACTGC TTCTGCTTCC ATCTCTGGAA
1361 CGCGTGGGAG GAGCCGGAGT CCGGCGAGGT GGTGGTAGTC
1401 GGCTCGTGCA TGACGCCGCC AGACTCAATA TTCAATGAAA 1441 ACGAGGAGAG CCTGAAGAGC ATTCTAACGG AGATCCGGCT 1481 CAACACGAGG ACAGGTGAGT CGACTCGCCG GACCATCATC 1521 GACCCGCAGA AGCCGTTGAA TTTGGAAGCT GGGATGGTGA 1561 ACCGGAATCG TTTGGGGAGG AAGACCCGGT TCGCGTATCT 1601 TGCCATTGCA GAGCCGTGGC CGAAGGTGTC GGGTATCGCG 1641 AAGGTGGATC TTGGGACGGG GGAGGTGAAC CGGTTTGTGT 1681 ATGGGGAGAG GCAGTTCGGT GGAGAACCGT ATTTCATTCC 1721 GAGAGAGCCG AGTACGTCGG GACGAGAGGA CGACGGGTAT 1761 GTGGTGTCGT TCATGCATGA CGAGAAGACG TCGAGGTCTG 1801 AGCTGCTTAT CTTGAATGCA ATGAATATGA GGTTGGAGGC 1841 GTCTGTGATG CTTCCTTCCA GAGTCCCATA TGGATTTCAT 1881 GGCACTTTTA TTAGTTCCAG GGACCTTGCA AAACAAGCCT 1921 GACACAGATC GGAGAGAGGA ACAAGACCCT GAGACTGAGT 1961 CGGAATCGTC TTCGTCTTCT TCTTCTTCTG ATTATTATTA 2001 GTGTTGTTAT TGTTGTTATC TTTTTTTAAG GGGAGATAAT 2041 ACCAGGGGGA TGAGTGGAGC TACGTCCCCG GAGTCTTCTC 2081 TTTTGCTATT ACAGGCCTTC TACGTTTGTG GGTTTTACGT 2121 GGTTTCTCTC TTCTTCTTCT GCTTCTTTAA ATATCTTTAA 2161 TTTGTTTGTT TTAGGTGTGG AACCAGCTCG AAGCTTGTTA 2201 GATTGTAGGT AGATTTGTAC CTTAGCTGGT TCTCTATAAT 2241 TATTTTACTC TAGTGTGAAT GAATTTATGA TCTTACTAGT 2281 GGTTACTATG CAAAGAAAAA AAAAAAAAAA
In other embodiments, the invention can be practiced using NCED-3 polypeptides or nucleic acids from cowpea (Vigna unguiculata ). An example of an NCED-3 polypeptide from cowpea is provided below (SEQ ID NO:33).
1 MLVKGAWEA PPSVSPSSQG GSGAASKKQL RVLVAGGGIG
41 GLVFALAAKK KGFDVWFEK DLSAIRGEGQ YRGPIQIQSN
81 ALAALEAIDS EVAEEVMRVG CITGDRINGL VDGVSGSWYV 121 KFDTFTPAVE RGLPVTRVIS RMVLQEILAR AVGEDIIMNA
161 SNWNFVDDG NKVTVELENG QKYEGDILVG ADGIWSKVRK
201 QLFGHKEAVY SGYTCYTGIA DFVPADIETV GYRVFLGHKQ 241 YFVSSDVGAG KMQWYAFHKE PPGGVDGPNG KKERLLKIFE 281 GWCDNAVDLI LATEEDAILR RDIYDRIPTL TWGKGRVTLL 321 GDSVHAMQPN MGQGGCMAIE DSYQLALELD NAWEQSVKSG
361 SPIDIDSSLR SYERERKLRV AIIHGMARMA ALMASTYKAY 401 LGVGLGPLEF LTKFRIPHPG RVGGRFFVDI MMPSMLSWVL 441 GGNSSKLΞGR PLSCRLSDKA NDQLRQWFΞD DEALERAING 481 EWILIPHGDG TSLSKPIVLS RNEMKPFIIG SAPAEDHPGT 521 SVTIPSPQVS PRHARINYKD GAFFLIDLRS EHGTWIIDNE 561 GKQYRVPPNY PARIRPSEAI QFGSEKVSFR VKVTRSVPRI 601 SENERPLTLQ EA
An example of an NCED-3 nucleic acid from cowpea is provided below (SEQ ID NO:34).
1 AATTCGGCAC GAGGATTTTC CTACGTGGGC GAGCTTACAA
41 CATACACACC ACTCCCATCC ATGACCACAA TTAAGAACCC
81 ACTTTTCAGT TCCCTTGAAT AAAGAACTTC CATTGGATGC 121 TTCACTTCTT GTTGGCTATA ACTGTCCCCT GGGATGCAGA
161 ACCAGGAAGC AGAGGAGGAA AGTGATGCTT GTGAAAGGTG
201 CGGTGGTAGA GGCTCCACCA AGTGTTTCAC CCTCGTCACA
241 AGGTGGAAGT GGGGCCGCTT CAAAGAAGCA GCTTCGGGTA
281 CTTGTTGCTG GTGGAGGGAT TGGAGGGTTG GTCTTTGCGT 321 TGGCTGCGAA GAAAAAGGGG TTTGATGTGG TGGTGTTTGA
361 GAAGGACCTG AGTGCTATAA GAGGGGAGGG ACAGTATAGG
401 GGTCCAATTC AGATTCAGAG CAATGCTTTG GCTGCTTTGG
441 AAGCTATAGA TTCAGAGGTT GCAGAGGAAG TTATGAGAGT 481 TGGTTGCATC ACCGGTGATA GAATCAATGG ACTTGTAGAT
521 GGGGTTTCTG GTTCTTGGTA CGTCAAGTTT GATACATTCA
561 CTCCAGCTGT GGAACGTGGG CTTCCAGTCA CAAGGGTTAT
601 TAGTCGAATG GTTTTACAAG AGATCCTTGC CCGCGCAGTT
641 GGGGAAGATA TCATTATGAA TGCTAGTAAT GTTGTTAATT 681 TTGTGGATGA TGGAAACAAG GTAACAGTAG AACTTGAGAA
721 TGGTCAGAAA TATGAAGGAG ATATATTGGT TGGAGCGGAT
761 GGTATATGGT CGAAGGTGAG GAAGCAATTA TTTGGGCACA
801 AAGAAGCTGT TTACTCTGGC TACACTTGTT ACACTGGCAT
841 TGCAGATTTT GTGCCTGCTG ACATTGAAAC TGTTGGATAC 881 CGGGTATTCT TGGGACACAA ACAATACTTT GTATCTTCAG
921 ATGTTGGTGC TGGAAAGATG CAATGGTATG CATTCCACAA
961 AGAACCTCCT GGTGGTGTTG ATGGCCCCAA CGGAAAAAAG
1001 GAAAGGCTGC TTAAGATATT TGAGGGTTGG TGTGATAATG
1041 CTGTAGATCT GATACTTGCC ACAGAAGAAG ATGCAATTCT 1081 AAGAAGAGAC ATATATGACA GGATACCGAC ATTGACATGG
1121 GGAAAGGGTC GTGTGACTTT GCTTGGGGAT TCCGTCCATG
1161 CCATGCAGCC AAACATGGGC CAAGGAGGGT GCATGGCTAT
1201 TGAGGACAGT TATCAACTTG CATTGGAGTT GGACAATGCA 1241 TGGGAACAAA GTGTTAAATC AGGGAGTCCA ATTGACATTG 1281 ATTCTTCCCT AAGGAGCTAC GAGAGAGAAA GAAAACTACG
1321 AGTTGCCATC ATTCATGGAA TGGCTAGAAT GGCCGCTCTC
1361 ATGGCTTCAA CTTACAAGGC ATATCTGGGT GTTGGTCTTG 1401 GCCCTTTAGA ATTTTTGACC AAGTTTCGCA TACCACATCC 1441 TGGAAGAGTT GGAGGAAGGT TTTTCGTTGA CATCATGATG 1481 CCTTCTATGT TGAGCTGGGT CTTAGGTGGC AATAGCTCCA
1521 AACTTGAGGG TAGACCACTA AGTTGCAGGC TCTCAGACAA
1561 AGCTAATGAT CAGTTACGCC AATGGTTTGA AGACGATGAA
1601 GCCCTTGAGC GTGCTATTAA TGGAGAGTGG ATTTTAATAC
1641 CGCATGGAGA TGGAACAAGT CTTTCAAAGC CTATAGTTTT 1681 AAGTCGAAAT GAGATGAAAC CCTTTATAAT CGGGAGTGCA 1721 CCAGCGGAAG ATCATCCTGG CACTTCAGTT ACAATACCTT 1761 CTCCTCAGGT TTCTCCAAGG CATGCTCGAA TTAACTATAA 1801 GGATGGTGCC TTCTTCTTGA TTGATTTACG GAGTGAACAT 1841 GGCACCTGGA TCATTGACAA TGAAGGAAAG CAGTACCGGG 1881 TACCCCCTAA TTATCCTGCT CGCATTCGCC CATCTGAGGC 1921 TATTCAGTTT GGTTCTGAGA AGGTTTCATT TCGTGTTAAG 1961 GTGACAAGAT CTGTTCCAAG AATCTCAGAG AATGAAAGGC 2001 CTCTAACGTT GCAGGAAGCG TGAGTGGTTC TGTTCAGTTG 2041 CAGTTTGTAA GTAATGGAAA AGTTATACAA AGCAAATTTA 2081 CATTTGTAGA GCACTATCTG CGTTACTTTA GGGTGGGATA 2121 TTAAACAACG ATCCAGTTAT CTTAATGTTT ATATGGACCT 2161 TTAAGAGGGA TTGTTGGTTA TAAATTCGTT ACCCCACTAA 2201 AAAACTTTTT GTGTAATAAC ATTTGTTAGT TAGATAGATT 2241 TGTAAAATGA CTGAAACTTG CACCACATTA ATGTTGAATG 2281 GAGTAAGCAA TGCTAAGCTG AGAATTTTTT TCACTTTTAA 2321 AAAAAAAAAA AAAAAAAAAA AAAAAAAAA
The invention also relates to sequences that are complementary to the coding strand of an NCED nucleic acid. In particular, the invention relates to nucleic acids that are complementary to an RNA produced from an NCED nucleic acid, for example, a nucleic acid complementary to any of SEQ ID NO:l-9, SEQ ID NO: 10, SEQ ID NO:ll, SEQ ID NO:12, SEQ ID NO:14-20, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34. Such complementary nucleic acids have utility for inhibiting the function of an endogenous NCED RNA and thereby diminishing the synthesis of a function NCED enzyme. Fragment and variant nucleic acids that comprise SEQ ID NO: 1-9, SEQ
ID NO:10, SEQ ID NO:l l, SEQ ID NO:12, SEQ ID NO:14-20, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, or complementary sequences thereof, are also encompassed by the invention. Such nucleic acid "fragments" that encompassed by the invention are not full sequences but do perform their intended function (conferring resistance environmental stresses such as salt).
"Variants" are substantially similar or substantially identical to the sequences (or the complements of the sequences) provided herein. For nucleotide sequences that encode an inhibitory RNA, "variants" include those sequences that are sufficiently complementary to an endogenous NCED RNA to inhibit the function of such an endogenous NCED RNA. For nucleotide sequences that encode proteins, "variants" include those sequences that, because of the degeneracy of the genetic code, encode the identical amino acid sequence of the reference protein. Variant nucleic acids also include those nucleic acids that encode polypeptides that do not have amino acid sequences identical to that of the proteins identified herein, but which encode an active protein with conservative changes in the amino acid sequence.
As is known by one of skill in the art, the genetic code is "degenerate," meaning that several trinucleotide codons can encode the same amino acid. This degeneracy is apparent from Table 2.
Table 2
Second Position
Figure imgf000042_0001
Hence, many changes in the nucleotide sequence of the variant may be silent and may not alter the amino acid sequence encoded by the nucleic acid. Where nucleic acid sequence alterations are silent, a variant nucleic acid will encode a polypeptide with the same amino acid sequence as the reference nucleic acid.
Therefore, a particular nucleic acid sequence of the invention also encompasses variants with degenerate codon substitutions, and complementary sequences thereof, as well as the sequence explicitly specified by a SEQ ID NO.
Specifically, degenerate codon substitutions may be achieved by generating sequences in which the reference codon is replaced by any of the codons for the amino acid specified by the reference codon. In general, the third position of one or more selected codons can be substituted with mixed-base and/or deoxyinosine residues as disclosed by Batzer et al., Nucleic Acid Res., 19, 5081
(1991) and/or Ohtsuka et al., J. Biol. Chem., 260, 2605 (1985); Rossolini et al,
Mol. Cell. Probes, 8, 91 (1994). However, the invention is not limited to silent changes in the present nucleotide sequences but also includes variant nucleic acid sequences that conservatively alter the amino acid sequence of a polypeptide of the invention. According to the present invention, variant and reference nucleic acids of the invention may differ in the encoded amino acid sequence by one or more substitutions, additions, insertions, deletions, fusions and truncations, which may be present in any combination, so long as an active protein with activity similar to the protein encoded by the reference nucleic acid is encoded by the variant nucleic acid. Such variant nucleic acids will not encode exactly the same amino acid sequence as the reference nucleic acid, but have conservative sequence changes and an activity similar to the protein encoded by the reference nucleic acid.
The invention also embraces derivative nucleic acids. Derivative nucleic acids can encode an inhibitory RNA that has additional ribonucleotides or an inhibitory RNA with one or more nucleotide substitutions, deletions or insertions. Such a derivative nucleic acid can have an improved property, for example, greater stability, resistance to nucleases, or sequences that cause the inhibitory RNA to be transported into the cytoplasm or to be retained in the nucleus. Derivative nucleic acids that encode proteins include nucleic acids with non-conservative amino acid sequences changes. Such derivative nucleic acids can encode a protein with an improved property, for example, improved stability, improved longevity, or improved salt resistance activity. Such derivative nucleic acids can encode a protein that is similar to the protein encoded by the reference nucleic acid, but the derivative nucleic acid will not have exactly the same amino acid sequence as the reference nucleic acid. Instead, both conservative and non-conservative amino acid changes can be present in the protein encoded by the derivative nucleic acid. The encoded derivative protein still provides salt resistance when expressed in a plant cell, but such a derivative protein will provide some other benefit relative to the protein encoded by the reference nucleic acid.
Variant and derivative nucleic acids with silent, conservative and non- conservative changes can be defined and characterized by the degree of homology to the reference nucleic acid. Preferred variant and derivative nucleic acids are "substantially homologous" or "substantially identical" to the reference nucleic acids of the invention. As recognized by one of skill in the art, such substantially homologous or substantially identical nucleic acids can hybridize under stringent conditions with the reference nucleic acids identified by SEQ ID NO herein. All of these types of substantially homologous/identical nucleic acids are encompassed by this invention.
Generally, nucleic acid derivatives and variants of the invention will have at least 90%, 91%, 92%, 93% or 94% sequence identity to the reference nucleotide sequence defined herein. Preferably, nucleic acids of the invention will have at least at least 95%, 96%, 97%, to 98% sequence identity to the reference nucleotide sequence defined herein.
Variant and derivative nucleic acids can be detected and isolated by standard hybridization procedures. Hybridization to detect or isolate such sequences is generally carried out under stringent conditions. "Stringent hybridization conditions" and "stringent hybridization wash conditions" in the context of nucleic acid hybridization experiments such as Southern and Northern hybridization are sequence dependent, and are different under different environmental parameters. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Laboratory Techniques in Biochemistry and Molecular biology- Hybridization with Nucleic Acid Probes, page 1, chapter 2 "Overview of principles of hybridization and the strategy of nucleic acid probe assays" Elsevier, New York (1993). See also, J. Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, N.Y., pp 9.31-9.58 (1989); J. Sambrook et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, N.Y.(3rd ed. 2001).
The invention also provides methods for detection and isolation of derivative or variant nucleic acids encoding the proteins provided herein. The methods involve hybridizing at least a portion of a nucleic acid comprising any one of the primers or nucleic acids provided herein to a sample nucleic acid, thereby forming a hybridization complex; and detecting the hybridization complex. The presence of the complex correlates with the presence of a derivative or variant nucleic acid which can be further characterized by nucleic acid sequencing, expression of RNA and/or protein and testing to determine whether the derivative or variant retains activity. In general, the portion of a nucleic acid that is used for the inhibitory RNA or for hybridization is at least fifteen nucleotides. Hybridization performed in vitro is under hybridization conditions that are sufficiently stringent to permit detection and isolation of substantially homologous nucleic acids. In an alternative embodiment, variant nucleic acids are isolated by amplification of a selected nucleic acid sample using polymerase chain reaction and primer oligonucleotides selected from any one of the nucleic acids provided herein.
Generally, highly stringent hybridization and wash conditions are selected to be about 5 °C lower than the thermal melting point (Tm) for the specific double-stranded sequence at a defined ionic strength and pH. For example, under "highly stringent conditions" or "highly stringent hybridization conditions" a nucleic acid will hybridize to its complement to a detectably greater degree than to other sequences (e.g., at least 2- fold over background). By controlling the stringency of the hybridization and/or the washing conditions, nucleic acids having 100% complementary or other desirable parcentages of complementary can be identified and isolated. Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing). Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30°C for short probes (e.g., 10 to 50 nucleotides) and at least about 60°C for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulfate) at 37°C, and a wash in IX to 2X SSC (20X SSC = 3.0 M NaCl and 0.3 M trisodium citrate) at 50 to 55°C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37°C, and a wash in 0.5X to IX SSC at 55 to 60°C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 MNaCl, 1% SDS at 37°C, and a wash in 0.1X SSC at 60 to 65°C.
The degree of complementarity or homology of hybrids obtained during hybridization is typically a function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. The type and length of hybridizing nucleic acids also affects whether hybridization will occur and whether any hybrids formed will be stable under a given set of hybridization and wash conditions. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl Anal. Biochem. 138:267-284 (1984);
Tm = 81.5°C + 16.6 (log M) +0.41 (%GC) - 0.61 (% form) - 500/L
where M is the molarity of monovalent cations, %GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected for hybridization to derivative and variant nucleic acids having a Tm equal to the exact complement of a particular probe, less stringent conditions are selected for hybridization to derivative and variant nucleic acids having a Tm less than the exact complement of the probe. In general, Tm is reduced by about 1°C for each 1% of mismatching. Thus, Tm, hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired sequence identity. For example, if sequences with >90% identity are sought, the Tm can be decreased 10°C. Generally, stringent conditions are selected to be about 5°C lower than the thermal melting point (Tm) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4°C lower than the thermal melting point (Tm); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10°C lower than the thermal melting point (Tm); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20°C lower than the thermal melting point (Tm).
An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or Northern blot is 50% formamide with 1 mg of heparin at 42 °C, with the hybridization being carried out overnight. An example of highly stringent conditions is 0.1 5 M NaCl at 72 °C for about 15 minutes. An example of stringent wash conditions is a 0.2x SSC wash at 65°C for 15 minutes (see also, Sambrook, infra). Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal. An example of medium stringency for a duplex of, e.g., more than 100 nucleotides, is lx SSC at 45 °C for 15 minutes. An example low stringency wash for a duplex of, e.g., more than 100 nucleotides, is 4-6x SSC at 40 °C for 15 minutes. For short nucleic acids (e.g., about 10 to 50 nucleotides), stringent conditions typically involve salt concentrations of less than about l.OM Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is typically at least about 30 °C.
Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide. In general, a signal to noise ratio of 2x (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization. Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the proteins that they encode are substantially identical. This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code.
The following are examples of sets of hybridization/wash conditions that may be used to detect and isolate homologous nucleic acids that are substantially identical to reference nucleic acids of the present invention: a reference nucleotide sequence preferably hybridizes to the reference nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50°C with washing in 2X SSC, 0.1% SDS at 50°C, more desirably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50°C with washing in IX SSC, 0.1% SDS at 50°C, more desirably still in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50°C with washing in 0.5X SSC, 0.1% SDS at 50°C, preferably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50°C with washing in 0.1X SSC, 0.1% SDS at 50°C, more preferably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50 °C with washing in 0.1X SSC, 0.1% SDS at 65 °C.
If the desired degree of mismatching results in a Tm of less than 45 °C (aqueous solution) or 32°C (formamide solution), it is preferred to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes, Part 1, Chapter 2 (Elsevier, New York); and Ausubel et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley - friterscience, New York). See Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, New York).
Hence, for example, nucleic acids can be isolated from any number of plant or animal species and tested for variants and derivatives of the present nucleic acids by using the references and the teachings herein on the relationship between Tm, mismatch, and hybridization and wash conditions. Those of ordinary skill can readily generate variants and derivatives of the present nucleic acids.
Computer analyses can also be utilized for comparison of sequences to determine sequence identity. Such analyses include, but are not limited to: CLUSTAL in the PC/Gene program (available from fritelligenetics, Mountain View, California); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Version 8 (available from Genetics Computer Group (GCG), 575 Science Drive, Madison, Wisconsin, USA). Alignments using these programs can be performed using the default parameters. The CLUSTAL program is well described by Higgins et al. Gene 73:237 244 (1988); Higgins et al. CABIOS 5:151-153 (1989); Corpet et al. Nucleic Acids Res. 16:10881-90 (1988); Huang et al. CABIOS 8:155-65 (1992); and Pearson et al. Meth. Mol. Biol. 24:307-331 (1994). The ALIGN program is based on the algorithm of Myers and Miller, supra. The BLAST programs of Altschul et al., J. Mol. Biol. 215:403 (1990), are based on the algorithm of Karlin and Altschul supra. To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al. Nucleic Acids Res. 25:3389 (1997). Alternatively, PSI-BLAST (in BLAST 2.0) can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al., supra. When utilizing BLAST, Gapped BLAST, PSI-BLAST, the default parameters of the respective programs (e.g. BLASTN for nucleotide sequences, BLASTX for proteins) can be used. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=-4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA, 89, 10915 (1989)). See the website at ncbi.nlm.nih.gov. Alignment may also be performed manually by inspection. For purposes of the present invention, comparison of nucleotide sequences for determination of percent sequence identity to the nucleic acid sequences disclosed herein is preferably made using the BlastN program (version 1.4.7 or later) with its default parameters or any equivalent program. By "equivalent program" is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by the preferred program.
Decreasing Expression of Endogenous of 9-cis-epoxycarotenoid dioxygenase
According to the invention, the expression of a target gene can be reduced through inhibitory RNA interactions with target mRNA. Such regulation of expression in plant cells is achieved by integrating into the plant cell host a nucleic acid sequence in which the transcribed nucleic acid sequences are at least partially complementary to a nucleic acid sequence that is already transcribed by the host. The exogenous nucleic acid is under the transcriptional control of a transcriptional initiation region recognized by the plant cell host. Transcription of the exogenous nucleic acid may produce multiple copies of an antisense RNA that is complementary to an endogenous RNA of the host cell. This antisense mRNA reduces the functioning of the naturally existing RNA. Inhibitory RNA can be produced in the nucleus so as to and operate to inhibit the function of endogenous RNA within the nucleus. Moreover, inhibitory RNA can also be produced in the cytoplasm. Cytoplasmic expression of inhibitory RNA (specific for target genes) has some advantages over nuclear expression, for example, the ability to use high level expression vectors that are not suitable for nuclear expression. The use of such vectors is particularly advantageous in plants, because vectors capable of systemically infecting plants may be used to produce the inhibitory RNA. The invention described herein has many aspects. These aspects include novel genetic constructions for the expression of target gene inhibitory RNA in the cytoplasm of eukaryotic cells, cells transfected with these genetic constructions, multicellular organisms comprising the transfected cells, and methods for reducing the expression of selected genes in a cell by transforming a cell with a genetic construction of the invention.
Background on the use of inhibitory RNA for regulating and/or decreasing the function of an endogenous RNA can be found in the art. For example, Crowley et al, Cell (1985) 43:633-641, describe the use of an anti- sense construct of the discoidin gene transfected into Dictyostelium to repress expression of endogenous discoidin genes. See also references cited therein. Anti-sense regulation has also been described by Rosenberg et al, Nature (1985) 313:703-706; Preiss et al., Nature (1985) 313:27-32; Melton, Proc. Natl. Acad. Sci. USA (1985) 82:144-148; Izant and Weinfraub, Science (1985) 229:345-352; and Kim and Wold, Cell (1985) 42:129-138. See also, Izant and Weintraub Cell (1984) 36:1007-1075; Pestka et al., Proc. Natl. Acad. Sci. USA (1984) 81:7525- 7528; Mizuno et al., ibid (1984) 81:1966-1970; Coleman et al., Cell (1984) 37:683-691; Travers, Nature (1984) 311:410 and Weintraub et al., Trends in Genetics (1985) 1:22-25.
Methods and compositions are therefore provided herein for modulating RNA utilization, particularly modulation of amino acid biosynthesis in a plant host cell. The compositions involve transcription constructs having transcriptional initiation and termination regions separated by a sequence that is complementary to a sequence present in an endogenous RNA, particularly messenger RNA. Such a sequence is a 9-cis-epoxycarotenoid dioxygenase (NCED) inhibitory RNA encoding nucleic acid. When expressed within a plant cell, an NCED inhibitory RNA encoding nucleic acid reduces the production of the 9-cis-epoxycarotenoid dioxygenase protein and lower its effective activity.
The sequence of the NCED inhibitory RNA encoding nucleic acid that is complementary to a sequence of the endogenous messenger RNA is usually at least about 17 nucleotides, at least about 20 nucleotides, or at least about 25 nucleotides. The upper limit on the length is not critical but generally the NCED inhibitory RNA encoding nucleic acid is smaller than about 7000 nucleotides, about 5000 nucleotides, or about 2000 nucleotides. Convenient lengths for the NCED inhibitory RNA encoding nucleic acid are about 17 to about 200 nucleotides, about 20 to about 100 nucleotides, or about 25 to about 50 nucleotides.
The sequence may be complementary to any sequence of the endogenous NCED messenger RNA, that is, it may be proximal to the 5'-terminus or capping site, downstream from the capping site, between the capping site and the initiation codon and may cover all or only a portion of the non-coding region, may bridge the non-coding and coding region, be complementary to all or part of the coding region, complementary to the 3 '-terminus of the coding region, or complementary to the 3 '-untranslated region of the mRNA.
The particular site(s) to which the anti-sense sequence binds and the length of the anti-sense sequence will vary depending upon the degree of inhibition desired, the uniqueness of the sequence, the stability of the anti-sense sequence, or the like. Therefore, to some degree, these factors will be determined empirically based on the experience observed with a particular anti-sense sequence, such as the phenotype of resulting transgenic plants.
The sequence may be a single sequence or a repetitive sequence having two or more repetitive sequences in tandem, where the single sequence may bind to a plurality of messenger RNAs. In some instances, rather than providing for homoduplexing, heteroduplexing may be employed, where the same sequence may provide for inhibition of a plurality of messenger RNAs by having regions complementary to different messenger RNAs.
The antisense sequence may be complementary to a unique sequence or a repeated sequence, so as to enhance the probability of binding. Thus, the antisense sequence may be involved with the binding of a unique sequence, a single unit of a repetitive sequence or of a plurality of units of a repetitive sequence. The antisense sequence may result in the modulation of expression of a single gene or a plurality of genes.
There are numerous ways to produce the genetic constructions of the invention. Techniques for manipulating nucleic acids, e.g., restriction endonuclease digestion and Hgation, are well known to a person of ordinary skill in the art. These conventional polynucleotide manipulation techniques may be used to produce and use the genetic constructs of the invention. While some optimization of standard techniques may be employed to produce the subject genetic constructs, significant experimentation is not required to produce the genetic constructs or practice the claimed methods.
The transcriptional construct will be comprised of, in the direction of transcription, a transcriptional initiation region, the sequence coding for the antisense RNA on the sense strand, and a transcriptional termination region. The transcriptional initiation region may provide for constitutive expression or regulated expression. The transcriptional initiation regions comprise a promoter region in functional combination with an inhibitory RNA encoding nucleic acid. The promoter region is selected so as to be capable of driving the transcription of a polynucleotide sequence in a host cell of interest. A large number of promoters are available which are functional in plants. The promoter driving transcription of the inhibitory RNA is selected so as to achieve a level of transcriptional activity sufficient to attain the desired degree of expression of the target gene inhibitory RNA of interest. The promoter may be native or heterologous to the cell selected for genetic modification. The promoter may also be native or heterologous to the expression vector, i.e., the portion of the vector other than the promoter and the inhibitory RNA encoding region. The promoter may be inducible or constitutive. Strong promoters can be used to drive transcription of the inhibitory RNA encoding nucleic acid when the target RNA is highly expressed. These promoters may be obtained from Ti- or Ri-plasmids, from plant cells, plant viruses or other hosts where the promoters are found to be functional in plants. An RNA virus subgenomic promoter can be used as a promoter region. RNA virus subgenomic promoters are described, among other places in Dawson and Lehto, Advances in Virus Research, 38:307- 342, and in PCT published application WO 93/03161.
Illustrative promoters also include the octopine synthetase promoter, the nopaline synthase promoter, the manopine synthetase promoter, etc., as illustrative of promoters of bacterial origin functional in plants. Viral promoters include the cauliflower mosaic virus full length (35S) and region VI promoters, etc. Endogenous plant promoters include the ribulose-l,6-biphosphate (RUBP) carboxylase small subunit (ssu), the beta-conglycinin promoter, the phaseolin promoter, the ADH promoter, heat-shock promoters, tissue specific promoters, e.g., promoters associated with fruit ripening, etc. The transcriptional initiation region may be a naturally-occurring region, a RNA polymerase binding region freed of the regulatory region, or a combination of an RNA polymerase binding region from one gene and regulatory region from a different gene. The regulatory region may be responsive to a physical stimulus, such as heat, with heat shock genes, light, as with the RUBP carboxylase SSU, or the like. Alternatively, the regulatory region may be sensitive to differentiation signals, such as the β-conglycinin gene, the phaseolin gene, or the like. A third type of regulatory region is responsive to metabolites. The time and level of expression of the antisense RNA can have a definite effect on the phenotype produced. Thus the promoters chosen will determine the effect of the antisense RNA.
Any convenient termination region may be employed, conveniently the termination region of the RNA polymerase binding region, or a different termination region. Various termination regions are available and the choice is primarily one of convenience, where prior constructions or DNA sequences may be available. Conveniently, the opine termination regions may be employed, or termination regions from endogenous genes, such as the genes which have been described previously. The various fragments may be joined by linkers, adapters, or the like, or directly where convenient restriction sites are available. The DNA sequences, particularly bound to a replication system, may be joined stepwise, where markers present on the replication system may be employed for selection. The expression cassettes and vectors containing NCED inhibitory RNA encoding nucleic acid constructs of the invention may be introduced into the host cell in a variety of ways. Of particular interest is the use of Agrobacterium tumefaciens with protoplasts, injured leaves, or other explant tissues. Other techniques which may find use include electroporation with protoplasts, liposome fusion, microinjection, microprojectile bombardment, or the like. Other methods are described in more detail below. The particular method for transforming the plant cells is not critical to this invention.
To achieve cytoplasmic expression of an inhibitory RNA, various plant viruses and plant viral vectors can be employed. Tobamoviruses, whose genomes consist of one plus-sense RNA strand of approximately 6.4 kb, replicate solely in the cytoplasm, and can be used as episomal RNA vectors to generate inhibitory RNA within the cytoplasm of plant cells. Hybrid tobacco mosaic (TMV)/odontoglosum ringspot viruses (ORSN) have been used previously to express heterologous enzymes in transfected plants (Donson, et al., Proc. Νatl. Acad. Sci. USA 88:7204 (1991) and Kumagai, et al., Proc. Νatl. Acad. Sci. USA 90:427-430 (1993), minus-Sense RΝA Strand (Miller, et al.). Infectious RΝA transcripts from viral cDΝA clones encode proteins involved in RΝA replication, movement, and encapsidation. Subgenomic RΝA for messenger RΝA synthesis is controlled by internal promoters located on the minus-sense RΝA strand (Ν. benthamiana plants were inoculated with in vitro transcripts as described previously [W. O. Dawson, et al., Proc. Νatl. Acad. Sci. USA 83:1832 (1986)]). Insertion of foreign genes into a specific location under the control of an additional subgenomic RΝA promoter have resulted in systemic and stable expression of neomycin phosphotransferase and α-trichosanthin (Donson, et al., Proc. Νatl. Acad. Sci. USA 88:7204 (1991) and Kumagai, et al, Proc. Νatl. Acad. Sci. USA 90:427-430 (1993)).
RΝA plant virus vectors are positive strand single-stranded RΝA viruses. RΝA plant virus vectors may be conveniently manipulated and introduced into cells in a DNA form instead of working directly with RNA vectors. Viral vector derived from tobamoviruses are preferred for some embodiments. Descriptions of suitable plant virus vectors that may be modified so as to contain an inhibitory RNA encoding region in functional combination with a promoter, as well as how to make and use such vectors, can be found in, among other places, PCT publication number WO 93/03161, Kumagai et al., Proc. Natl. Acad. Sci. USA 90:427-430 (1993).
The genetic constructions for cytoplasmic expression of the NCED inhibitory RNA are capable of replication or maintenance, at least transiently, in the cytoplasm of plant cells of interest. Many vectors capable of replication (or stable maintenance) in different types of eukaryotic cells are known. For example, vectors for use in plant cells include vectors derived from cauliflower mosaic virus, tobacco mosaic virus, tomato mosaic virus, and the like. Information describing plant cell vectors and their use in plant cells can be found, among other places, in PCT published application WO 93/03161, and Donson, et al., Proc. Natl. Acad. Sci. USA 88:7204-7208 (1991).
The invention also provides methods of reducing the expression of a gene or genes of interest in a eukaryotic cell. As a consequence of providing the subject methods of reducing gene expression in eukaryotic cell, the subject invention also provides methods of producing a eukaryotic cell having reduced expression of a gene of interest and eukaryotic cells that have reduced expression of a gene of interest, as produced by the methods of the invention. Reduction of gene expression is achieved by introducing one or more of the vectors of the invention into a eukaryotic cell. The vector used to transform the cell of interest comprises an inhibitory RNA encoding polynucleotide that encodes an inhibitory RNA specific for the gene for which reduced expression is sought. The method of reducing expression of the gene of interest comprises the step of introducing the subject genetic vector into a host cell that is capable of expressing the gene of interest under certain environmental conditions. The vector may be introduced into a cell of interest by any of a variety of well known transformation methods. Such methods include: infection, transfection, electroporation, ballistic projectile transformation, conjugation, and the like. The inventive aspect of the subject methods is not dependent upon the particular means by which the inhibitory RNA encoding vector is introduced into the cell of interest. The particular methods of introducing the vector into a cell of interest is, in part, dependent upon the particular cell for modification and the precise type of vector selected.
Expression Cassettes
The nucleic acids of the invention can be placed within an expression cassette. Nucleic acids encoding an inhibitory NCED RNA or a NCED protein can be placed in an expression cassette. Such an expression cassette includes regulatory elements that are needed for transcription and/or expression of an
RNA or protein encoded by the nucleic acid. In general, the expression cassettes of the invention contain at least a promoter capable of expressing RNA in a plant cell and a terminator. However, other elements may also be present in the expression cassettes of the invention. For example, expression cassettes can also contain enhancers, infrons, untranslated leader sequences, cloning sites, elements of the Gateway recombination system, matrix attachment regions for silencing the effects of chromosomal control elements, and other elements known to one of skill in the art.
Expression cassettes have promoters that can regulate gene expression. Promoter regions are typically found in the flanking DNA sequence upstream from coding regions in both prokaryotic and eukaryotic cells. A promoter sequence provides for regulation of transcription of the downstream gene sequence and typically includes from about 50 to about 2,000 nucleotide base pairs. Promoter sequences also contain regulatory sequences such as enhancer sequences that can influence the level of gene expression. Many isolated promoter sequences can provide for gene expression of heterologous genes, that is, a gene different from the native or homologous gene.
Promoter sequences can be strong or weak or inducible. A strong promoter provides for a high level of gene expression, whereas a weak promoter provides for a very low level of gene expression. An inducible promoter is a promoter that can be turned on and off so that the encoded RNA is transcribed in response to an exogenously added agent or in response to an environmental or developmental stimulus. Promoters can also provide for tissue specific or developmental regulation.
An isolated promoter sequence that is a strong promoter for heterologous genes is advantageous because it provides for a sufficient level of gene expression to allow for easy detection and selection of transformed cells and provides for a high level of gene expression when desired.
Preferred promoters will generally include, but are not limited to, bacterial, bacteriophage or plant promoters. Useful promoters include the CaMV 35S promoter (Odell et al., Nature. 313. 810 (1985)), the CaMV 19S (Lawton et al., Plant Mol. Biol.. 9, 3 IF (1987)), nos (Ebert et al., PNAS USA. 84, 5745 (1987)), Adh (Walker et al., PNAS USA. 84, 6624 (1987)), sucrose synthase (Yang et al., PNAS USA. 87, 4144 (1990)), tubulin, napin, actin (Wang et al, Mol. Cell. Biol.. 12, 3399 (1992)), cab (Sullivan et al., Mol. Gen. Genet. 215. 431 (1989)), PEPCase promoter (Hudspeth et al., Plant Mol. Biol.. 12, 579 (1989)), the 7S-alpha'-conglycinin promoter (Beachy et al., EMBO J. 4, 3047 (1985)) or those associated with the R gene complex (Chandler et al, The Plant Cell 1, 1175 (1989)). Other useful promoters include the tomato E8, patatin, ubiquitin, mannopine synthase (mas), soybean seed protein glycinin (Gyl), soybean vegetative storage protein (vsp), bacteriophage SP6, T3, and T7 promoters. Other promoters useful in the practice of the invention that are known to those of skill in the art are also contemplated by the invention.
An inducible promoter can be turned on or off by an exogenously added agent so that expression of operably linked nucleic acids is also turned on or off. For example, a bacterial promoter such as the Ptac promoter can be induced to varying levels of gene expression depending on the level of isothiopropylgalactoside added to the transformed bacterial cells.
It may desirable to combine a nucleic acid of the invention with a promoter that provides tissue specific expression or developmentally regulated gene expression in plants. Tissue-specific promoters, including but not limited to, root-cell promoters (Conkling et al., Plant Physiol.. 93, 1203 (1990)), and tissue-specific enhancers (Fromm et al., The Plant Cell. I, 977 (1989)) are also contemplated to be particularly useful, as are inducible promoters such as ABA-inducible and turgor-inducible promoters, and the like. Placing a nucleic acid under the regulatory control of a promoter or a regulatory element means positioning the nucleic acid such that the expression of the nucleic acid is controlled by these sequences. In general, promoters are found positioned 5' (upstream) to the nucleic acid that that they control. Thus, in the construction of heterologous promoter/nucleic acid combinations, the promoter is preferably positioned upstream to the nucleic acid and at a distance from the transcription start site of the nucleic acid that the distance between the promoter and the transcription star site approximates the distance observed in the natural setting. As is known in the art, some variation in this distance can be tolerated without loss of promoter function. Similarly, the preferred positioning of a regulatory element with respect to a heterologous nucleic acid placed under its control is the natural position of the regulatory element relative to the structural gene it naturally regulates. Again, as is known in the art, some variation in this distance can be accommodated. Promoter function during expression of a heterologous nucleic acid under its regulatory control can be tested at the transcriptional stage using reverse transcription/PCR methods and or DNA-RNA hybridization assays ("Northern" blots). Promoter function at the translational stage can be tested by using specific functional assays for the protein synthesized (for example, by enzymatic activity or by immunoassay of the protein).
In addition, transcription enhancers or duplications of enhancers can be used to increase expression from a particular promoter. Examples of such enhancers include, but are not limited to, elements from the CaMV 35S promoter and octopine synthase genes (Last et al., U.S. Patent No. 5,290,924, issued March 1, 1994). For example, it is contemplated that vectors for use in accordance with the present invention may be constructed to include the octopine synthase gene (ocs) enhancer element. This element was first identified as a 16 bp palindromic enhancer from the octopine synthase (ocs) gene of Agrobacterium (Ellis et al., EMBO J.. 6, 3203 (1987)), and is present in at least ten other promoters (Bouchez et al., EMBO J.. 8, 4197 (1989)). It is proposed that the use of an enhancer element, such as the ocs element and particularly multiple copies of the element, will act to increase the level of transcription from adjacent promoters when applied in the context of monocot transformation. It is known that the nucleotide sequence between the transcription initiation site and the start of the coding sequence, i.e., the untranslated leader sequence, can influence gene expression. Accordingly, leader sequences can also be employed with the nucleic acids of the invention. Preferred leader sequences include those that direct optimum expression of the attached gene, for example, consensus leader sequences that can increase or maintain mRNA stability and prevent inappropriate initiation of translation (Joshi, Nucl. Acid Res., 15, 6643 (1987)). Sequences that are derived from genes that are highly expressed in dicots, such as those in soybeans, and monocots, such as those in corn, are preferred. Those of skill in the art can readily identify and incorporate such sequences into the present vectors.
In one embodiment, the promoter is a ubiquitin regulatory system described, for example, in U.S. Patent 6,054,574, which in addition to a promoter, has an intron sequence before the initiation codon. Such a ubiquitin regulatory system is approximately 2 kb and includes nucleic acids sequences that are 5' to the translation start site of the maize ubiquitin gene. The ubiquitin regulatory system has sequences that direct initiation of transcription, regulation of transcription, control of expression level, induction of stress genes and enhancement of expression in response to stress. Expression cassettes of the invention also include a sequence near the 3' end of the cassette that acts as a signal to terminate transcription from a heterologous nucleic acid and that directs polyadenylation of the resultant mRNA. Some 3' elements that can act as termination signals include those from the nopaline synthase gene of Agrobacterium tumefaciens (Bevan et al., Nucl. Acid Res., 11, 369 (1983)), the terminator for the T7 transcript from the octopine synthase gene of Agrobacterium tumefaciens, the 3' end of the protease inhibitor I or II genes from potato or tomato, the vegetative storage protein (vsp), and the geminiviral short intergenic (sir) termination sequences. Other 3' elements known to those of skill in the art also can be used in the vectors of the invention. Regulatory elements such as Adh intron 1 (Callis et al., Genes Develop..
1, 1183 (1987)), sucrose synthase intron (Vasil et al., Plant Phvsiol.. 91, 5175 (1989)) or TMV omega element (Gallie et al., The Plant Cell. 1, 301 (1989)) may further be included where desired. These 3' nontranslated regulatory sequences can be obtained as described in An, Methods in Enzymology, 153, 292 (1987) or are already present in plasmids available from commercial sources such as Clontech, Palo Alto, California. The 3' nontranslated regulatory sequences can be operably linked to the 3 'terminus of any heterologous nucleic acid to be expressed by the expression cassettes contained within the present vectors. Other such regulatory elements useful in the practice of the invention are known to those of skill in the art and can also be placed in the vectors of the invention.
Additionally, expression cassettes may be constructed and employed to target the heterologous gene product to a desired intracellular compartment within a plant cell or to direct the heterologous gene product to the extracellular environment. This will generally be achieved by joining a DNA sequence encoding a transit or signal peptide sequence to the coding sequence of a particular gene. The resultant transit, or signal, peptide will transport the protein to a particular intracellular, or extracellular destination, respectively, and will then be post-translationally removed. Transit or signal peptides act by facilitating the transport of proteins through intracellular membranes, e.g., vacuole, vesicle, plastid and mitochondrial membranes, whereas signal peptides direct proteins through the extracellular membrane. By facilitating transport of the protein into compartments inside or outside the cell, these sequences may increase the accumulation of gene product.
Vectors that are used for expression of a protein of the invention can be optimized for protein expression in plants by having one or more codons of selcted coding regions degenerate to corresponding codons that are preferably translated by the translation machinery of the plant species in which the vector is used.
Selectable Markers
Selectable marker genes or reporter genes can also be linked to the nucleic acids of the invention, for example, by placing such genes within a vector that contains the nucleic acid of the invention. When expressed, such selectable markers or reporter genes can impart a distinct phenotype to a host cell and thus allow that host cell to be distinguished from cells that do not have the marker or reporter gene. Some selectable marker genes confer a trait which one can 'select' for by chemical means, for example, through the use of a selectable agent such as a herbicide, antibiotic, or the like. Reporter genes confer a trait that one can identify through observing, testing, or 'screening' for the trait. Other examples of suitable marker genes are known to the art and can be employed in the practice of the invention.
Included within the terms selectable marker or reporter genes are also genes which encode a "secretable marker" whose secretion can be detected as a means of identifying or selecting for transformed cells. Examples include markers that encode a secretable antigen that can be identified by antibody interaction, or a secretable enzyme that can be detected by its catalytic activity. Secretable proteins fall into a number of classes, including small, diffusible proteins detectable, e.g., by ELISA; and proteins that are inserted or trapped in the cell wall (e.g., proteins that include a leader sequence such as that found in the expression unit of extensin or tobacco PR-S).
In one embodiment, the selectable or reporter marker can encode a protein that becomes sequestered in the cell wall, and that includes a unique epitope that is considered to be advantageous. Such a secreted antigen marker would ideally employ an epitope sequence that would provide low background in plant tissue, a promoter-leader sequence that would impart efficient expression and targeting across the plasma membrane, and would produce protein that is bound in the cell wall and yet accessible to antibodies. A normally secreted wall protein modified to include a unique epitope would satisfy all such requirements. One example of a protein suitable for modification in this manner is extensin, or hydroxyproline rich glycoprotein (HPRG). The use of the maize HPRG (Steifel et al., The Plant Cell. 2, 785 (1990)) is preferred as this molecule is well characterized in terms of molecular biology, expression, and protein structure. However, any one of a variety of extensins and/or glycine-rich wall proteins (Keller et al., EMBO J.. 8, 1309 (1989)) could be modified by the addition of an antigenic site to create a reporter marker.
Possible selectable markers for use in connection with the present invention include, but are not limited to, a neo gene (Potrykus et al., Mol. Gen. Genet., 199, 183 (1985)) which codes for kanamycin resistance and can be selected for using kanamycin, G418, and the like; a bar gene which codes for bialaphos resistance; a gene which encodes an altered EPSP synthase protein (Hinchee et al., Biotech., 6, 915 (1988)) thus conferring glyphosate resistance; a nitrilase gene such as bxn from Klebsiella ozaenae which confers resistance to bromoxynil (Stalker et al., Science, 242, 419 (1988)); a mutant acetolactate synthase gene (ALS) which confers resistance to imidazolinone, sulfonylurea or other ALS-inhibiting chemicals (European Patent Application 154,204, 1985); a methotrexate-resistant DHFR gene (Thillet et al, J. Biol. Chem.. 263. 12500 (1988)); a dalapon dehalogenase gene that confers resistance to the herbicide dalapon; or a mutated anthranilate synthase gene that confers resistance to 5- methyl tryptophan. Where a mutant EPSP synthase gene is employed, additional benefit may be realized through the incorporation of a suitable chloroplast transit peptide (CTP). Selectable markers can also be, for example, luciferase, glucuronosidase (GUS), or green fluorescent protein (GFP).
An illustrative embodiment of a selectable marker gene capable of being used in systems to select transformants is the gene set that encodes the enzyme phosphinothricin acetyltransferase, such as the bar gene from Streptomyces hygros copious or the pat gene from Streptomyces viridochromogenes (U.S. Pat. No. 5,550,318, which is incorporated by reference herein). The enzyme phosphinothricin acetyl transferase (PAT) inactivates the active ingredient in the herbicide bialaphos, phosphinothricin (PPT). PPT inhibits glutamine synthetase, (Murakami et al., Mol. Gen. Genet.. 205. 42 (1986); Twell et al., Plant Physiol. 91. 1270 (1989)) causing rapid accumulation of ammonia and cell death. Selectable or reporter markers that may be employed include, but are not limited to, a glucuronidase or uidA gene (GUS) which encodes an enzyme for which various chromogenic substrates are known; an R-locus gene, which encodes a product that regulates the production of anthocyanin pigments (red color) in plant tissues (Dellaporta et al, in Chromosome Structure and Function. pp. 263-282 (1988)); a lactamase gene (Sutcliffe, PNAS USA. 75, 3737 (1978)), which encodes an enzyme for which various chromogenic substrates are known (e.g., PAD AC, a chromogenic cephalosporin); axylE gene (Zukowsky et al, Proc. Nat'l. Acad. Sci. USA. 80, 1101 (1983)) which encodes a catechol dioxygenase that can convert chromogenic catechols; an amylase gene (Ikuta et al, Biotech.. 8, 241 (1990)); a tyrosinase gene (Katz et al, J. Gen. Microbiol. 129, 2703 (1983)) which encodes an enzyme capable of oxidizing tyrosine to DOPA and dopaquinone which in turn condenses to form the easily detectable compound melanin; a galactosidase gene, which encodes an enzyme for which there are chromogenic substrates; a luciferase (lux or luc) gene (Ow et al, Science, 234, 856 (1986)), which allows for bioluminescence detection; or even an aequorin gene (Prasher et al, Biochem. Biophys. Res. Comm.. 126. 1259 (1985)), which provides calcium-sensitive bioluminescence detection, or a green fluorescent protein gene (Niedz et al, Plant Cell Reports. 14, 403 (1995)). The presence of the lux gene in transformed cells may be detected using, for example, X-ray film, scintillation counting, fluorescent spectrophotometry, low- light video cameras, photon-counting cameras, or multiwell luminometry. It is also envisioned that a such a detectable marker may be used for populational screening for bioluminescence, such as on tissue culture plates, or even for whole plant screening.
Host Cells
The nucleic acids, expression cassettes and/or vectors of the invention are introduced into prokaryotic or eukaryotic host cells by available methods.
Methods of transformation include, but are not limited to, the syringe infiltration method, the vacuum infiltration method (Bechtold et al, C.R. Acad. Sci. Paris, 316:1194-1199 (1993)), the microprojectile bombardment of immature embryos (U.S. Pat. No. 5,990,390) or Type II embryogenic callus cells as described by W.J. Gordon-Kamm et al (Plant Cell 2, 603 (1990)), M.E. Fromm et al (Bio/Technology. 8, 833 (1990)) and D.A. Walters et al. (Plant Molecular Biology, 18. 189 (1992)), or by electroporation of type I embryogenic calluses described by D'Halluin et al. (The Plant Cell. 4, 1495 (1992)), or by Krzyzek (U.S. Patent No. 5,384,253, issued January 24, 1995). Transformation of plant cells by vortexing with DNA-coated tungsten whiskers (Coffee et al, U.S. Patent No. 5,302,523, issued April 12, 1994) and transformation by exposure of cells to DNA-containing liposomes can also be used. Other methods include micropipette injection, polyethylene glycol (PEG) mediated transformation of protoplasts, and gene gun or particle bombardment techniques. Host cells containing the nucleic acids or vectors of the invention can be selected or isolated using the selectable markers or reporter genes described herein. Host cells are cultured using available tissue culture and conditions optimized to allow growth and accumulation of host cells containing the nucleic acids or vectors of the invention.
Transient Plant Transformation Nucleic acids of the invention can be introduced into plant cells or plants by the methods described above under the section entitled Host Cells. For transient expression and transformation of plants, the infiltration method is preferred, for example, as described by Bechtold et al, (1993); see also U.S. Patent 6,291,742. In general, intact plants are immersed in a suspension of nucleic acid, vector, or bacteria containing the nucleic acid or vector, then transferred to a vacuum chamber and placed under vacuum until the plant tissues appear uniformly water-soaked. Plants are then grown under standard conditions.
Transiently transformed plants have some advantageous properties. For example, expression at discrete time periods in a plant's life cycle may be desirable and higher levels of expression can often be obtained when a protein is transiently expressed. Moreover, plants that do not stably transmit a genetic trait encoded in the vectors of the invention are not capable of dispersing that trait to related plants. Accordingly, other plants will not be inadvertently altered by the genetic trait. Moreover, the public may exhibit less concern that the environment will be adversely affected by genetically engineered organisms than if the plant were stably transformed and capable of transmitting the genetic trait to other plants.
Accordingly, the invention provides a method of transiently expressing a nucleic acid (e.g. an inhibitory NCED RNA) or a NCED protein of the invention in a plant that includes contacting a plant with a vector or nucleic acid of the invention, replicating the vector or nucleic acid within the plant and expressing a protein encoded by the nucleic acid or the vector. Such a nucleic acid may present in an expression cassette and/or within the vector. This method involves amplifying, i.e., increasing the copy number, of a nucleic acids or vectors of the invention, thereby permitting expression of an encoded protein over basal levels obtained in the absence of amplification. hi another embodiment, the nucleic acid or vector is provided in the plant but is not stably integrated into the germ line of the plant, and the method involves replicating the nucleic acid or vector within the plant and expressing an encoded protein. Such a nucleic acid may be present in an expression cassette and/or within a vector. The invention also provides a method of amplifying a nucleic acid of the invention that involves replicating a nucleic acid or vector of the invention within a host cell. The host cell can be any host cell, for example, any of those described herein, as well as any organism or plant contemplated herein.
Stable Plant Transformation
Nucleic acids of the invention can be introduced into plant cells or plants by the methods described above under the section entitled Host Cells. The infiltration method can also be used for stable transformation of whole plants, plant calli or plant cuttings by exposing the plants, calli and cuttings to the present vectors, and identifying transformants. Transformed embryogenic calli, meristemate tissue, embryos, leaf discs and the like can be used to generate transgenic plants that exhibit stable inheritance of the nucleic acids of the invention. Plant cell lines having the nucleic acids of the invention are put through a plant regeneration protocol to obtain mature plants and seeds expressing the traits by methods well known in the art (for example, see U.S. Pat. Nos. 5,990,390, 5,489,520; and Laursen et al, Plant Mol Biol.24, 51 (1994)). The plant regeneration protocol allows the development of somatic embryos and the subsequent growth of roots and shoots. To determine that the vector is present in differentiated organs of the plant, and not solely in undifferentiated cell culture, regenerated plants can be assayed for the selectable markers and/or reporter genes described herein, in various portions of the plant relative to regenerated, non-transformed plants. Transgenic plants and seeds can be generated from transformed cells and tissues having the present nucleic acids by using standard methods.
Mature plants can be obtained from cell lines that contain the present vectors. If possible, the regenerated plants are self-pollinated. In addition, pollen obtained from the regenerated plants is crossed to seed grown plants of agronomically important inbred lines. In some cases, pollen from plants of these inbred lines is used to pollinate regenerated plants. The nucleic acids and vectors of the invention are genetically traced by evaluating the segregation of the selectable marker or reporter gene in first and later generation progeny. The heritability and expression in plants of traits selected in tissue culture are of particular importance if the traits are to be commercially useful.
The commercial value of the plants of the invention can be optimized by providing different combinations of hybrids. The farmer typically grows more than one kind of hybrid based on such differences as maturity, standability or other agronomic traits. Additionally, hybrids adapted to one part of the country are not adapted to another part because of differences in such traits as maturity, disease, and insect resistance. Because of this, it is preferable to breed the nucleic acids into a large number of parental lines so that many hybrid combinations can be produced. A conversion process, known as backcrossing, is carried out by crossing the original producing line to normal elite lines and then crossing the progeny back to the normal parent. The progeny from this cross will segregate such that some plants carry the gene responsible for production whereas some do not. Plants carrying such genes will be crossed again to the normal parent resulting in progeny that segregate for production and normal production once more. This is repeated until the original normal parent has been converted to an producing line, yet possesses all other important attributes as originally found in the normal parent. A separate backcrossing program is implemented for every elite line that is to be converted to production line capable of expressing the heterologous nucleic acids in the expression cassettes of the invention.
Subsequent to the backcrossing, the new producing lines and the appropriate combinations of lines that make good commercial hybrids are evaluated for production as well as a battery of important agronomic traits. Producer lines and hybrids are produced which are true to type of the original normal lines and hybrids. This requires evaluation under a range of environmental conditions where the lines or hybrids will generally be grown commercially. Parental lines of hybrids that perform satisfactorily are increased and used for hybrid production using standard hybrid seed production practices. Transgenic plants may find use in the commercial manufacture of proteins or other molecules, where the molecule of interest is extracted or purified from plant parts, seeds, and the like. Cells or tissue from the plants may also be cultured, grown in vitro, or fermented to manufacture such molecules. The transgenic plants may also be used in commercial breeding programs, or may be crossed or bred to plants of related crop species. Improvements encoded by the recombinant DNA may be transferred, e.g., from cells of one species to cells of other species, e.g., by protoplast fusion.
The invention also provides for a method of stably expressing a protein of the invention in a plant, which includes, contacting the plant cell with a nucleic acid or vector of the invention that has an associated selectable marker gene, under conditions effective to infect or transfect the plant cell. The nucleic acid of the invention can be provided with an expression cassette as described herein. A promoter within the expression cassette can be any of the promoters provided herein, for example, a constitutive promoter, an inducible promoter, a tissue-specific promoter or a fruit ripening-dependent promoter. Such promoters can provide expression of an encoded protein at a desired time, or at a desired developmental stage, or in a desired tissue.
The invention also provides for a method of stably expressing an inhibitory RNA or a NCED protein of the invention in a plant, which includes, contacting the plant cell with a nucleic acid encoding the an inhibitory RNA or a NCED protein of the invention, under conditions effective to transfer and integrate the nucleic acid into the nuclear genome of the cell. After integration, a plant may be generated from the plant cell using available methods, including those described herein. The plant or the plant cell may be exposed to a chemical or developmental agent, which induces expression of the inhibitory RNA or protein in the cell. The nucleic acid may be present in a vector that can also include a selectable marker gene. When using such a vector with Agrobacterium tumefaciens, the vector can have an Agrobacterium tumefaciens origin of replication.
Plants Plants for use with the NCED nucleic acids and polypeptides of the invention include dicots and monocots, including but not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B. juncea), particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatus), cassava (Manihot esculenta), coffee (Cofea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado (Persea americana), fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica), olive (Olea europaea), papaya (Carica papaya), cashew (Anacardium occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, barley, vegetables, ornamentals, and conifers; duckweed (Lemna, see WO 00/07210, which includes members of the family Lemnaceae. There are known four genera and 34 species of duckweed as follows: genus Lemna (L. aequinoctialis, L. disperma, L. ecuadoriensis, L. gibba, L. japonica, L. minor, L. miniscula, L. obscura, L. perpusilla, L. tenera, L. trisulca, L. turionifera, L. valdiviana); genus Spirodela (S. intermedia, S. polyrrhiza, S. punctata); genus Woffia (Wa. angusta, Wa. arrhiza, Wa. australina, Wa. borealis, Wa. brasiliensis, Wa. columbiana, Wa. elongata, Wa. globosa, Wa. microscopica, Wa. neglecta) and genus Wofiella (WI. caudata, WI. denticulata, WI. gladiata, WI. hyalina, WI. lingulata, WI. repunda, WI. rotunda, and WI. neotropica). Any other genera or species of Lemnaceae, if they exist, are also aspects of the present invention. Lemna gibba, Lemna minor, and Lemna miniscula are preferred, with Lemna minor and Lemna miniscula being most preferred. Lemna species can be classified using the taxonomic scheme described by Landolt, Biosystematic Investigation on the Family of Duckweeds: The family of Lemnaceae - A Monograph Study. Geobatanischen Institut ETH, Stiftung Rubel, Zurich (1986)); vegetables including tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo). Ornamentals include azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum. Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata), Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga canadensis); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and balsam fir (Abies balsamea); and cedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis); and leguminous plants.
Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc. Legumes include, but are not limited to, Arachis, e.g., peanuts, Vicia, e.g., crown vetch, hairy vetch, adzuki bean, mung bean, and chickpea, Lupinus, e.g., lupine, trifolium, Phaseolus, e.g., common bean and lima bean, Pisum, e.g., field bean, Melilotus, e.g., clover, Medicago, e.g., alfalfa, Lotus, e.g., trefoil, lens, e.g., lentil, and false indigo. Other plants for use with the nucleic acids and proteins of the invention include Acacia, aneth, artichoke, arugula, blackberry, canola, cilantro, Clementines, escarole, eucalyptus, fennel, grapefruit, honey dew, jicama, kiwifruit, lemon, lime, mushroom, nut, okra, orange, parsley, persimmon, plantain, pomegranate, poplar, radiata pine, radicchio, Southern pine, sweetgum, tangerine, triticale, vine, yams, apple, pear, quince, cherry, apricot, melon, hemp, buckwheat, grape, raspberry, chenopodium, blueberry, nectarine, peach, plum, strawberry, watermelon, eggplant, pepper, cauliflower, Brassica, e.g., broccoli, cabbage, brussel sprouts, onion, carrot, leek, beet, broad bean, celery, radish, pumpkin, endive, gourd, garlic, snapbean, spinach, squash, turnip, asparagus, and zucchini and ornamental plants include impatiens, Begonia, Pelargonium, Viola, Cyclamen, Verbena, Vinca, Tagetes, Primula, Saint Paulia, Agertum, Amaranthus, Antihirrhinum, Aquilegia, Cineraria, Clover, Cosmo, Cowpea, Dahlia, Datura, Delphinium, Gerbera, Gladiolus, Gloxinia, Hippeastrum, Mesembryanthemum, Salpiglossos, and Zinnia.
Absisci Acid Biosynthetic Pathway and NCED3
The NCED3 gene encodes the 9-cis-epoxycarotenoid cleavage enzyme that is thought to catalyze a rate-limiting reaction in ABA biosynthesis (luchi et al, 2001). The gene encoding this enzyme is induced by osmotic stress in Arabidopsis and several other species and, according to the invention, this NCED3 gene plays a key role in ABA-mediated responses to osmotic stress such as increased seed dormancy, reduced seedling growth, stomatal behavior, increased osmotic adjustment and transition to flowering (Leon-Kloosterziel et al, 1996 ). In Arabidopsis there is a small family of at least seven NCED genes, luchi et al. (2001), have shown that the NCED3 and to a small extent NCED9 genes in Arabidopsis are desiccation-induced but other members of the NCED gene family are not. Ablation of the ABA response in plants with a mutated nced3 gene leads to many changes in gene expression. Prior to the invention, however, only a few changes in such expressionhave been examined. Anti-sense expression of the NCED 3 gene leads to suppression of desiccation induction of the RD29B gene but not the RAB18 or KIN1 genes. According to the invention, the transcript of the ABA-induced ICK1 gene also fails to accumulate in NaCl- treated stol/nced3 plants. The affects of the nced3 mutation on other gene expression and physiological responses may depend on the specific effects of this mutation on tissue and cell-specific perturbations in ABA content. Disruption of the NCED3 gene has revealed that in Arabidopsis this leads to a syndrome of phenotypic changes that indicates that there may be a number of ABA-associated responses to stress that are not always necessarily coupled in previously assumed ways. For instance, it has been generally believed that when plants are exposed to decreased water potential, cell growth ceases or slows due to inadequate solute potential needed to compensate for the water potential imbalance with the environment (Morgan et al, 1984; Bressan et al., 1990). The resulting low tissue water potential leads to increased ABA or some other signal response, which in turn affects osmotic adjustment that compensates for the reduced turgor, allowing resumption of water uptake and re-growth (Wilkinson et al, 2002; Bressan et al, 1990). This relationship between osmotic adjustment and growth of plants during desiccation or other osmotic stresses has been explored by workers in the art (Sharp et al, 1994; Morgan et al, 1984). ABA therefore has an important role in coordinating growth and osmotic adjustment responses to environments with decreased availability of water has been well established (see Sharp et al, 1994; Giraudat, 1995). However, the primary affects of ABA in this co-ordination are complex and never have been clearly defined. Some general principals, such as increased ABA accumulation in plants resulting from osmotic stress often facilitates root growth and restricts shoot growth, have emerged from the observations of many studies using hormone and other pharmacological treatments, (Spollen et al, 2000). Surprising, few studies have attempted to clarify this issue using recently available ABA biosynthesis mutants that are available in Arabidopsis and other species (Sharp et al, 2000; Sharp, 2002; Sharp and Le Noble, 2002). This invention identifies the stol/nced3 mutant of Arabidopsis as a mutant that exhibits enhanced germination, and increased root and shoot growth at low water potentials, (Figures 1, 2 and 3) indicates that ABA increase during osmotic stress in wild type plants reduces growth. In fact, not only do root and shoots of stol nced3 mutant seedlings grow faster than wild type plants at low water potentials caused by salinized medium but they also have significantly more positive osmotic potentials (lower osmotic adjustment). These results indicate that the effect of ABA on growth can be direct and not always dependent on ABA effects on osmotic adjustment. In fact, the greater osmotic adjustment in wild type plants may largely be facilitated by ABA-mediated reduction of growth allowing passive solute accumulation. Nuccio et al. (1999) calculated that reduced cell growth rate after adaptation to salt may account for 60% of the observed accumulation of the solute proline. Even though results indicate that in response to osmotic stress, ABA-mediated signaling affecting osmotic adjustment is at least partially uncoupled from growth, the mechanism of uncoupling remains unclear. Cell growth rate obviously must depend on and thus appears to be tightly linked to osmotic adjustment (Bressan et al, 1990) perhaps as in yeast where the same receptor mediates both cell growth and osmotic adjustment pathways (Maggio et al, In press).
Another interesting possibility regarding stress-induced growth reduction arises from our observations of the growth of stol nced3 mutant plants. Both NaCl and sorbitol treated stol/nced3 plants have sufficient osmotic adjustment to sustain growth, since their apparent turgor levels (assuming both are at water potential equilibrium with the medium inside the closed Petri plates) are similar to unstressed plants. However, only the NaCl-treated stol/nced3 plants do not exhibit normal stress-induced growth inhibition. Sorbitol-treated plants, however, actually exhibit more growth inhibition (compared to wild-type plants). Apparently, under these conditions osmotic stress-induced growth inhibition caused by salt, is largely dependent on ABA, and ablation of the stress-induced increase in ABA accumulation in stol/nced3 mutant plants allows faster growth. However non-ionic osmotic stress mediated by sorbitol can apparently inhibit growth by an ABA-independent pathway, since stol/nced3 plants exhibit osmotic-stress induced growth reduction without the normal increased ABA accumulation associated with osmotic stress (Figure 4). In fact, increased ABA appears to be required for growth maintenance during nonionic osmotic stress as reported previously (Sharp, 2002). This strongly implies that plants are able to sense ionic and non-ionic osmotic stresses differently.
The role of ABA in non-turgor dependent growth inhibition has recently received more experimental attention (Sharp et al, 2000). Recent studies have revealed that there is a very close connection between ABA and C2FJ , and that the interaction of these two hormones may often affect plant tissue growth rates at low water potentials (Sharp, 2002; Sharp and LeNoble, 2002). Spollen et al. (2000) have reported that in maize, ABA is required to maintain root growth at low water potentials and that this effect can be related to dependence of growth on ABA-restricted ethylene production. In addition Arabidopsis seed germination and growth can be stimulated by ethylene (Ghassemian et al, 2000). However, ethylene treatment oϊstol/nced3 mutant seeds did not further stimulate germination and growth as it does in wild type seeds and plants (Figure 13). Furthermore, consistent with the maintenance of a basal level of ABA, ethylene levels in the stol/nced3 mutant were modestly higher than wild type seedlings (Figure 12), suggesting that impaired ABA production during osmotic stress in stol/nced3 plants may also affect their sensitivity to ethylene, allowing faster germination and growth (Ghassemian et al, 2000).
Whatever the involvement of ABA and ethylene in controlling stress- induced growth reduction, the mechanism by which ABA level exerts its influence on growth is unknown. This mechanism should, however, involve control of cell division, since the rate of leaf formation of stol/nced3 plants during stress was also accelerated compared to controls (Figure 13B). This indicates that there is a clear increase in rate of leaf cell division and not just cell enlargement in stol/nced3 plants during salt exposure compared to wild type plants. Considerable progress in elucidating important regulators of plant cell division has been made in recent years (Wang et al, 1998; De Neylder et al, 2001) and the ICK1 gene encoding a cyclin-dependent kinase inhibitor appears to play a crucial role in cell cycle regulation in Arabidopsis. Furthermore, this gene is regulated by ABA and has been proposed to mediate ABA effects on cell growth and development (Wang et al, 1998; Wang et al, 2000). Plants with a defective NCED3 gene fail to increase ABA accumulation in response to salt stress and also fail to increase levels of ICK1 transcript under the same conditions. This is further evidence that the almost universally observed decrease in plant growth after exposure to osmotic stress is mediated by signal transduction events directly leading to growth through altered activities of cell cycle division and other growth processes rather than indirectly affecting only the physical-chemical changes controlling water flux (Wang et al, 1998). luchi et al. (2001) have reported that overexpression of the NCED3 gene results in plants with increased ability to survive severe desiccation stress. However, they did not compare growth responses of either nced3 mutant plants or plants overexpressing nced3 on salinized versus desiccated soil. In addition, our results imply that NCED3 overexpressing plants may display reduced growth even in the absence of stress that is independent of the consequences of increased ABA on plant water status.
This invention has identified the specific characteristics of the stol/nced3 mutant that influence ABA in directly controlling stress-induced growth and development. These effects include ABA effects on stomatal function and indicate that the diminished capacity of stol/nced3 plants to accumulate ABA at low water potentials dramatically alters stomatal behavior (Figure 14). Other studies on stomatal have not explored the relationship between these alterations in ABA physiology and the diurnal cycle of stomatal movements that is largely controlled by light and CO levels (Hedrich et al, 2001). Most studies have employed epidermal peels (Raschke et al, 1979) which are, of course, disconnected from mesophyl, root and other tissues. Experiments provided by the invention reveal that a failure to increase ABA levels after osmotic stress in stol/nced3 plants leads to very normal (without stress) diurnal stomatal movements with only altered upper and lower limits of stomatal aperature being imposed by the level of ABA. As soil desiccation is increased, diurnal opening is suppressed and diurnal closing is enhanced by the normal, wild type accumulation of ABA (Figure 14B). Changes in the diurnal range of stomatal aperture were correlated with reduced ABA levels in stol/nced3 plants. Even under continually desiccating conditions of the soil that eventually lead to plant death, the degree of water loss rate in stol/nced3 plants was increased only about 20%. This indicates that relatively small changes in the dynamics of water absorption and loss can result in dramatic consequences for plant growth and survival.
The invention will now be illustrated by the following non-limiting Examples. EXAMPLE: Stress Resistant Plants
This Example illustrates the isolation and characterization of a stol (for salt tolerant) mutation that lead to the identification of the nced3 gene as an important regulator of tolerance to environmental stress. As shown herein both mutation and over-expression of the nced3 gene can lead to tolerance by plants to environmental stress.
Experimental procedures
Plant material and growth conditions Arabidopsis thaliana C24 line homozygous for the chimeric
RD29A::LUC reporter gene (Ishitani et α/.,1997) was provided by Professor J.K. Zhu, University of Arizona. A T-DNA population was obtained after Agrobacterium tumefaciens floral transformation with GV3101 (pMP90RK) carrying the binary vector pSK1015 and selection based on Liberty (bialaphos) (30 mg/1) resistance (Koiwa et al. , 2002). Herbicide resistant plants were combined into 10 plant pools and T seeds were collected for screening. Plants from T2 seeds were grown either in a controlled environment room with 16 hr of light at 22° C and 8 hr in darkness at 18° C or in a greenhouse. The screening was performed in vitro for the ability of the seeds to germinate in a media containing 145 mM NaCl Seeds were surface sterilized (2% sodium hypocloride for 15 min.), sowed onto medium containing Murashige and Skoog (MS) basal salt mixture, 2% sucrose, 145 mM NaCl, solidified with 1% agar (pH 5.7). After sowing the seeds were stratified for 2 to 4 days at 4°C. For the mutant characterization in vitro, MS either contained no supplement or was supplemented with 100, 130, 145, 150, 200, 250 mM NaCl±ABA, 20 mM
LiCl±ABA, or 160 mM KC1. For hygromicin selection, seeds were plated onto medium containing 1/4X MS salt, 30μg/ml hygromicin B, 100 μg/ml tiamine and 1% agar.
Germination assay
^t-C24-(RD29::LUC) wild type (wt) and t-C24-(RD29::LUC) stol (stol) mutant seeds were sterilized and sowed on Petri plates containing either basic MS agar medium or MS supplemented with 100, 130, 150, 160, 200, 250 mM NaCl, 160mM KCl or 20 mM LiCl, stratified at 4 °C for 4 days and transferred in a growth chamber with 16 h of light at 22°C and 8 h of darkness at 18°C. Fourteen days after sowing, the number of germinated seeds was assessed. After 7 additional days of growth on saline media plant fresh weight was measured.
Growth on saline medium after germination on non-saline medium
Wild type and stol mutant plants were germinated in vitro on MS medium. Seven-day old seedlings were transferred onto MS medium or MS medium supplemented with 160mM NaCl, 160mM KCl or 20mM LiCl After 20 days from transferring the plants, they were collected for fresh weight measurements.
Germination and growth on non ionic osmotic stress medium ^t-C24-(RD29::LUC) wild type (wt) and ^t-C24-(RD29::LUC) stol
(stol) mutant seeds were sterilized and sowed on Petri plates containing either basic MS agar medium or MS supplemented with 300 mM sorbitol, stratified at 4 °C for 4 days and transferred in a growth chamber with 16 h of light at 22°C and 8 h of darkness at 18°C. Twenty one days after sowing, the number of germinated seeds was assessed. Wild type and stol mutant plants were germinated in vitro on MS medium, 3day old seedlings were transferred onto MS medium or MS medium supplemented with 300mM sorbitol. After 14 days from transferring the plants, they were collected for fresh weight and roots length measurements.
Desiccation stress and salts stress tolerance in soil
Seeds of wild type and stol mutant plants were directly sowed in turface (MPN Bancroft, Bag Inc., Louisiana, USA). Fifty uniform plants from the wild type and stol/nced3 populations were selected and grown in the greenhouse using a standard irrigation regime. After 15 days, when plantlets had reached the stage of 5-6 fully expanded leaves, irrigation was stopped for half of the plants (25 for each genotype), whereas the other half was grown under standard irrigation regime as a control. After 15 days, water stressed plants were re- watered and for 2 additional days were allowed to recover before measuring plant fresh weight. To assess salt stress tolerance in soil under saturated atmospheric humidity, Arabidopsis seeds were directly sowed in turface and allowed to grow for one week under non-saline irrigation. At this stage, five groups of 20 plants each were placed under PNC domes and were daily irrigated with saline water [50, 100, 150, 200mM ΝaCl plus a non- salinized control). After 28 days plants were collected for fresh weight measurements.
Identification of the T-DNA insertion region, Northern blot analyses andRT- PCR
Genomic sequence flanking the T-DΝA insertion was determined by using Thermal Asymmetric Interlaced-PCR (TAIL-PCR) procedure of Liu et al.
(1995) with primers corresponding to the nested regions internal to the left border and degenerate primers as listed below in Table 3. Primers 1, 2, 3, 4, 5 were used for the TAIL-PCR analysis. Primers 3, 6 and 7 were used for the identification of the TDΝA genotype. Primers 6 and 7 were used for the detection of ΝCED-4 gene. Primers 8 and 9 were used to synthesize the probe for the Northern blot hybridization.
Table 3: Primer Sequences
Name Experiment Sequence SEQ ID NO:
1 LB1 TAIL-PCR 5- atacgacggatcgtaatttgtc-3 1
2 LB2 TAIL-PCR 5- taataacgctgcggacatctac-3 2
3 LB3 TAIL-PCR 5- ttgaccatcatactcattgctg-3 3 diagnostic PCR
4 DEG1 TAIL-PCR 5- wgcnagtnagwanaag-3 4
5 DEG2 TAIL-PCR 5- awgcangncwganata-3 5
6 NCED F Gene cloning 5- tggtctctccactgcgttacc-3 6
6 NCED F Gene cloning 5-gggctctgttatgaggcaaagacgc-3 17
7 NCED R T-DNA detection 5-cagatgaagtcgtcgtgatga-3 7
7 NCED R Gene cloning 5 -ggtggatcccatcagtgtgg-3 18
8 NCED F Norten's probe 5- cgtgaaatccgtacggaacc-3 8
8 NCED F Gene cloning 5 -ccacactgatgggatccacc-3 19 9 ncedR Norten's probe 5- ccggaatccggtgaactctt-3 9
9 NCED R Gene cloning 5 -agctgagctcgaacggctag-3 20
10 NCED F T-DNA detection 5-tggtctctccactgcgttacc-3 6 diagnostic PCR
11 NCED R T-DNA detection 5-cagatgaagtcgtcgtgatga-3 diagnostic PCR
Primers for Northern probes
12 NCED F 5- cgtgaaatccgtacggaacc-3 21 13 NCED R 5- ccggaatccggtgaactctt-3 22 14 ICK1 F 5-ccgtcgtcggtgataatgga-3 23 15 ICK1 R 5-ctaatggcttctccttctcg-3 24
Total RNA was isolated from wild type and stol/nced3 plants germinated in control medium or in medium containing 145mM NaCl. Using the RNAeasy total RNA isolation kit (Quiagen, Valencia, CA, USA), 10 μg of total RNA were isolated and electrophoretically separated on denaturing formaldehyde-agarose gels and blotted onto nylon membrane (Schleicher & Schuell, Keene, NH, USA). RNA was crosslinked to the membrane and the membrane was hybridized with DIG-labeled DNA probe (Roche, Indianapolis, IN, USA). The probe was produced by PCR reaction using the primers listed in Table 3. The blots were washed twice in 2 X SSC and 0.1% (w/v) SDS at 25°C, and twice in 0.5 X SSC and 0.1 (w/v) SDS at 65°C.
Total RNA for RT-PCR was extracted as described. First strand cDNA was synthesized using the Superscript II kit (Gibco BRL, Rockville, MD, USA). First-strand cDNA of total RNA (4ug) from shoots of three- week old plants was used for PCR amplification. PCR was carried out using ExTaq DNA polymerase (TaKaRa, Shiga, Japan) and gene-specific primers for stol/nced3 as described in Table 3.
Genetic analysis and complementation
Stable F3 stol mutant plants were backcrossed with the parental C24 wild type plants and co-segregation for the stol salt tolerance (germination assay) and herbicide resistance phenotypes was determined in FI and F2 generations.
Three separate fragments of 2.2, 0.8, and 2.3 kbp, respectively were amplified from the BAC clone MOA2.4 and sub-cloned into pBluescript. The resulting 4.5 kbp DNA fragment was digested with Smal(5') and Kpnl(3') and ligated into the pBIB vector (Higromycin+). The plasmid was transferred into Agrobacterium strain GV3101. The Agrobacterium transformed colonies were selected with 50mg/l kanamicin (binary vector marker), 30mg/l rifampicin (agro strain marker) and 30mg/l gentamycin (Ti-plasmid marker). Single transformed colonies were isolated and grown in liquid medium, confirmed for their insert size by PCR, and stored frozen at -80°C. A 5μl aliquot from the -80°C stock was used to inoculate 250ml of Yeast Extract Phosphate (YEP) medium (DIFCO, Becton Dickinson & Co., Sparks, MD, USA) plus appropriate antibiotics and incubated on a shaker in the dark at 28°C and allow to grow to an OD60oof >1.5 to 2.0 (16-20 hr). The bacteria were then centrifuged for 10 min. at 4000rpm and the resulting pellet was re-suspended in 500ml of Agrobacterium infiltration medium (2.3g/l MS salt, 50g/l sucrose, O.Olmg/1 N6-benzilaminopurine, 200μl/l Silwet L-77 (pH 5.7). Flower buds of 30day old stol plants were sprayed with the infiltration solution and kept at high humidity for 24 hr. Plants were then transferred to the green house and grown under standard conditions. FI seeds were collected and selected for hygromycin resistance on MS medium. F2 plants from five Hyg+ lines that were confirmed homozygous for the insertion in the NCED 3 gene were grown and analyzed by RT-PCR for the expression of the NCDE3 gene. One of the 5 transgenic lines (4-6) was tested for salt tolerance using the germination assay and for soil desiccation tolerance.
ABA extraction and quantification
ABA was extracted as described by Xiong et al. (2001) from 3week old wild type and stol/nced3 plants grown in Petri plates on standard MS or MS supplemented with 145 mM sorbitol. ABA was quantified using an immunoassay ELISA kit according to the manufacturer's instructions (Phytodetek ABA, AGDIA, Elkhart, IN, USA). Osmotic potential measurements
The sap osmotic potential of wild type and stol/nced3 plants was measured after germination and growth on NaCl- and sorbitol- containing media. Fifteen days after germination, plantlets were collected, frozen in liquid nitrogen, and centrifuged for 20 min. at 4000 rpm in microcentrifuge tubes. Further separation of the cellular fluid from plant debris was obtained by centrifugation at 10000 rpm for 10 min. and osmotic potential was measured using lOμl samples with a Wescor 5500 vapor pressure osmometer (Wescor Inc. Logan, Utah, USA). The same procedure was followed for plants sown and grown for 7 days on basic MS medium and then transferred and grown for an additional 15 days on NaCl or sorbitol media before measuring the osmotic potential.
Transpiration measurements Wild type and stol/nced3 mutant plants were grown in turface in 100ml pots. At day 21 after sowing, each pot was covered with a plastic bag with the sealed shoot protruding outside the bag. This system was used to avoid water loss from the soil surface. Each plant was then placed on an electronic balance under a light intensity of 140μmol m"2 s"1 at 25° C, and the weight loss was automatically measured every hour for 24 hours using PC software. Water loss values were normalized for plants dry weight taken at the end of the experiment.
Pharmacological complementation of the stol salt tolerant phenotype
Wild type and stol/nced3 mutant seeds were sterilized and sown in vitro on MS medium or MS medium supplemented with 160mM NaCl±20μM ABA, stratified at 4°C for 4 days and placed in a growth chamber with 16 hr of light at 22° C and 8 hr of darkness at 18° C. The number of germinated seeds was determined periodically over a 21 day time interval.
Pharmacological complementation of LiCl sensitivity of stol plants
Wild type and stol/nced3 mutant plants were germinated in vitro on MS medium. Seven-day old seedlings were transferred onto MS medium or MS medium supplemented with 20mM LiCl±20μM ABA. Seedlings were allowed to grow for additional 7 days before visual assessment of LiCl sensitivity.
Ethylene treatment and measurements Wild type and stol/nced3 mutant plants were germinated on MS medium. Seven-day old seedlings were transferred onto MS medium or MS supplemented with 160mM NaCl, 160mM KCl or 20mM LiCl. Ten plates (each containing 20 seedlings per each genotype) were placed in two sealed Plexiglas chambers (5 plates per chamber). Ethylene was added in one of the two chambers to a final concentration of 20ppm. After 10 days, plant growth and development was quantified by counting the number of new leaves.
Ethylene production in wild type and stol/nced3 mutant plants was assayed on 7day old seedlings germinated on basic MS medium and then transferred in liquid medium. Seedlings were allowed to grow for 7 days in 3 ml of a 6 ml plastic syringe filled with liquid MS or MS supplemented with 160mM NaCl. Ethylene accumulated during this time in the remaining 3ml volume of the syringe and was collected by injecting the non-liquid volume (air) of the syringe in sealed vials. The ethylene concentration was subsequently quantified using standard GC analysis and normalized per 0.5 g of plant FW.
Results Identification of the stol mutant from a T-DNA mutagenized population of Arabidopsis thaliana
A population of over 300,000 T-DNA tagged Arabidopsis thaliana (ecotype C24) mutants was generated as described in Koiwa et al. (2002).
Approximately 11,000 T2 lines were screened based on their ability to germinate and grow on MS media containing 145mM NaCl. Two stable genetic mutants able to germinate and grow faster than wild type were isolated and confirmed. One of these two mutants, designated stol (for salt tolerant) was selected for further characterization (Figure 1). Germination assays on MS media plus or minus salt revealed a normal phenotype of the stol seeds in the absence of salt and enhanced germination in the presence of both KCl- and NaCl (Figure 1 A). Fourteen days after sowing, 80% and 60% of stol seeds germinated on 160mM KCl- and NaCl-containing media, respectively, whereas wild type seeds showed 95% (NaCl) or 80% (KCl) inhibition compared to germination on MS control media (Figure IB). Within the first 7 days after germination, stol seedlings developed normal cotyledons and true leaves. In vitro (Figure 2A) and in soil under high atmospheric humidity (Figure 2B) dose response of stol seedlings to increasing NaCl concentrations confirmed their enhanced ability to germinate and subsequently grow faster in presence of high salt.
Genetic Analysis Genetic analysis was performed on the isolated mutants. Arabidopsis thaliana C24 RD29::luc genetic background T3 were crossed with Arabidopsis thaliana C24 (RD29::LUC) nced-4 mutant T3. Four hundred FI plants were tested for the herbicide resistance and for the salt resistant phenotype, 400 F2 plants were tested for the salt resistant phenotype and the herbicide resistant phenotype. In the figure are indicated the percentage of herbicide resistance of the FI and F2 plants and the number of FI and F2 plants showing the salt resistant phenotype and the percentage of F2 plants showing mutant or the wild type phenotype.
Table 4 illustrates the genetic analysis performed on plants bearing the mutant nced-4 allele.
Figure imgf000083_0001
These results indicate that the nced-4 mutation isolated is a recessive mutation in a single nuclear gene. In F2 progeny the ratio of salt tolerance to salt sensitivity is 1:3. The salt resistance phenotype of mutant nced-4 plants also cosegregates with the bialaphos resistance phenotype. hi F2 progeny the ratio of bialaphos resistance to salt sensitivity is 3:1.
Ionic specificity of the enhanced growth response of stol plants
Because germination and growth in the presence of NaCl may involve distinct physiological adaptive responses to stress, stol seedlings were allowed to first germinate on non-saline media and then transferred (at the stage of fully expanded cotyledons) to hyperosmotic media to examine their growth response independent of germination. In the presence of both elevated KCl and NaCl, stol plantlets were able to withstand the abrupt hyperosmotic stress and grow until flowering (data not shown), whereas wild type seedlings became chlorotic upon exposure to high salinity and they never reached flowering (Figure 3). However, in the presence of LiCl, salt commonly used at low concentrations to discriminate between ionic toxicity and osmotic effects of nutrient media (Rus et al, 2001), stol was remarkably impaired in its normal growth (Figure 3), indicating that the stol seedlings are hypersensitive to Li+ ions, possibly via altered activity of an ion transport system specific to Li+ or to an alteration in the expression of a Li sensitive component such as HAL2 (Serrano and Rodriguez- Navarro, 2001). Hypersensitivity of stol seed germination to Li+ was also observed (data not shown). Non-ionic osmotic stress tolerance of stol plants
The osmotic stress tolerance of stol mutants was assessed upon exposure to 300 mM sorbitol (Figure 4). Seeds of stol plants were able to germinate slightly earlier than wild type at 300 mM sorbitol (Figure 4A). In contrast to salt treatment (NaCl and KCl), growth of stol plants on sorbitol medium after germination on medium without sorbitol was inhibited more than the wild type (Figure 4B,C and D). These results indicate that osmotic stress-induced growth inhibition is reduced in stol plants only in salt stress medium.
Desiccation and salt stress tolerance of stol plants grown in soil
The tolerance of stol plants to desiccation stress was also evaluated on soil-grown plants. Irrigation was interrupted at the stage of 6-7 fully expanded leaves and plant response to gradual dehydration of the soil was assessed visually and quantified in terms of plant fresh weight. Mutant stol plants were much more sensitive than wild type to soil desiccation. After one week from interruption of irrigation, stol plants were wilted and weighted approximately 30%) of the wild type plants (Figure 5B). These results are in sharp contrast to those observed during growth of stol plants in Petri plates with saturated humidity and exposed to ion stress (Figure 2A). In fact, when stol plants are grown in soil and exposed to salt stress under high atmospheric humidity (>95%) (Figure 2B) they grow faster than wild type plants exposed to the same stress conditions.
Genetic analysis of stol mutant plants and identification of the STOl locus The stol mutants were crossed to C24 wild type and the resulting FI progeny all presented the wild type salt sensitive phenotype and were Bialaphos resistant (Bialaphos herbicide resistance was the selection marker of the activation tagging vector), indicating that the mutation is recessive (Table 4). F2 seedlings from selfed FI plants revealed a segregation ratio of approximately 3 : 1 for NaCl sensitiviy (C24)/NaCl tolerance (stol) phenotypes (X2 test, P>0.05), which co-segregated with the herbicide resistant phenotype. It was concluded that the stol phenotype was caused by a single recessive nuclear mutation. Thermal asymmetric interlaced-PCR analysis of DNA from stol plants (Koiwa et al, 2002) (Figure 6A), located a single T-DNA insertion in an ORF of Chromosome III (position 11989 of PI clone MOA2.4; Genebank accession #AB028617). Examination of the predicted cDNA nucleotide sequence revealed that the T-DNA was located inside the coding region (-13 bp from the 3 'end) of a gene (NCED3) encoding a putative 9-cis-epoxicarotenoid dioxygenase (similar to 9-cis-epoxicarotenoid dioxygenase GB: AAF26356 Phaseoulus vulgaris), a key enzyme in the ABA biosynthetic pathway (Figure 6C and Table 3).
Molecular and functional evidence for inactivation of the NCED3 (9-cis- epoxicarotenoid dioxygenase) gene in stol mutants
STOl /NCED 3 transcript is expressed in both leaf and root (not shown) tissue of unstressed wild type plants and its level is increased moderately upon 145 mM NaCl treatment (Figure 7) as previously reported (luchi et al, 2001). The ST01/NCED3 transcript abundance was substantially reduced in unstressed stol /need plants compared to wild type plants, possibly due to instability of the transcript (3'). Upon 145 mM NaCl treatment, there was an increase of the ST01/NCED3 transcript abundance in the mutant plants, but the level remained well below that observed in stressed wild type plants (Figure 7). Consistent with the fact that the ST01/NCED3 gene encodes for a key enzyme in ABA biosynthesis, the level of this hormone was significantly affected in stol/nced3 plants (Table 5).
Table 5: ABA Content in Wild Type and stol Plants (ng/g fresh weight)
Figure imgf000085_0001
Values are the mean values of three plants + S.E.
As illustrated in Table 5, the ABA content was lower in stol/nced3 compared to wild type unstressed plants yet, more importantly, it did not accumulate following exposure to hyperosmotic stress. These results indicate that deficiency in the NCED3 enzyme blocked the stress-induced increase in ABA while having little or no effect on the ABA content of unstressed leaves.
Genetic and pharmacological complementation of the stol/nced3 mutant phenotype confirm that inactivation of the ST01/NCED3 gene is responsible for enhanced germination on salt and hyper sensitivity to desiccation and LiCl
To determine whether the mutated stollnced3 gene was responsible for the stol/nced3 mutant phenotype in terms of both enhanced seed germination on hyperosmotic medium and soil desiccation tolerance, a 4.5 kb Smal(5yKpnl(3') genomic fragment, including the full length ST01/NCED3 gene and its promoter, was cloned from wild type C24 plants and introduced via agrobacterium transformation (pBIB vector) into stol/ncedS mutant plants. Ten independent hygromycin-resistant TI transformants were confirmed by RT-PCR analysis and one was selected for further study. Phenotypic and molecular evaluation of line 4-6 revealed that expression of the wild type ST01/NCED3 gene in mutant plants (Figure 8 A) eliminated their enhanced ability to germinate on salt (data not shown) and hypersensitivity to desiccation (Figure 8B). Pharmacological complementation of stol Vnced3 plants by addition of ABA to the medium also reverted both their enhanced germination on NaCl medium (Figure 9) and growth sensitivity in LiCl (Figure 10).
Enhanced growth of stol Mced3 plants on hyperosmotic medium is associated with blockage of ABA-mediated growth inhibition independent of the degree of osmotic adjustment To verify whether the enhanced growth of stol Vnced3 plants was correlated with an increased accumulation of solutes, osmotic potentials in the absence or presence of stress were measured. Surprisingly, cellular saps from stol/nced3 plants had less negative osmotic potential under stress compared to wild type plants (Table 6). Table 6: Osmotic Potential (MPa)a
Control (MS) NaCl Sorbitol
Germinationb wild type -2.2±0.1 -5.3±0.2 -3.4 ±0.2 stol -2.2±0.15 -1.6±0.7 -2.4 ±0.1
Growthc wild type -2.3±0.13 -3.1±0.8 -3.2 ±0.1 stol -2.1±0.09 -1.9±0.1 -2.2 ±0.1 a Nalues are means of 3 seedling preparations ± S.E. b Nalues refer to seeds germinated and grown on non-saline (control), ΝaCl or sorbitol media. c Nalues refer to seeds germinated on non-saline medium and subsequently transferred and grown on non-saline, ΝaCl or sorbitol media (see Experimental procedure for details).
Since the growth of stol Vnced3 plants was not associated with an increased osmotic adjustment, it appears that ABA-mediated stress-induced growth reduction can be uncoupled from osmotic adjustment. It follows that insufficient osmotic adjustment is not the cause of stress-induced growth reduction. Rather, reduced growth during ΝaCl stress appears more the result of direct stress/ABA-mediated changes in growth regulation, h fact, growth related genes, such as cyclin kinase inhibitors (ICK) have been reported to be activated under stress (Wang et al., 1998). Interestingly, we also detected an increase of ICKl transcript level in ΝaCl stressed wild type plants, which in contrast did not change in stol/nced3 plants (Figure 11).
Ethylene treatment of wild type plants phenocopies the stol/nced3 mutation
Since the restriction of ethylene production is a well-established function of ABA and, moreover, considering that ethylene also affects seed germination and growth (Sharp and Le Noble, 2002; Beaudoin et al, 2000), we examined the possibility of a link between ABA and ethylene levels in stol/nced3 plants. Consistent with other observations, (Ghassemian et al, 2000) the ethylene concentration in stol/nced3 was slightly higher compared to the wild type (Figure 12). The ethylene level was also moderately decreased in wild type salt- stressed plants as previously reported, yet it was unaffected in stressed stol/nced3 mutant plants. Ethylene treatment of wild type seeds allowed rapid germination similar to that observed with seeds of the stol/nced3 mutant. Exogenous applications of ethylene also phenocopied the stol/nced3 mutation by suppressing the NaCl-induced growth inhibition and LiCl hypersensitivity of wild type plants (Figure 13). Since the ethylene level of stol Vnced3 mutant plants was only marginally increased, the reduced ABA of this mutant may have also resulted in increased sensitivity to ethylene.
Effects ofstol/nced3 mutation on stomatal function do not override the diurnal effects of the day/night cycle
Because ABA is also directly involved in the regulation of stomatal aperture, the water loss characteristics of stol/nced3 plants were examined. Wild type and mutant plants were grown in the soil for two weeks under a normal irrigation regime. At the stage of 6-8 fully expanded leaves, irrigation was interrupted and plant water loss via transpiration was monitored over a 7day time period (Figure 14A). Mutant stol/nced3 plants always transpired more then wild type plants until day 5, after which they begun to lose turgor and to exhibit a wilty appearance. This result is consistent with an impaired stomatal response to dehydration and to the previously observed desiccation sensitivity of plants with impaired NCED3 expression (Figure 5) (luchi et al, 2001). Because we found that the osmotic stress- induced ABA level was reduced in stol/nced3 mutant plants, stomatal malfunction was expected to occur also during midday water stress. Measurements of daily fluctuations of transpiration fluxes over a 7day time period confirmed higher transpiration of stol/nced3 plants during the midday photoperiod. However, to our surprise our results also revealed higher transpiration fluxes of these plants during night hours (Figure 14B). The upper and lower limits of stomatal aperture but not the amplitude (max-min) of the daily transpiration flux changed in the mutant plants (Figure 14B). We can not fully explain the reduced night stomatal closure of stol/nced3 plants. However, this may be caused by a residual effect of an altered diurnal activity of NCED3 enzyme (Wilkinson and Davies, 2002) affecting ABA levels that subsequently impair stomatal closure at night. Changes in guard cell ABA levels may result from a complex interaction of ABA synthesis, catabolism storage and transport (Wilkinson and Davies, 2002). Nevertheless, the amount of ABA accumulation (Table 5) in the leaves that is controlled by NCED3 appears not to be able to override the diurnal cycle behavior of stomatal aperture which is apparently determined by the composite affects of several simultaneous signals (Shinozaki and Yamaguchi-Shinozaki, 1996; Bray, 2001a; Giraudat and Schroeder, 2001).
Therefore complementation of the altered growth and desiccation tolerance phenotypes of stol Vnced3 plants by transformation with a wild-type NCED3 gene confirmed the identity of the locus responsible for the phenotypic syndrome of the stol/nced3 mutation. Also, application of exogenous ABA to stol/nced3 plants is able to induce a phenotype that mimics wild type.
EXAMPLE 2: NCED-3 Over-Expression Increases Plant Salt Tolerance
This Example illustrates that overexpressing NCED-3 gene in Arabidopsis thaliana plants generates plants that are more tolerant to the salt and the drought stress than in similar plants where the NCED-3 gene is not expressed. Arabidopsis thaliana wild type plants, stol/nced-3 mutant plants and C24 transgenic plants over-expressing the gene NCED-3 under the control of the 35S promoter (named 5-1) were germinated in vivo on control media. Seven days after germination, the plants were watered with a solution containing 160mM NaCl for 15 days, or the plants were exposed for 15 days to drought stress. On the 16th day the plants were rewatered and after 2 days the number of surviving plants was assessed. The results of these experiments are provided in Table 7. Table 7
Figure imgf000090_0001
Table 7 illustrates that over-expression of NCED-3 leads to increased plant survival under stressful conditions such as high salt or low water conditions.
Overexpression of the NCED3 gene in Arabidopsis was achieved in another experiment that employed the cauliflower mosaic virus promoter (35S), or the superpromoter (Super) in an (OCS)3 Mas-bar cassette (see Narasilhulu et al, 1996 Early transcription of Agrobacterium T-DNA genes in tobacco and maize. Plant Cell 8:873-886). Plants were watered normally in 2" pots containing soil for two weeks (6 leaf stage) after which water was withheld for 12 days. Plants were then rewatered and scored as either surviving or not, two weeks following rewatering.
Table 8 illustrates that the abundance of NCED3 transcripts (relative to C24rd29 control plants receiving vectors only) correlates with the percent survival of plant under such dessicating conditions. NCED3 transcripts were detected using the primers for Northern probes that are listed in Table 3.
Table 8
Figure imgf000090_0002
All publications, patents and patent applications are incorporated herein by reference. While in the foregoing specification this invention has been described in relation to certain preferred embodiments thereof, and many details have been set forth for purposes of illustration, it will be apparent to those skilled in the art that the invention is susceptible to additional embodiments and that certain of the details described herein maybe varied considerably without departing from the basic principles of the invention.
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Claims

WHAT IS CLAIMED:
1. A mutant plant comprising a mutated 9-cis-epoxycarotenoid dioxygenase gene so that, as compared to a plant not comprising said mutated gene, the mutant plant exhibits increased salt tolerance or increased stress resistance.
2. A plant comprising a null mutation in an endogenous 9-cis- epoxycarotenoid dioxygenase gene so that, compared to a plant of the same genetic background but without the null mutation in the endogenous 9-cis-epoxycarotenoid dioxygenase gene, the plant exhibits increased salt resistance.
3. A transgenic plant comprising an isolated 9-cis-epoxycarotenoid dioxygenase nucleic acid having SEQ ID NO: 10, SEQ ID NO:ll, SEQ ID NO:12, SEQ ID NO:14-16, SEQ ID NO:26, SEQ ID NO:28, SEQ ID
NO:30, SEQ ID NO:32, SEQ ID NO:34, or a complement thereof, operably linked to a promoter functional in a plant cell, wherein the transgenic plant exhibits increased salt resistance relative to a plant of the same genetic background but without the isolated 9-cis-epoxycarotenoid dioxygenase nucleic acid.
4. A transgenic plant comprising an isolated nucleic acid that encodes an inhibitory 9-cis-epoxycarotenoid dioxygenase RNA that, when expressed from a promoter functional in a plant cell, inhibits the function of endogenous RNA encoding a 9-cis-epoxycarotenoid dioxygenase enzyme; wherein the transgenic plant exhibits increased salt resistance relative to a plant of the same genetic background but without the isolated 9-cis-epoxycarotenoid dioxygenase nucleic acid.
5. The transgenic plant of claim 4, wherein the inhibitory RNA is substantially complementary to the endogenous RNA encoding a 9-cis- epoxycarotenoid dioxygenase enzyme.
6. The transgenic plant of claim 4, wherein the inhibitory RNA is substantially complementary to SEQ ID NO: 1-9, SEQ ID NO: 10, SEQ ID NO:l 1, SEQ ID NO: 12, SEQ ID NO: 14-20, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34.
7. The transgenic plant of claim 4, wherein the inhibitory RNA hybridizes under moderately stringent hybridization conditions to the endogenous RNA encoding a 9-cis-epoxycarotenoid dioxygenase enzyme comprising SEQ ID NO:13, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID NO:33.
8. The transgenic plant of claim 7, wherein the moderately stringent hybridization conditions comprise hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37°C- and a wash in 0.5X to IX SSC at 55 to 60°C.
9. The transgenic plant of claim 4, wherein the inhibitory RNA hybridizes under highly stringent hybridization conditions to the endogenous RNA encoding a 9-cis-epoxycarotenoid dioxygenase enzyme comprising SEQ ID NO: 13, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID
NO:33.
10. The transgenic plant of claim 9, wherein the highly stringent conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0. IX SSC at 60 to 65°C.
11. The plant of claim 3 or 4, wherein the promoter functional in a plant cell is a viral coat protein promoter, a tissue-specific promoter, a ubiquitin promoter, a CaMV 35S promoter, a CaMV 19S promoter, a nos promoter, an Adh promoter, a sucrose synthase promoter, a tubulin promoter, a napin promoter, an actin promoter, a cab promoter, a PEPCase promoter, a 7S-alpha'-conglycinin promoter, an R gene complex promoter, a tomato E8 promoter, a patatin promoter, a mannopine synthase promoter, a soybean seed protein glycinin promoter, a soybean vegetative storage protein promoter, a bacteriophage SP6 promoter, a bacteriophage T3 promoter, a bacteriophage T7 promoter, a Ptac promoter, a root-cell promoter, an ABA-inducible promoter or a turgor-inducible promoter.
12. The plant of claim 2, 3 or 4 wherein the plant develops in the presence of a concentration of salt that would normally inhibit the development of the plant.
13. The plant of claim 2, wherein the plant germinates faster or develops leaves faster than a plant of the same genetic background but without the null mutation.
14. The transgenic plant of claim 3 or 4 wherein the plant germinates faster or develops leaves faster than a plant of the same genetic background but without the isolated nucleic acid.
15. The transgenic plant of claim 2, 3 or 4, wherein the plant is alfalfa, avocado, Brassica campestris, canola, cantaloupe, cotton, cowpea, cranberry, cucumber, eucalyptus, fescue, flax, gladiolus, lettuce, liliacea, maize, mellon, millet, muskmelon, oat, oil palm, olive, papaya, peanut, perennial ryegrass, potato, rapeseed, rice, rye, safflower, sorghum, soybean, sugarbeet, sugarcane, sunflower, tritordeum, turfgrass, or wheat.
16. The transgenic plant of claim 2, 3 or 4, wherein the plant is a dicot.
17. The transgenic plant of claim 16, wherein the dicot is soybean.
18. The transgenic plant of claim 2, 3 or 4, wherein the plant is a monocot.
19. The transgenic plant of claim 18, wherein the monocot is corn, rice, rye, oats or wheat.
20. Food or feed produced from the transgenic plant of claim 2, 3 or 4.
21. A progeny plant obtained from the transgenic plant of claim 2, wherein the progeny plant comprises the null mutation, and wherein the progeny plant is able to develop in the presence of a concentration of salt that inhibits the development of a plant not comprising the null mutation.
22. A transgenic progeny plant obtained from the transgenic plant of claim 3 or 4, wherein the progeny plant comprises the isolated 9-cis- epoxycarotenoid dioxygenase nucleic acid, and wherein the progeny plant is able to develop in the presence of a concentration of salt that inhibits the development of a plant not comprising the 9-cis- epoxycarotenoid dioxygenase nucleic acid.
23. A seed obtained from the plant of claim 2, wherein said seed comprises the null mutation, and wherein the sees is able to develop in the presence of a concentration of salt that inhibits the development of a seed not comprising the null mutation.
24. A progeny plant obtained from the seed of claim 23.
25. A transgenic seed obtained from the transgenic plant of claim 3 or 4, wherein said seed comprises the isolated 9-cis-epoxycarotenoid dioxygenase nucleic acid, and wherein the seed is able to develop in the presence of a concentration of salt that inhibits the development of a seed not comprising the 9-cis-epoxycarotenoid dioxygenase nucleic acid.
26. A progeny plant obtained from the seed of claim 25.
27. A transgenic plant comprising an isolated recombinant DNA comprising a promoter functional in a plant cell that is operably linked to a DNA encoding a 9-cis-epoxycarotenoid dioxygenase or a functional subunit thereof so that RNA is expressed from the recombinant DNA sequence in the transgenic plant so as to increase at least one of the drought, cold, salt, osmotic or pathogen tolerance of the transgenic plant.
28. The transgenic plant of claim 25 wherein the promoter is induced by stress.
29. The transgenic plant of claim 25 wherein the promoter functional in a plant cell is a viral coat protein promoter, a tissue-specific promoter, a ubiquitin promoter, a CaMV 35S promoter, a CaMV 19S promoter, a nos promoter, an Adh promoter, a sucrose synthase promoter, a tubulin promoter, a napin promoter, an actin promoter, a cab promoter, a
PEPCase promoter, a 7S-alpha'-conglycinin promoter, an R gene complex promoter, a tomato E8 promoter, a patatin promoter, a mannopine synthase promoter, a soybean seed protein glycinin promoter, a soybean vegetative storage protein promoter, a bacteriophage SP6 promoter, a bacteriophage T3 promoter, a bacteriophage T7 promoter, a
Ptac promoter, a root-cell promoter, an ABA-inducible promoter or a turgor-inducible promoter.
30. The transgenic plant of claim 25 wherein the a 9-cis-epoxycarotenoid dioxygenase or a functional subunit thereof is expressed at higher levels than in a plant of the same genetic background that does not comprise the isolated recombinant DNA.
31. The transgenic plant of claim 25 wherein the recombinant DNA encodes a 9-cis-epoxycarotenoid dioxygenase-3 enzyme.
32. The transgenic plant of claim 31 wherein the 9-cis-epoxycarotenoid dioxygenase enzyme comprises SEQ ID NO: 13, SEQ HD NO:25, SEQ HD NO:27, SEQ HD NO:31 or SEQ ID NO:33.
33. A method of increasing salt resistance in a plant comprising:
(a) transforming a plant cell with an isolated nucleic acid that encodes an inhibitory 9-cis-epoxycarotenoid dioxygenase RNA that, when expressed from a promoter functional in a plant cell, inhibits the function of endogenous RNA encoding a 9-cis- epoxycarotenoid dioxygenase enzyme, so as to generate a transformed plant cell;
(b) regenerating the transformed plant cell into a transgenic plant that has increased resistance to salt relative to a non-transgenic plant with the same genetic background but without the isolated nucleic acid.
34. The method of claim 33, wherein the inhibitory RNA is complementary to the endogenous RNA encoding a 9-cis-epoxycarotenoid dioxygenase enzyme.
35. The method of claim 33, wherein the inhibitory RNA is substantially complementary to SEQ ID NO: 1-9, SEQ ID NO: 10, SEQ ID NO:l 1, SEQ ID NO: 12, SEQ ID NO: 14-20, SEQ ID NO:26, SEQ ID NO:28, SEQ HD NO:30, SEQ HD NO:32, or SEQ ID NO:34.
36. The method of claim 33, wherein the inhibitory RNA hybridizes under moderately stringent hybridization conditions to the endogenous RNA encoding an 9-cis-epoxycarotenoid dioxygenase enzyme comprising SEQ HD NO: 13, SEQ HD NO:25, SEQ ID NO:27, SEQ ID NO:31 or SEQ ID NO:33.
37. The method of claim 33 , wherein the moderately stringent hybridization conditions comprise hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37°C, and a wash in 0.5X to IX SSC at 55 to 60°C.
38. The method of claim 33 , wherein the inhibitory RNA hybridizes under highly stringent hybridization conditions to the endogenous RNA encoding an 9-cis-epoxycarotenoid dioxygenase enzyme comprising SEQ HD NO: 13, SEQ HD NO:25, SEQ ID NO:27, SEQ HD NO:31 or SEQ ID NO:33.
39. The method of claim 33, wherein the highly stringent conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0. IX SSC at 60 to 65°C.
40. The method of claim 33, wherein the promoter functional in a plant cell that is a viral coat protein promoter, a tissue-specific promoter, a ubiquitin promoter, a CaMN 35S promoter, a CaMN 19S promoter, a nos promoter, an Adh promoter, a sucrose synthase promoter, a tubulin promoter, a napin promoter, an actin promoter, a cab promoter, a PEPCase promoter, a 7S-alpha'-conglycinin promoter, an R gene complex promoter, a tomato E8 promoter, a patatin promoter, a mannopine synthase promoter, a soybean seed protein glycinin promoter, a soybean vegetative storage protein promoter, a bacteriophage SP6 promoter, a bacteriophage T3 promoter, a bacteriophage T7 promoter, a Ptac promoter, a root-cell promoter, an ABA-inducible promoter or a turgor-inducible promoter.
41. The method of claim 33 , wherein the development of the plant is not inhibited in the presence of a concentration of salt that inhibits the development of the plant of the same genetic background but without the isolated nucleic acid.
42. The method of claim 33, wherein the development of the plant is faster than the development of the plant of the same genetic background but without the isolated nucleic acid.
43. The method of claim 33, wherein the plant develops leaves faster than a plant of the same genetic background but without the isolated nucleic acid.
44. The method of claim 33, wherein the plant is alfalfa, avocado, Brassica campestris, canola, cantaloupe, cotton, cowpea, cranberry, cucumber, eucalyptus, fescue, flax, gladiolus, lettuce, liliacea, maize, mellon, millet, muskmelon, oat, oil palm, olive, papaya, peanut, perennial ryegrass, potato, rapeseed, rice, rye, safflower, sorghum, soybean, sugarbeet, sugarcane, sunflower, tritordeum, turfgrass, or wheat.
45. The method of claim 33, wherein the plant is a dicot.
46. The method of claim 45, wherein the dicot is soybean.
47. The method of claim 33, wherein the plant is a monocot.
48. The method of claim 47, wherein the monocot is corn, rice, rye, oats or wheat.
49. Food or feed produced from the transgenic plant of the method of claim 33.
50. A transgenic progeny plant obtained from the transgenic plant produced by the method of claim 33 wherein the progeny plant comprises the isolated nucleic acid, and wherein the progeny plant is able to develop in the presence of a concentration of salt that inhibits the development of a plant not comprising the isolated nucleic acid.
51. A transgenic seed obtained from the plant produced by the method of claim 33 wherein said seed comprises the isolated nucleic acid, and wherein the transgenic seed is able to germinate in the presence of a concentration of salt that inhibits the germination of a seed not comprising the isolated nucleic acid.
52. A transgenic progeny plant obtained from the transgenic seed of claim 51 wherein the progeny plant comprises the isolated nucleic acid.
53. A method for increasing at least one of the drought, cold, salt, osmotic or pathogen tolerance of a plant comprising:
(a) introducing into regenerable cells of a plant a DNA sequence encoding a 9-cis-epoxycarotenoid dioxygenase or a functional subunit thereof operably linked to a promoter functional in the cells of the plant to yield transformed plant cells; and
(b) regenerating a plant from said transformed plant cells wherein the cells of said plant express the NCED or functional subunit thereof encoded by the DNA sequence in an amount effective to increase at least one of the drought, cold, salt, osmotic or pathogen tolerance of a plant.
54. The method of claim 53 wherein the 9-cis-epoxycarotenoid dioxygenase is a 9-cis-epoxycarotenoid dioxygenase-3.
55. The method of claim 53 wherein the promoter is induced by stress.
56. The method of claim 53 wherein the plant is a monocot.
57. The method of claim 53 wherein the plant is a dicot.
58. The method of claim 53 further comprising (c) obtaining a transgenic seed from the plant of step (b), wherein the transgenic seed comprises said DNA sequence.
59. The method of claim 58 further comprising (d) obtaining a transgenic progeny plant from the transgenic seed of step (c) wherein the cells of the progeny plant express a 9-cis-epoxycarotenoid dioxygenase or functional subunit thereof encoded by the DNA sequence in an amount effective to increase at least one of the drought, cold, salt, osmotic or pathogen tolerance of a plant.
60. A plant obtained from the transformed plant cells of claim 53 wherein cells of the plant express the 9-cis-epoxycarotenoid dioxygenase or functional subunit thereof encoded by the DNA sequence in an amount effective to increase at least one of the drought, cold, salt, osmotic or pathogen tolerance of a plant.
61. A transgenic seed obtained from the plant of claim 60 wherein said transgenic seed comprises said DNA sequence.
62. A method for increasing the salt tolerance or the stress resistance of a plant comprising:
(a) altering the DNA of regenerable cells of said plant to introduce a mutation into a nucleic acid encoding a 9-cis-epoxycarotenoid dioxygenase in said plant cells so as to decrease the amount or activity of a 9-cis-epoxycarotenoid dioxygenase gene product produced by the DNA; and
(b) regenerating a plant from said plant cells having increased salt tolerance or increased stress resistance as compared to a plant not comprising said mutation.
63. The method of claim 62 wherein the 9-cis-epoxycarotenoid dioxygenase is 9-cis-epoxycarotenoid dioxygenase-3.
64. The method of claim 62 wherein the plant is a monocot.
65. The method of claim 62 wherein the plant is a dicot.
66. The method of claim 62 further comprising (c) obtaining a seed from the plant of step (b), wherein the seed comprises said mutation.
67. The method of claim 62further comprising (d) obtaining a progeny plant from the seed of step (c) wherein the cells of the progeny plant comprise said mutation so that the plant exhibits at least one of increased salt tolerance or increased stress resistance as compared to a plant not comprising said mutation.
68. A plant obtained from the transformed plant cells of claim 62 wherein the cells of the plant comprise said mutation so that the plant exhibits at least one of increased salt tolerance or increased stress resistance as compared to a plant not comprising said mutated gene.
69. A seed obtained from the plant of claim 62 wherein said seed comprises said mutation.
70. The plant of claim 2, 3 or 4, wherein the plant has altered abscisic acid signaling as compared to a wild-type plant.
71. An isolated polynucleotide comprising a nucleotide sequence that is substantially identical to SEQ HD NO: 10 or a fragment thereof and which comprises a promoter region.
72. An isolated polynucleotide comprising a nucleotide sequence that is substantially complementary to SEQ HD NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ HD NO:26, SEQ HD NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, or a fragment thereof, wherein the isolated polynucleotide can inhibit RNA transcription from a DNA comprising
SEQ ID NO:10, SEQ ID NO:ll, SEQ HD NO:12, SEQ HD NO:26, SEQ HD NO:28, SEQ HD NO:30, SEQ HD NO:32, SEQ ID NO:34.
73. The isolated polynucleotide of claim 72, wherein the isolated polynucleotide hybridizes under moderately stringent hybridization conditions to an RNA encoding a 9-cis-epoxycarotenoid dioxygenase enzyme comprising SEQ HD NO:13, SEQ ID NO:25, SEQ HD NO:27, SEQ HD NO:29, SEQ HD NO:31, or SEQ ID NO:33.
74. The isolated polynucleotide of claim 72, wherein the moderately stringent hybridization conditions comprise hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37°C, and a wash in 0.5X to IX SSC at 55 to 60°C.
75. The isolated polynucleotide of claim 72, wherein the isolated polynucleotide hybridizes under highly stringent hybridization conditions to an RNA encoding a 9-cis-epoxycarotenoid dioxygenase enzyme comprising SEQ ID NO: 13, SEQ HD NO:25, SEQ ID NO:27, SEQ ID
NO:29, SEQ HD NO:31, or SEQ ID NO:33.
76. The isolated polynucleotide of claim 75, wherein the highly stringent conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37°C, and a wash in 0. IX SSC at 60 to 65°C.
77. The isolated polynucleotide of claim 72 wherein the nucleotide sequence is at least 66% complementary to any one of SEQ ID NO: 10, SEQ HD NO:l 1, SEQ HD NO:12, SEQ HD NO:26, SEQ HD NO:28, SEQ HD NO:30, SEQ ID NO:32, SEQ ID NO:34.
78. The isolated polynucleotide of claim 72 wherein the nucleotide sequence is at least 90% complementary to any one of SEQ JX> NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ HD NO.26, SEQ HD NO:28, SEQ HD NO:30, SEQ HD NO:32, SEQ ID NO:34.
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