WO2001014561A1 - Compositions de gene nor et leurs procedes d'utilisation - Google Patents

Compositions de gene nor et leurs procedes d'utilisation Download PDF

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WO2001014561A1
WO2001014561A1 PCT/US2000/019071 US0019071W WO0114561A1 WO 2001014561 A1 WO2001014561 A1 WO 2001014561A1 US 0019071 W US0019071 W US 0019071W WO 0114561 A1 WO0114561 A1 WO 0114561A1
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plant
nucleic acid
acid sequence
gene
transgenic plant
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PCT/US2000/019071
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James Giovannoni
Steven Tanksley
Julia Vrebalov
Frederick Noensie
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The Texas A & M University System
Cornell Research Foundation, Inc.
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Priority to AU60942/00A priority Critical patent/AU6094200A/en
Publication of WO2001014561A1 publication Critical patent/WO2001014561A1/fr

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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
    • 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
    • C12N15/8291—Hormone-influenced development
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/415—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from plants
    • 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
    • C12N15/8242—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
    • C12N15/8243—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine
    • C12N15/8249—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine involving ethylene biosynthesis, senescence or fruit development, e.g. modified tomato ripening, cut flower shelf-life
    • 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
    • C12N15/8242—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
    • C12N15/8243—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine
    • C12N15/825—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine involving pigment biosynthesis

Definitions

  • the present invention relates generally to the NOR gene. More specifically, it relates to methods and compositions for the modification of plant phenotypes with the NOR gene.
  • the ripe phenotype is the summation of biochemical and physiological changes occurring at the terminal stage of fruit development rendering the organ edible and desirable to seed dispersing animals and valuable as an agricultural commodity. These changes, although variable among species, generally include modification of cell wall ultrastructure and texture, conversion of starch to sugars, increased susceptibility to post-harvest pathogens, alterations in pigment biosynthesis/accumulation, and heightened levels of flavor and aromatic volatiles (Rhodes, 1980; Hobson and Grierson, 1993). Several of theses ripening attributes translate to decreased shelf-life and high input harvest, shipping and storage practices, particularly via changes in firmness and the overall decrease in resistance to microbial infection of ripe fruit.
  • Climacteric fruit such as tomato, cucurbits, avocado, banana, peaches, plums, and apples
  • non-climacteric fruits such as strawberry, grape and citrus
  • Ethylene has been shown to be necessary for the coordination and completion of ripening in climacteric fruit via analysis of inhibitors of ethylene biosynthesis and perception (Yang, 1985; Tucker and Brady, 1987), in transgenic plants blocked in ethylene biosynthesis (Klee et al, 1991; Oeller et al., 1991; Picton et al., 1993a), and through examination of the None-ripe (Nr) ethylene perception mutant of tomato (Lanahan et al., 1994).
  • ripening genes including ACC synthase and ACC oxidase, have been shown via antisense gene repression to have profound influences on the onset and degree of ripening (Hamilton et al, 1990; Oeller et al, 1991). Although the sum effect of this research has been a wealth of information pertaining to the regulation of ethylene biosynthesis and its role in ripening, the molecular basis of developmental cues which initiate ripening- related ethylene biosynthesis, and additional aspects of ripening not directly influenced by ethylene, remain largely unknown (Theologis et al, 1993).
  • Nr mutation has been identified and represents a gene responsible for ethylene perception and/or signal transduction and is a tomato homologue of the Arabidopsis Ethylene response 1 (Etrl) gene (Yen et al, 1995; Wilkinson et al, 1995).
  • Tomato has served as a model for ripening of climacteric fruit.
  • Ripening-related genes have been isolated via differential gene expression patterns (Slater et al, 1985, Lincoln et al, 1987, Pear et al, 1989, Picton et al, 1993b) and biochemical function (DellaPenna et al, 1986; Sheehy et al, 1987; Ray et al, 1988; Biggs and Handa, 1989; Harriman and Handa, 1991 ; Oeller et al, 1991; Yelle et al, 1991).
  • Promoter analysis of ripening genes has been performed via examination of promoter/reporter construct activities in transient assay systems and transgenic plants.
  • ripening-related genes including polygalacturonase, pectinmethylesterase, ACC synthase, ACC oxidase, and phytoene synthase have been tested via antisense gene repression and/or mutant complementation in transgenic tomatoes.
  • the cell wall pectinase, polygalacturonase was shown to be necessary for ripening- related pectin depolymerization and pathogen susceptibility, however, the inhibition of PG expression had minimal effects on fruit softening (Smith et al., 1988, Giovannoni et al, 1989, Kramer et al, 1990).
  • transgenic tomatoes inhibited in ethylene biosynthesis demonstrates that climacteric ripening represents a combination of both ethylene mediated and developmental control (Theologis et al, 1993).
  • antisense ACC synthase tomatoes which failed to produce ethylene did not ripen
  • gene expression analysis demonstrated that several ripening-related genes, including polygalacturonase and E8 are expressed in the absence of ethylene. This observation confirms the presence of a developmental (or non-ethylene regulated) component of ripening.
  • the current invention provides an isolated nucleic acid sequence comprising the NOR gene.
  • the NOR gene may be further defined as isolatable from the nucleic acid sequence of SEQ ID NO:l, SEQ ID NO:6 or SEQ ID NO:7.
  • the invention provides an isolated nucleic acid corresponding to an open reading frame of the NOR cDNA, for example, which may be denoted by the nucleotides as indicated by bold letters in FIG. 6.
  • the invention provides an isolated nucleic acid sequence having from about 17 to about 1209, about 25 to about 1209, about 30 to about 1209, about 40 to about 1209, about 60 to about 1209, about 100 to about 1209, about 200 to about 1209, about 400 to about 1209, about 600 to about 1209, about 800 to about 1209, or about 1000 to about 1209 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:6 or SEQ ID NO:7.
  • the invention provides such nucleic acid segments from SEQ ID NO:l .
  • the nucleic acid sequences of SEQ ID NO:6 and SEQ ID NO:7 are provided.
  • a nucleic acid sequence of the invention may further comprising an enhancer, such as an intron.
  • a nucleic acid sequence of the invention may also include a transcriptional terminator. Such sequences may be native to the NOR gene or heterologous from potentially any species.
  • the invention provides an expression vector comprising a NOR gene.
  • NOR gene may be in accordance with any of the NO ⁇ -containing sequences described herein.
  • the expression vector may comprise the NOR gene operably linked to a native or heterologous promoter, either in sense or antisense orientation relative to the promoter.
  • any heterologous promoter may be used, for example, a promoter is selected from the group consisting of CaMV 35S, CaMV 19S, nos, Adh, actin, histone, ribulose bisphosphate carboxylase, R-allele, root cell promoter, ⁇ -tubulin, ABA-inducible promoter, turgor-inducible promoter, rbcS, corn sucrose synthetase 1, corn alcohol dehydrogenase 1 , corn light harvesting complex, corn heat shock protein, pea small subunit RuBP carboxylase, Ti plasmid mannopine synthase, Ti plasmid nopaline synthase, petunia chalcone isomerase, bean glycine rich protein 1, CaMV 35s transcript, Potato patatin, actin, cab, PEPCase and S-E9 small subunit RuBP carboxylase promoter.
  • a promoter is selected from the group consisting of CaMV 35S, CaMV 19S, nos
  • the expression vector may comprise any selectable marker, for example, a selectable marker selected from the group consisting of phosphinothricin acetyltransferase, glyphosate resistant EPSPS, aminoglycoside phosphotransferase, hygromycin phosphotransferase, neomycin phosphotransferase, dalapon dehalogenase, bromoxynil resistant nitrilase, anthranilate synthase and glyphosate oxidoreductase.
  • a selectable marker selected from the group consisting of phosphinothricin acetyltransferase, glyphosate resistant EPSPS, aminoglycoside phosphotransferase, hygromycin phosphotransferase, neomycin phosphotransferase, dalapon dehalogenase, bromoxynil resistant nitrilase, anthranilate synthase and
  • the expression vector may be either circular, for example, as in the case of a plasmid vector, or could be a linear nucleic acid segment, such as an expression cassette isolated from a plasmid.
  • the vector is a plasmid vector.
  • the expression vector may further comprise other elements, such as a nucleic acid sequence encoding a transit peptide, or potentially any terminator, for example, a heterologous terminator such as the nos terminator.
  • the invention provides a transgenic plant comprising a stably transformed expression vector, such as those described above.
  • the transgenic plant may be any type of plant, and in particular embodiments of the invention is a tomato plant.
  • the transgenic plant may be a fertile Ro transgenic plant.
  • a seed of such a fertile R 0 transgenic plant wherein said seed comprises said expression vector.
  • the transgenic plant may be a progeny plant of any generation of a fertile R 0 transgenic plant, wherein said R 0 transgenic plant comprises said expression vector.
  • the invention also includes a seed of such a progeny plant, wherein said seed comprises said expression vector.
  • the invention provides a crossed fertile transgenic plant prepared according to the method comprising the steps of: (i) obtaining a fertile transgenic plant comprising a selected DNA comprising a NOR gene; (ii) crossing said fertile transgenic plant with itself or with a second plant lacking said selected DNA to prepare the seed of a crossed fertile transgenic plant, wherein said seed comprises said selected DNA; and (iii) planting said seed to obtain a crossed fertile transgenic plant.
  • a seed is provided of such a crossed fertile transgenic plant, wherein said seed comprises said selected DNA.
  • the crossed fertile transgenic plant may be of any species, for example, a tomato plant. The plant may also be inbred or hybrid.
  • the invention provides a method of manipulating the phenotype of a plant comprising the steps of: (i) obtaining an expression vector comprising a NOR gene in sense or antisense orientation; (ii) transforming a recipient plant cell with said expression vector; and (iii) regenerating a transgenic plant from said recipient plant cell, wherein the phenotype of said plant is altered based on the expression of said NOR gene in sense or antisense orientation.
  • Any method of transforming a plant may be used in accordance with the invention, including, microprojectile bombardment, PEG mediated transformation of protoplasts, electroporation, silicon carbide fiber mediated transformation, or Agrobacterium-mediated transformation.
  • the invention provides a method of plant breeding comprising the steps of: (i) obtaining a transgenic plant comprising a selected DNA comprising a NOR gene; and (ii) crossing said transgenic plant with itself or a second plant.
  • the plant may be of any species and may be inbred or hybrid.
  • this method further comprises the steps of: (iii) collecting seeds resulting from said crossing; (iv) growing said seeds to produce progeny plants; (v) identifying a progeny plant comprising said selected DNA; and (vi) crossing said progeny plant with itself or a third plant.
  • the second plant and third plant are of the same genotype.
  • the second and third plants may also be inbred plants.
  • the invention provides a transgenic plant cell stably transformed with a selected DNA comprising a NOR gene.
  • the cell may be from any plant species, for example, a cell from a tomato plant.
  • the selected may comprise any of the NOR gene comprising nucleic acid compositions disclosed herein, for example, the expression vector compositions described herein above.
  • Such compositions include the open reading frame of the NOR gene, as provided in SEQ ID NO:6 or SEQ ID NO:7 and demarcated in FIG. 6.
  • FIG. 1 T-DNA constructs for delivery of sense or antisense NOR gene cDNA (CD- 11) sequences into plant genomes.
  • the base plasmid termed NOR-pBI121 Sense/ Antisense (Kanamicin resistant - NPTII), had an approximate size of 13.0 kb.
  • FB, LB right and left T-DNA borders, respectively;
  • Nos-pro nopaline synthase promoter driving expression of the NPTII gene;
  • NPTII neomycin phosphotransferase (kanamycin resistance) gene;
  • nos-ter transaction termination sequence from the nopaline synthase gene;
  • Sma/EcoRV the resulting chimeric sequence is recognized by neither enzyme.
  • FIG. 2 Manipulation of fruit ripening and carotenoid accumulation with the tomato NOR gene. Shown are representative control and transformed fruit from tomato a line of the genotype nor/nor in the cultivar MHl and transformed with NOR-pBI121 Sense (FIG. 1). Primary transformants (TO) were confirmed for transgene integration via DNA gel-blot analysis and subsequently self-pollinated. Resulting seed were harvested and grown (TI generation) and analyzed for transgene segregation. Representative fully mature fruit from TI nor /nor individuals that either harbor the sense NOR transgene (+) or have segregated it out (-) are shown.
  • TO Primary transformants
  • transgene expression in the mutant background partially recovers the non-ripening phenotype and confers ripening.
  • relatively low expression of the transgene was observed as compared to expression of NOR in normally ripening (Nor/Nor) fruit.
  • Representative normal (Nor/Nor) and nearly isogenic mutant (nor/nor) cultivar MHl tomato fruit are shown as controls.
  • the partial recovery of ripening in the nor/nor fruit harboring the NOR-pBI121 (+) transgene verified the isolation of the NOR gene.
  • FIG. 3 DNA agarose gel showing the Nor versus nor alleles as PCR amplification products. Genomic DNA was isolated from normal (N/N) and homozygous nor mutant (n/n) nearly isogenic control lines (cultivar MHl), in addition to individuals from a Nor/Nor X Nor/nor back-cross (BC) population.
  • N/N normal
  • n/n homozygous nor mutant
  • BC Nor/Nor X Nor/nor back-cross
  • DNA was amplified with one PCR primer common to the coding region of both the Nor and nor alleles and separately with either one primer specific to the Nor or nor alleles, respectively.
  • the allele-specific primers were based on the 2 bp deletion which distinguished the normal (Nor) versus mutant (nor) allele (see FIG. 5). PCR reactions with the normal (Nor) allele primer were loaded on the top portion of the gel, and those employing the mutant (nor) allele primer were loaded on the bottom portion of the gel. PCR reactions from the same individual plant but amplified separately with each allele- specific primer were loaded directly above and below each other to facilitate scoring.
  • the normal (N) and mutant (n ) alleles are indicated above each lane and represent the corresponding genotype as determined by analysis of band amplification.
  • FIG. 4 Expression of the NOR gene through plant development and in normal and mutant fruit. RNA gel-blot analysis of expression using the NOR full-length cDNA as probe. Expression was induced in the transition from mature green to breaker fruit but was not detected in any additional tissues examined including combined cotyledons and hypocotyls (C H), leaves, senescing leaves (S Leaf), stems or roots. It was noted that expression was also reduced in identically aged nor (nor/nor) mutant fruit.
  • C H combined cotyledons and hypocotyls
  • S Leaf senescing leaves
  • FIG. 5 DNA sequence of the region of tomato chromosome 10 harboring the NOR gene (SEQ ID NO: 7).
  • the sense genomic DNA sequence of the complete transcribed region is shown in the 5' - 3' orientation.
  • the coding sequence is in upper case while non-translated sequences including the two NOR gene introns are in lower case.
  • FIG. 6 Corrected DNA sequence of the NOR full-length cD ⁇ A (CD-11) (SEQ ID ⁇ :6).
  • the full cDNA sequence is shown in 5' - 3' orientation. Lower case letters refer to non-translated portions of the transcript while the upper case letters refer to the translated (coding) sequence.
  • the ripening of fleshy fruits represents a system of eukaryotic development unique to plants as well as an important component of agricultural quality and productivity. Greater understanding of the genetic and molecular basis of the ripening process will promote both our collective understanding of plant development and yield tools useful for sustaining and improving agricultural productivity and quality, while minimizing impact on the resources necessary for production.
  • the current invention provides such understanding by providing the nucleic acids encoding the NOR gene. By providing these sequences, the invention provides, for the first time, the ability to use genetic transformation techniques to manipulate a variety of plant characteristics which are associated with these genes in ways that cannot be accomplished via traditional breeding strategies including direct D ⁇ A transfer to species other than tomato.
  • ripening occurs over a period of several days, depending on variety, and is characterized by softening, pectin solubilization, increased respiration and ethylene biosynthesis, enhanced pathogen susceptibility, heightened palatability, and accumulation of the characteristic red and orange carotenoid pigments lycopene and beta-carotene, respectively.
  • NOR and also the fruit ripening gene RIN segregate as single traits, result in nearly complete inhibition of normal ripening as defined above, and their effects on ripening cannot be restored via application of exogenous ethylene (Tigchelaar et al, 1978).
  • the ripening phenotypes displayed by RIN and NOR demonstrate that the gene products encoded by the normal alleles at these loci are involved in the primary regulation of ripening (Hobson and Grierson, 1993; Giovannoni 1993; Gray et al, 1994). Because virtually nothing is known of the expression patterns or biochemical nature of the normal NOR gene product, the inventors initiated a genetic map-based cloning strategy for isolation of the corresponding normal allele.
  • Tomato has served for decades as a model system for both plant genetics and fruit ripening, in part resulting in the availability of the tools for ripening gene isolation mentioned above.
  • Numerous mutations regulating various aspects of tomato fruit ripening have been identified over the years, most of which result in alteration of pigment biosynthesis and/or accumulation without significant effects on additional ripening characteristics (Rick, 1980; Grierson, 1986; Gray et al, 1994). Examples include the greenflesh (gf; Ramirez and Tomes, 1964) and yellowflesh (r; Darby, 1978) mutants which inhibit ripening-related chlorophyll degradation and lycopene accumulation, respectively.
  • Tomato mutations exerting complete or nearly complete inhibition of overall ripening (i.e. blocking changes not just in color but also texture, ethylene biosynthesis, pathogen susceptibility, flavor and aroma) are few, the most extreme being rin and nor.
  • homozygous rin and nor mutant fruit fail to display climacteric respiration and ethylene biosynthesis characteristic of normally ripening tomatoes (Tigchelaar et al, 1978), are highly resistant to microbial infection (Grierson, 1986), and are inhibited in their expression of ripening-related genes (DellaPenna et al, 1989; Picton et al, 1993). Although often referred to as recessive mutations, both rin and nor heterozygotes show significant effects on some ripening parameters, including reduced pathogen susceptibility and softening, resulting in extended shelf-life (Tigchelaar et al, 1978; Biggs and Handa, 1989).
  • Ripening is a unique and important plant process whose understanding has great significance in the agricultural arts. Isolation of genes regulating both the ethylene and non- ethylene mediated components of fruit ripening represents an important step in understanding the genetic basis of this complex developmental pathway. Although most research emphasis in recent years has been focused on elucidating the biosynthesis and function of ethylene during climacteric fruit ripening, the genetic and molecular basis of the developmental regulators which initiate ripening ethylene biosynthesis, and control the non-ethylene mediated ripening pathway, had remained a mystery.
  • the mutant phenotypes of the targeted nor locus demonstrates that this gene is essential for normal ripening to occur and is a developmental regulator both of ethylene biosynthesis and non-ethylene regulated aspects of ripening.
  • this gene may be related to those involved in the regulation of other developmental programs. Insights gained into the ripening process as a result of the current invention will not only aid our understanding of overall plant development, but may enhance understanding of developmental processes in other eukaryotes as well.
  • ripening confers both positive and negative attributes to the resulting commodity. While ripening imparts desirable flavor, color, and texture, considerable expense and crop loss result as a consequence of negative ripening characteristics. For example, ripening related increases in fruit pathogen susceptibility is a major contributor to fruit loss both before and after harvest. This genetically regulated change in fruit physiology currently necessitates the use of pesticides, post-harvest fumigants, and controlled atmosphere storage and shipping mechanisms in attempts to minimize loss. In addition to being wasteful of energy and potentially harmful to the environment, such practices represent major expenses in fruit production.
  • NOR ripening regulatory gene
  • Tomato is the best available system for the map-based cloning of ripening genes because of the availability of: 1) single locus mutations inhibiting normal fruit ripening, 2) a high density RFLP map, 3) large populations segregating for targeted ripening loci, 4) a YAC library, and 5) established procedures for transformation and regeneration.
  • gene products have not been identified for either of the target genes, thus precluding immunological cloning strategies.
  • previous to the invention one could only speculate concerning patterns of normal NOR gene expression, thus exacerbating the already difficult task of identifying appropriate stages for differential screening strategies. Therefore, the current invention represents a major advance over the prior art, potentially allowing for the first time the creation of transgenic plants having greatly enhanced agronomic characteristics.
  • NOR non-ripening
  • Fruit ripening is a complex process ultimately rendering the fruit palatable and/or susceptible to biotic or abiotic process which result in seed liberation and dispersal. While specific ripening attributes vary among species, the following general process are common to many fruits (see Seymour et al, 1993 for review), including tomato, and are all have been shown to be influenced by the NOR gene via characterization of the corresponding mutant: A) Degradation of the photosynthetic pigment chlorophyll and accumulation of various pigment compounds (often carotenoids and flavonoids) resulting in changes of both color and nutritional composition (Tigchellar et al, 1978; Yen et al, 1997).
  • NOR gene compositions provided by the inventors may find numerous uses in manipulation of plant phenotypes. Exemplary uses for the NOR gene are described herein below, although those of skill in the art will recognize that the examples are in no way limiting.
  • the nor mutation is currently used in tomato breeding for development of hybrid lines with slow-ripening/long-shelf-life characteristics.
  • the NOR gene could similarly be used for manipulation and control of ripening with potential for accelerated ripening of important early season crops, controlled or delayed ripening of crops permitting longer shipping handling, storage and post-retail shelf-life.
  • the fact that the inventors have provided the cloned NOR gene will permit its utilization in species other than tomato. Specific examples of use would be in accelerated ripening of early season melons for favorable market position and pricing, and ripening control of bananas and strawberry - fruits which typically have short shelf-lives making shipping and handling more costly.
  • modified expression of the NOR gene in ripening fruits may find use in elevating levels of important processing and nutritional compounds such as antioxidant flavonoids and carotenoids in fruits and non-fruit tissues.
  • An example would be potential over-expression in maize seeds to enhance accumulation of antioxidant compounds for nutritional enhancement of the crop or for extraction.
  • NOR gene orthologues functional equivalents
  • expression of NOR gene orthologues (functional equivalents) in other species may regulate maturation of seed pods (which are also carpels or "fruits", for example in soybean, pea, common bean) and/or cereal grains (e.g., rice, maize, wheat, sorghum).
  • seed pods which are also carpels or "fruits", for example in soybean, pea, common bean
  • cereal grains e.g., rice, maize, wheat, sorghum
  • Protracted or accelerated maturation via manipulation of the NOR gene may additionally impact quality characteristics such as total protein content, carbohydrate loading, nutritional composition (e.g., via altered levels of carotenoids such as beta-carotene and lycopene) and total yield.
  • FIG. 1 shows that delivery of the normal Nor allele into the genome of mutant plants results in conversion of fruit from unripe to ripe and results in a range of degrees of ripening and pigment accumulation.
  • the NOR gene controls fruit senescence as demonstrated by the lack of senescence in tomato fruits harboring the nor mutation. Senescence or tissue death is thus clearly regulated by NOR in fruit and may be manipulated in non-fruit tissues via regulated expression of the NOR gene. Examples of use may include late fruit-ripening repression in banana or other tropical or sub-tropical fruits subject to rapid decay to permit desirable ripening but not advanced tissue damage reducing fruit quality and desirability. Over-expression in anthers may result in senescence yielding male-sterility, while if this gene is normally expressed in other senescing tissues, gene repression may be useful to inhibit senescence for example in vegetables (spinach, lettuce, cabbage, broccoli).
  • Fruit tissue from nor mutant tomato plants are highly resistant to infection by opportunistic microbial pathogens (Tigchellar et al, 1978).
  • Post-ripening repression (antisense or co-suppression) of the gene in tomato, or other species could thus be useful in inhibiting subsequent over-ripening and pathogen susceptibility of fruit.
  • activity of the NOR gene may participate in non-fruit pathogen resistance for example via repression of low-level of tissue or cell specific expression in response to pathogen attack. Consequently NOR gene repression may thus be used to provide a positive impact on pathogen resistance in fruit and non-fruit tissues.
  • Specific examples of use might include 1) synchronized and controlled maturation of cereal grains via high level NOR expression late in seed development, 2) high level expression of NOR later in the growing season to induce senescence and defoliation of cotton via over-expression in leaves prior to boll harvest, and 3) synchronized'and accelerated or protracted maturation of seed pods via over-expression or repression, respectively of NOR in soybean.
  • stress responses such as responses to pathogen infection, and abiotic stress (temperature, water, mechanical damage) are mediated in part by ethylene
  • over- expression of the NOR gene may positively impact the ability of plants to withstand biotic and abiotic insults, thus resulting in enhanced crop performance and yield.
  • D ⁇ A markers based on sequence variation between the normal versus mutant tomato genotypes. Use of such markers allows for definitive genotyping of seedlings in a matter of 1 - 5 days.
  • An example of a D ⁇ A marker system based on the nor mutation is shown in FIG. 3.
  • the 2 bp deletion resulting in the mutation is exploited to develop a set of PCR primers which distinguishes the normal versus mutant allele.
  • the sequence variation between the normal versus mutant alleles would be the basis for development of virtually all types of DNA-based markers for determining nor locus genotype through the use of sequences located precisely at (thus 100% accurate) the nor locus.
  • the NOR gene cD ⁇ A was identified by the inventors and termed CD- 11.
  • the gene shows similar transcript size in mutant versus normal fruit (FIG. 4) though it does show reduced accumulation in the mutant.
  • the inventors have also shown that the nor mutation results from a 2 bp deletion in the coding sequence which results in introduction of a premature stop codon through comparative sequencing of the normal versus mutant alleles of the nor locus (FIG. 5).
  • the NOR gene is related to a family of plant transcription factors associated with multiple aspects of plant development including meristem and cotyledon development and leaf senescence (Sour et al, 1996; Aida et al, 1997; John et al, 1997).
  • FIG. 6 depicts the D ⁇ A sequence NOR cD ⁇ A sequence.
  • the invention provides novel methods for the modification of plant phenotypes.
  • the invention allows the creation of plants with modified phenotypes.
  • the inventors specifically contemplate the use of the NOR sequence, as well as all of the derivatives thereof which are provided by the invention, to genetically transform plant species for the purpose of altering plant phenotypes.
  • Exemplary phenotypic effects are those which are associated with fruit ripening or ethylene response.
  • the inventors contemplate increasing the expression of NOR in order to increase fruit ripening and/or ethylene responsiveness, or alternatively, decreasing the effective expression of the NOR gene in order to delay, protract, and/or inhibited fruit ripening or ethylene responses.
  • NOR sequences in accordance with the invention may be carried out using the native promoter, or alternatively, promoters that are inducible, viral, synthetic, constitutive as described (Poszkowski et al, 1989; Odell et al, 1985), and temporally regulated, spatially regulated (e.g., tissue-specific), and spatio-temporally regulated (Chau et al, 1989).
  • Types of effects which could be recognized on fruit ripening include, as described in detail above, processes related to changes in color, texture, flavor, aroma, shelf-life, ethylene responses, nutrient composition, cell wall metabolism, and susceptibility to pathogenesis associated with the ripening process.
  • effects on ethylene responsiveness which could be effected with the invention include either increased or decreased responsiveness to ethylene. Changes in response to ethylene may effect fruit ripening, organ abscission, seed or pollen dehiscence/shattering, tissue senescence, disease resistance, and response to environmental stresses including but not limited to drought, flooding, heat, cold, nutrient deficiency, high or low light intensity, mechanical damage and insect or pathogen infection. Modification of any of the foregoing effects in a plant, as well as any other effects associated with the NOR gene, is specifically contemplated by the inventors and a part of the current invention.
  • any method employing the sequences described by the inventors may be used to realize the above-mentioned phenotypic effects in potentially any plant species, although fruiting effects can be expected to be realized only in species producing fruit.
  • fruit ripening or ethylene responsiveness could be decreased in a given plant by transformation of the plant with an expression vector comprising an antisense NOR gene.
  • Such a NOR gene could comprise the sequences provided herein, or could represent copies of homologous sequences from other plants isolated using the sequences of the invention. Decreases in fruit ripening or ethylene responsiveness could alternatively be realized by use of co-suppression by way of introduction of additional NOR sequences into a host genome.
  • NOR sequences preferably comprising a functional expression unit
  • cosuppression of any functional native NOR sequences could be realized, and thereby the phenotype of the plant be modified with respect to traits effected by NOR expression.
  • the effect could be realized potentially by use of the NOR promoter, coding sequences or terminators, or using heterologous versions thereof.
  • transgene comprising a sequence of the invention
  • that transgene may be passed to any subsequent generation by standard plant breeding protocols.
  • Such breeding can allow the transgene to be introduced into different lines, preferably of an elite agronomic background, or even to different species which can be made sexually compatible with the plant having the transgene. Breeding protocols may be aided by the use of genetic markers which are closely linked to the genes of interest.
  • a plant prepared in accordance with the invention will be a fruiting plant, for example, tomato, berries such as strawberries and raspberries, banana, kiwi, avocado, melon, mango, papaya, lychee, pear, stone fruits such as peach, apricot, plum and cherry, in addition to true (anatomical) fruits commonly referred to as "vegetables” including peppers, eggplant, okra, and other non-melon curcubuts such as cucumber and squash.
  • an expression vector containing a sense or antisense NOR coding region and an appropriate selectable marker may be used in accordance with the invention, for example, use of Agrobacteri m-mediated D ⁇ A transfer, microprojectile bombardment, direct D ⁇ A transfer into pollen, by injection of D ⁇ A into reproductive organs of a plant, or by direct injection of D ⁇ A into the cells of immature embryos followed by the rehydration of desiccated embryos, or by direct D ⁇ A uptake by protoplasted cells.
  • transgenic plants created in accordance with the current invention may be used for virtually any purpose deemed of value to the grower or to the consumer.
  • the fruit of tomato plants with enhanced fruit ripening characteristics may be harvested and sold to consumers or used in the production of various food products.
  • seed could be harvested from the fruit of a plant prepared in accordance with the instant invention, and the seed may be sold to farmers for planting in the field or may be directly used as food, either for animals or humans.
  • products may be made from the seed itself, for example, oil, starch, pharmaceuticals, and various industrial products. Such products may be made from particular plant parts or from the entire plant.
  • vectors which may be employed in conjunction with plant transformation techniques according to the invention will be known to those of skill of the art in light of the present disclosure (see, for example, Sambrook et al, 1989; Gelvin et al, 1990).
  • the techniques of the current invention are thus not limited to any particular nucleic acid sequences in conjunction with the NOR nucleic acid sequences provided herein.
  • Exemplary sequences for use with the invention include those provided in SEQ ID ⁇ :l, SEQ ID N ⁇ :6 and SEQ ID NO:7.
  • sequences of the invention will be in the alteration of plant phenotypes by genetic transformation of plants with sense or antisense NOR genes.
  • the NOR gene may be provided with other sequences.
  • an expressible coding region that is not necessarily a marker coding region is employed in combination with a marker coding region, one may employ the separate coding regions on either the same or different D ⁇ A segments for transformation. In the latter case, the different vectors are delivered concurrently to recipient cells to maximize cotransformation.
  • any additional elements used in conjunction with the NOR sequences will often depend on the purpose of the transformation.
  • One of the major purposes of transformation of crop plants is to add commercially desirable, agronomically important traits to the plant.
  • Such traits include, but are not limited to, processes related to changes in fruit color, texture, flavor, aroma, shelf-life, ethylene responses, nutrient composition, cell wall metabolism, susceptibility to pathogenesis associated with the ripening process, organ abscission, seed or pollen dehiscence/shattering, tissue senescence, disease resistance, and response to environmental stresses including but not limited to drought, flooding, heat, cold, nutrient deficiency, high or low light intensity, mechanical damage and insect or pathogen infection.
  • the present inventors contemplate the transformation of a recipient cell with more than transformation construct.
  • Two or more transgenes can be created in a single transformation event using either distinct selected-gene encoding vectors, or using a single vector incorporating two or more gene coding sequences.
  • viral vectors for plant transformation.
  • Such vectors include, for example, wheat dwarf virus (WDV) "shuttle" vectors, such as pWl-11 and PW1-GUS (Ugaki et al, 1991). These vectors are capable of autonomous replication in plant cells as well as E. coli, and as such may provide increased sensitivity for detecting DNA delivered to transgenic cells.
  • WDV wheat dwarf virus
  • a replicating vector also may be useful for delivery of genes flanked by DNA sequences from transposable elements such as Ac, Ds, or Mu.
  • transposable elements would be useful for introducing DNA fragments lacking elements necessary for selection and maintenance of the plasmid vector in bacteria, e.g., antibiotic resistance genes and origins of DNA replication. It also is proposed that use of a transposable element such as Ac, Ds, or Mu would actively promote integration of the desired DNA and hence increase the frequency of stably transformed cells.
  • Co-transformation may be achieved using a vector containing the marker and another gene or genes of interest.
  • different vectors e.g., plasmids
  • the plasmids may be concurrently delivered to the recipient cells.
  • Vectors used for plant transformation may include, for example, plasmids, cosmids, YACs (yeast artificial chromosomes), BACs (bacterial artificial chromosomes) or any other suitable cloning system.
  • vector or "expression vector”
  • all of the foregoing types of vectors, as well as nucleic acid sequences isolated therefrom, are included. It is contemplated that utilization of cloning systems with large insert capacities will allow introduction of large DNA sequences comprising more than one selected gene. Introduction of such sequences may be facilitated by use of bacterial or yeast artificial chromosomes (BACs or YACs, respectively), or even plant artificial chromosomes.
  • BACs for Agrobacterium-mzdiated transformation was disclosed by Hamilton et ⁇ l. (1996).
  • DNA segments used for transforming plant cells will, of course, generally comprise the cDNA, gene or genes which one desires to introduced into and have expressed in the host cells. These DNA segments can further include, in addition to a NOR coding sequence, structures such as promoters, enhancers, polylinkers, or even regulatory genes as desired.
  • the D ⁇ A segment or gene chosen for cellular introduction will often encode a protein which will be expressed in the resultant recombinant cells resulting in a screenable or selectable trait and/or which will impart an improved phenotype to the resulting transgenic plant. However, this may not always be the case, and the present invention also encompasses transgenic plants incorporating non-expressed transgenes.
  • Preferred components likely to be included with vectors used in the current invention are as follows.
  • Preferred constructs will generally include a plant promoter such as the CaMV 35S promoter (Odell et al, 1985), or others such as CaMV 19S (Lawton et al, 1987), nos (Ebert et al, 1987), Adh (Walker et al, 1987), sucrose synthase (Yang & Russell, 1990), a-tubulin, actin (Wang et al, 1992), cab (Sullivan et al, 1989), PEPCase (Hudspeth & Grula, 1989) or those associated with the R gene complex (Chandler et al, 1989).
  • a plant promoter such as the CaMV 35S promoter (Odell et al, 1985), or others such as CaMV 19S (Lawton et al, 1987), nos (Ebert et al, 1987), Adh (Walker et al, 1987), sucrose synthase (Yang & Russell, 1990), a-tubulin, actin (Wang
  • Tissue specific promoters such as root cell promoters (Conkling et al, 1990) and tissue specific enhancers (Fromm et al, 1989) are also contemplated to be particularly useful, as are inducible promoters such as ABA- and turgor-inducible promoters.
  • leader sequences are contemplated to include those which include sequences predicted to direct optimum expression of the attached gene, i.e., to include a preferred consensus leader sequence which may increase or maintain mRNA stability and prevent inappropriate initiation of translation.
  • sequences will be known to those of skill in the art in light of the present disclosure. Sequences that are derived from genes that are highly expressed in plants, and in tomato in particular, will be most preferred.
  • vectors for use in accordance with the present invention may be constructed to include the 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, 1987), and is present in at least 10 other promoters (Bouchez et al, 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 plant transformation.
  • NOR coding sequences may be introduced under the control of novel promoters or enhancers, etc., or perhaps even homologous or tissue specific (e.g., root-, collar/sheath-, whorl-, stalk-, earshank-, kernel- or leaf-specific) promoters or control elements. Indeed, it is envisioned that a particular use of the present invention will be the targeting sense or antisense NOR expression in a tissue-specific manner. For example, these sequences could be targeted to the fruit.
  • tissue specific e.g., root-, collar/sheath-, whorl-, stalk-, earshank-, kernel- or leaf-specific
  • tissue-specific promoters for use in tissue-specific targeting of genes in transgenic plants will typically include tissue-specific promoters and may also include other tissue-specific control elements such as enhancer sequences. Promoters which direct specific or enhanced expression in certain plant tissues will be known to those of skill in the art in light of the present disclosure. These include, for example, the rbcS promoter, specific for green tissue; the ocs, nos and mas promoters which have higher activity in roots or wounded leaf tissue; a truncated (-90 to +8) 35S promoter which directs enhanced expression in roots, and an a-tubulin gene that directs expression in roots.
  • tissue specific expression may be functionally accomplished by introducing a constitutively expressed gene (all tissues) in combination with an antisense gene that is expressed only in those tissues where the gene product is not desired.
  • a gene coding for a NOR sequence may be introduced such that it is expressed in all tissues using the 35S promoter from Cauliflower Mosaic Virus. Expression of an antisense transcript of the same NOR gene in the fruit of a plant would prevent expression of the NOR gene only in the fruit.
  • tissue-specific promoter sequences for use in accordance with the present invention.
  • one may first isolate cD ⁇ A clones from the tissue concerned and identify those clones which are expressed specifically in that tissue, for example, using Northern blotting.
  • tissue concerned a tissue concerned
  • identify those clones which are expressed specifically in that tissue for example, using Northern blotting.
  • the promoter and control elements of corresponding genomic clones may then be localized using the techniques of molecular biology known to those of skill in the art.
  • NOR genes in transgenic plants may in some cases be desired only under specified conditions. It is contemplated that expression of such sequences at high levels may have detrimental effects. It is known that a large number of genes exist that respond to the environment. For example, expression of some genes such as rbcS, encoding the small subunit of ribulose bisphosphate carboxylase, is regulated by light as mediated through phytochrome. Other genes are induced by secondary stimuli. A number of genes have been shown to be induced by ABA (Skriver and Mundy, 1990). Therefore, in particular embodiments, inducible expression of the nucleic acid sequences of the invention may be desired.
  • NOR gene in some embodiments of the present invention expression of a NOR gene will be desired only in a certain time period during the development of the plant. Developmental timing is frequently correlated with tissue specific gene expression. For example, expression of certain genes associated with fruit ripening will only be expressed at certain stages of fruit development.
  • vectors may be constructed and employed in the intracellular targeting of a specific gene product within the cells of a transgenic plant or in directing a protein to the extracellular environment. This will generally be achieved by joining a D ⁇ A 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.
  • intracellular membranes e.g., vacuole, vesicle, plastid and mitochondrial membranes
  • a particular example of such a use concerns the direction of a herbicide resistance selectable marker gene, such as the EPSPS gene, to a particular organelle such as the chloroplast rather than to the cytoplasm.
  • a herbicide resistance selectable marker gene such as the EPSPS gene
  • organelle such as the chloroplast rather than to the cytoplasm.
  • rbcS transit peptide which confers plastid-specific targeting of proteins.
  • D ⁇ A itself within a cell.
  • it may be useful to target introduced D ⁇ A to the nucleus as this may increase the frequency of transformation.
  • Within the nucleus itself it would be useful to target a gene in order to achieve site specific integration.
  • Transformation constructs prepared in accordance with the invention will typically include a 3' end D ⁇ A sequence that acts as a signal to terminate transcription and allow for the poly-adenylation of the mR ⁇ A produced by coding sequences operably linked to a NOR gene.
  • the native NOR gene is used.
  • a heterologous 3' end may enhance the expression of sense or antisense NOR sequences.
  • Terminators which are deemed to be particularly useful in this context include those from the nopaline synthase gene of Agrobacterium tumefaciens (nos 3' end) (Bevan et al, 1983), the terminator for the T7 transcript from the octopine synthase gene of Agrobacterium tumefaciens, and the 3' end of the protease inhibitor I or II genes from potato or tomato.
  • Adh intron (Callis et al, 1987), sucrose synthase intron (Vasil et al, 1989) or TMV omega element (Gallie et al, 1989), may further be included where desired.
  • Transit or Signal Peptides Sequences that are joined to the coding sequence of an expressed gene, which are removed post-translationally from the initial translation product and which facilitate the transport of the protein into or through intracellular or extracellular membranes, are termed transit (usually into vacuoles, vesicles, plastids and other intracellular organelles) and signal sequences (usually to the endoplasmic reticulum, golgi apparatus and outside of the cellular membrane). By facilitating the transport of the protein into compartments inside and outside the cell, these sequences may increase the accumulation of gene product protecting them from proteolytic degradation. These sequences also allow for additional mRNA sequences from highly expressed genes to be attached to the coding sequence of the genes.
  • translatable mRNA in front of the gene may increase the overall stability of the mRNA transcript from the gene and thereby increase synthesis of the gene product. Since transit and signal sequences are usually post-translationally removed from the initial translation product, the use of these sequences allows for the addition of extra translated sequences that may not appear on the final polypeptide. It further is contemplated that targeting of certain proteins may be desirable in order to enhance the stability of the protein (U.S. Patent No. 5,545,818, incorporated herein by reference in its entirety).
  • vectors may be constructed and employed in the intracellular targeting of a specific gene product within the cells of a transgenic plant or in directing a protein to the extracellular environment. This generally will 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.
  • Marker genes are genes that impart a distinct phenotype to cells expressing the marker protein and thus allow such transformed cells to be distinguished from cells that do not have the marker. Such genes may encode either a selectable or screenable marker, depending on whether the marker confers a trait which one can "select” for by chemical means, i.e., through the use of a selective agent (e.g. , a herbicide, antibiotic, or the like), or whether it is simply a trait that one can identify through observation or testing, i.e., by "screening”' (e.g., the green fluorescent protein).
  • a selective agent e.g. , a herbicide, antibiotic, or the like
  • screening e.g., the green fluorescent protein
  • selectable or screenable markers also are genes which encode a "secretable marker" whose secretion can be detected as a means of identifying or selecting for transformed cells. Examples include markers which are secretable antigens that can be identified by antibody interaction, or even secretable enzymes which can be detected by their catalytic activity.
  • Secretable proteins fall into a number of classes, including small, diffusible proteins detectable, e.g., by ELISA; small active enzymes detectable in extracellular solution (e.g., ⁇ -amylase, ⁇ -lactamase, phosphinothricin acetyltransferase); 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).
  • small, diffusible proteins detectable e.g., by ELISA
  • small active enzymes detectable in extracellular solution e.g., ⁇ -amylase, ⁇ -lactamase, phosphinothricin acetyltransferase
  • 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.
  • a gene that encodes a protein that becomes sequestered in the cell wall, and which protein includes a unique epitope is considered to be particularly 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.
  • NOR sequences of the present invention including, but not limited to, neo (Potrykus et al, 1985), which provides kanamycin resistance and can be selected for using kanamycin, G418, paromomycin, etc.; bar, which confers bialaphos or phosphinothricin resistance; a mutant EPSP synthase protein (Hinchee et al, 1988) conferring glyphosate resistance; a nitrilase such as bxn from Klebsiella ozaenae which confers resistance to bromoxynil (Stalker et al, 1988); a mutant acetolactate synthase (ALS) which confers resistance to imidazolinone, sulfonylurea or other ALS inhibiting chemicals (European Patent Application 154,204, 1985); a methotrexate resistant DHFR (Thillet et al, 1988), a dalapon de
  • Patent No. 5,188,642 or OTP U.S. Patent No. 5,633,448
  • selectable marker capable of being used in systems to select transformants are those that encode the enzyme phosphinothricin acetyltransferase, such as the bar gene from Streptomyces hygroscopicus or the pat gene from Streptomyces viridochromogenes.
  • the enzyme phosphinothricin acetyl transferase (PAT) inactivates the active ingredient in the herbicide bialaphos, phosphinothricin (PPT). PPT inhibits glutamine synthetase, (Murakami et al, 1986; Twell et al, 1989) causing rapid accumulation of ammonia and cell death.
  • Screenable markers that may be employed include a ⁇ -glucuronidase (GUS) or uidA gene 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, 1988); a ⁇ -lactamase gene (Sutcliffe, 1978), which encodes an enzyme for which various chromogenic substrates are known (e.g., PAD AC, a chromogenic cephalosporin); a xylE gene (Zukowsky et ⁇ l., 1983) which encodes a catechol dioxygenase that can convert chromogenic catechols; an ⁇ -amylase gene (Ikuta et ⁇ l, 1990); a tyrosinase gene (Katz et ⁇ l, 1983) which encodes an enzyme capable of oxidizing ty
  • Genes from the maize R gene complex can also be used as screenable markers.
  • the R gene complex in maize encodes a protein that acts to regulate the production of anthocyanin pigments in most seed and plant tissue.
  • Maize strains can have one, or as many as four, R alleles which combine to regulate pigmentation in a developmental and tissue specific manner.
  • an R gene introduced into such cells will cause the expression of a red pigment and, if stably incorporated, can be visually scored as a red sector.
  • a maize line carries dominant alleles for genes encoding for the enzymatic intermediates in the anthocyanin biosynthetic pathway (C2, Al, A2, Bzl and Bz2), but carries a recessive allele at the R locus, transformation of any cell from that line with R will result in red pigment formation.
  • Exemplary lines include Wisconsin 22 which contains the rg-Stadler allele and TR112, a K55 derivative which is r-g, b, PI.
  • any genotype of maize can be utilized if the Cl and R alleles are introduced together.
  • Another screenable marker contemplated for use in the present invention is firefly luciferase, encoded by the lux gene.
  • 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 also is envisioned that this system may be developed for populational screening for bioluminescence, such as on tissue culture plates, or even for whole plant screening.
  • the gene which encodes green fluorescent protein (GFP) is contemplated as a particularly useful reporter gene (Sheen et al, 1995; Haseloff et al, 1997; Reichel et al, 1996; Tian et al, 1997; WO 97/41228). Expression of green fluorescent protein may be visualized in a cell or plant as fluorescence following illumination by particular wavelengths of light. Where use of a screenable marker gene such as lux or GFP is desired, the inventors contemplated that benefit may be realized by creating a gene fusion between the screenable marker gene and a selectable marker gene, for example, a GFP-NPTII gene fusion. This could allow, for example, selection of transformed cells followed by screening of transgenic plants or seeds.
  • a selectable marker gene for example, a GFP-NPTII gene fusion. This could allow, for example, selection of transformed cells followed by screening of transgenic plants or seeds.
  • Negative Selectable Markers Introduction of genes encoding traits that can be selected against may be useful for eliminating undesirable linked genes. It is contemplated that when two or more genes are introduced together by cotransformation that the genes will be linked together on the host chromosome. For example, a gene encoding Bt that confers insect resistance on the plant may be introduced into a plant together with a bar gene that is useful as a selectable marker and confers resistance to the herbicide Liberty® on the plant. However, it may not be desirable to have an insect resistant plant that also is resistant to the herbicide Liberty®. It is proposed that one also could introduce an antisense bar gene that is expressed in those tissues where one does not want expression of the bar gene, e.g., in whole plant parts. Hence, although the bar gene is expressed and is useful as a selectable marker, it is not useful to confer herbicide resistance on the whole plant. The bar antisense gene is a negative selectable marker.
  • a homologous recombinant may be identified through the inactivation of a gene that was previously expressed in that cell.
  • the antisense gene to neomycin phosphotransferase II (NPT II) has been investigated as a negative selectable marker in tobacco (Nicotiana tabacum) and Arabidopsis thaliana (Xiang. and Guerra, 1993).
  • NPT II neomycin phosphotransferase II
  • both sense and antisense NPT II genes are introduced into a plant through transformation and the resultant plants are sensitive to the antibiotic kanamycin.
  • negative selectable markers also may be useful in other ways.
  • One application is to construct transgenic lines in which one could select for transposition to unlinked sites.
  • the transposable element In the process of tagging it is most common for the transposable element to move to a genetically linked site on the same chromosome.
  • a selectable marker for recovery of rare plants in which transposition has occurred to an unlinked locus would be useful.
  • the enzyme cytosine deaminase may be useful for this purpose (Stouggard, 1993). In the presence of this enzyme the compound 5-fluorocytosine is converted to 5-fluorouracil which is toxic to plant and animal cells.
  • transposable element is linked to the gene for the enzyme cytosine deaminase
  • the parental plants and plants containing transpositions to linked sites will remain sensitive to 5- fluorocytosine.
  • Resistance to 5-fluorocytosine is due to loss of the cytosine deaminase gene through genetic segregation of the transposable element and the cytosine deaminase gene.
  • Other genes that encode proteins that render the plant sensitive to a certain compound will also be useful in this context.
  • T-DNA gene 2 from Agrobacterium tumefaciens encodes a protein that catalyzes the conversion of ⁇ -naphthalene acetamide (NAM) to ⁇ - naphthalene acetic acid (NAA) renders plant cells sensitive to high concentrations of NAM (Depicker et ⁇ /., 1988).
  • NAM ⁇ -naphthalene acetamide
  • NAA ⁇ - naphthalene acetic acid
  • negative selectable markers may be useful in the construction of transposon tagging lines.
  • an autonomous transposable element such as Ac, Master Mu, or En/Spn
  • a negative selectable marker By marking an autonomous transposable element such as Ac, Master Mu, or En/Spn with a negative selectable marker, one could select for transformants in which the autonomous element is not stably integrated into the genome. It is proposed that this would be desirable, for example, when transient expression of the autonomous element is desired to activate in trans the transposition of a defective transposable element, such as Ds, but stable integration of the autonomous element is not desired. The presence of the autonomous element may not be desired in order to stabilize the defective element, i.e., prevent it from further transposing. However, it is proposed that if stable integration of an autonomous transposable element is desired in a plant the presence of a negative selectable marker may make it possible to eliminate the autonomous element during the breeding process.
  • DNA may be introduced into plants for the purpose of expressing RNA transcripts that function to affect plant phenotype yet are not translated into protein.
  • RNA transcripts that function to affect plant phenotype yet are not translated into protein.
  • antisense RNA which is discussed in detail below
  • RNA with ribozyme activity Both may serve possible functions in reducing or eliminating expression of native or introduced plant genes, for example, a NOR gene.
  • D ⁇ A need not be expressed to effect the phenotype of a plant.
  • Genes also may be constructed or isolated, which when transcribed, produce R ⁇ A enzymes (ribozymes) which can act as endoribonucleases and catalyze the cleavage of R ⁇ A molecules with selected sequences.
  • the cleavage of selected messenger R ⁇ As can result in the reduced production of their encoded polypeptide products.
  • These genes may be used to prepare novel transgenic plants which possess them.
  • the transgenic plants may possess reduced levels of polypeptides including, but not limited to, the polypeptides cited above.
  • Ribozymes are R ⁇ A-protein complexes that cleave nucleic acids in a site-specific fashion. Ribozymes have specific catalytic domains that possess endonuclease activity (Kim and Cech, 1987; Gerlach et al, 1987; Forster and Symons, 1987). For example, a large number of ribozymes accelerate phosphoester transfer reactions with a high degree of specificity, often cleaving only one of several phosphoesters in an oligonucleotide substrate (Cech et al, 1981; Michel and Westhof, 1990; Reinhold-Hurek and Shub, 1992). This specificity has been attributed to the requirement that the substrate bind via specific base- pairing interactions to the internal guide sequence ("IGS") of the ribozyme prior to chemical reaction.
  • IGS internal guide sequence
  • Ribozyme catalysis has primarily been observed as part of sequence-specific cleavage/ligation reactions involving nucleic acids (Joyce, 1989; Cech et al, 1981).
  • U. S. Patent 5,354,855 reports that certain ribozymes can act as endonucleases with a sequence specificity greater than that of known ribonucleases and approaching that of the DNA restriction enzymes.
  • RNA cleavage activity examples include sequences from the Group I self splicing introns including Tobacco Ringspot Virus (Prody et al, 1986), Avocado Sunblotch Viroid (Palukaitis et al, 1979), and Lucerne Transient Streak Virus (Forster and Symons, 1987). Sequences from these and related viruses are referred to as hammerhead ribozyme based on a predicted folded secondary structure.
  • ribozymes include sequences from RNase P with RNA cleavage activity (Yuan et al, 1992, Yuan and Altman, 1994, U. S. Patents 5,168,053 and 5,624,824), hairpin ribozyme structures (Berzal-Herranz et al, 1992; Chowrira et al, 1994) and Hepatitis Delta virus based ribozymes (U. S. Patent 5,625,047).
  • the general design and optimization of ribozyme directed RNA cleavage activity has been discussed in detail (Haseloff and Gerlach, 1988, Symons, 1992, Chowrira et al, 1994; Thompson et al, 1995).
  • Ribozymes are targeted to a given sequence by virtue of annealing to a site by complimentary base pair interactions. Two stretches of homology are required for this targeting. These stretches of homologous sequences flank the catalytic ribozyme structure defined above. Each stretch of homologous sequence can vary in length from 7 to 15 nucleotides. The only requirement for defining the homologous sequences is that, on the target RNA, they are separated by a specific sequence which is the cleavage site.
  • the cleavage site is a dinucleotide sequence on the target RNA is a uracil (U) followed by either an adenine, cytosine or uracil (A,C or U) (Perriman et al, 1992; Thompson et al, 1995).
  • U uracil
  • A,C or U adenine, cytosine or uracil
  • the frequency of this dinucleotide occurring in any given RNA is statistically 3 out of 16. Therefore, for a given target messenger RNA of 1000 bases, 187 dinucleotide cleavage sites are statistically possible.
  • Designing and testing ribozymes for efficient cleavage of a target RNA is a process well known to those skilled in the art. Examples of scientific methods for designing and testing ribozymes are described by Chowrira et al, (1994) and Lieber and Strauss (1995), each incorporated by reference. The identification of operative and preferred sequences for use in down regulating a given gene is simply a matter of preparing and testing a given sequence, and is a routinely practiced "screening" method known to those of skill in the art.
  • genes may be introduced to produce novel transgenic plants which have reduced expression of a native gene product by the mechanism of co-suppression, thus this technique could be used in accordance with the invention. It has been demonstrated in tobacco, tomato, and petunia (Goring et al, 1991; Smith et al, 1990; Napoli et al, 1990; van der Krol et al. , 1990) that expression of the sense transcript of a native gene will reduce or eliminate expression of the native gene in a manner similar to that observed for antisense genes. The introduced gene may encode all or part of the targeted native protein but its translation may not be required for reduction of levels of that native protein. IV. Antisense Constructs
  • Antisense treatments are one way of altering fruit quality and/or ethylene response and the characteristics associated therewith in accordance with the invention.
  • constructs comprising the NOR gene in antisense orientation may be used to decrease or effectively eliminate the expression of the gene in a plant.
  • antisense technology may be used to "knock-out" the function of a NOR gene or homologous sequences thereof, thereby causing the delay, protraction or inhibition of fruit ripening and/or decreased ethylene responsiveness, as well as the effects associated therewith.
  • Antisense methodology takes advantage of the fact that nucleic acids tend to pair with "complementary" sequences.
  • complementary it is meant that polynucleotides are those which are capable of base-pairing according to the standard Watson-Crick complementarity rules. That is, the larger purines will base pair with the smaller pyrimidines to form combinations of guanine paired with cytosine (G:C) and adenine paired with either thymine (A:T) in the case of D ⁇ A, or adenine paired with uracil (A:U) in the case of R ⁇ A.
  • Inclusion of less common bases such as inosine, 5-methylcytosine, 6-methyladenine, hypoxanthine and others in hybridizing sequences does not interfere with pairing.
  • Antisense polynucleotides when introduced into a target cell, specifically bind to their target polynucleotide and interfere with transcription, R ⁇ A processing, transport, translation and/or stability.
  • Antisense R ⁇ A constructs, or D ⁇ A encoding such antisense R ⁇ A's, may be employed to inhibit gene transcription or translation or both within a host cell, either in vitro or in vivo, such as within a host animal, including a human subject.
  • Antisense constructs may be designed to bind to the promoter and other control regions, exons, introns or even exon-intron boundaries of a gene. It is contemplated that the most effective antisense constructs will include regions complementary to intron/exon splice junctions. Thus, it is proposed that a preferred embodiment includes an antisense construct with complementarity to regions within 50-200 bases of an intron-exon splice junction. It has been observed that some exon sequences can be included in the construct without seriously affecting the target selectivity thereof. The amount of exonic material included will vary depending on the particular exon and intron sequences used. One can readily test whether too much exon DNA is included simply by testing the constructs in vitro to determine whether normal cellular function is affected or whether the expression of related genes having complementary sequences is affected.
  • complementary or “antisense” means polynucleotide sequences that are substantially complementary over their entire length and have very few base mismatches. For example, sequences of fifteen bases in length may be termed complementary when they have complementary nucleotides at thirteen or fourteen positions. Naturally, sequences which are completely complementary will be sequences which are entirely complementary throughout their entire length and have no base mismatches. Other sequences with lower degrees of homology also are contemplated. For example, an antisense construct which has limited regions of high homology, but also contains a non-homologous region (e.g., ribozyme; see above) could be designed. These molecules, though having less than 50% homology, would bind to target sequences under appropriate conditions.
  • genomic DNA may be combined with cDNA or synthetic sequences to generate specific constructs.
  • a genomic clone will need to be used.
  • the cDNA or a synthesized polynucleotide may provide more convenient restriction sites for the remaining portion of the construct and, therefore, would be used for the rest of the sequence.
  • Suitable methods for plant transformation for use with the current invention are believed to include virtually any method by which DNA can be introduced into a cell, such as by direct delivery of DNA such as by PEG-mediated transformation of protoplasts (Omirulleh et al, 1993), by desiccation/inhibition-mediated DNA uptake (Potrykus et al, 1985), by electroporation (U.S. Patent No. 5,384,253, specifically incorporated herein by reference in its entirety), by agitation with silicon carbide fibers (Kaeppler et al, 1990; U.S. Patent No. 5,302,523, specifically incorporated herein by reference in its entirety; and U.S. Patent No.
  • Agrobacterium-mediated transfer is a widely applicable system for introducing genes into plant cells because the DNA can be introduced into whole plant tissues, thereby bypassing the need for regeneration of an intact plant from a protoplast.
  • the use of Agrobacterium-mediated plant integrating vectors to introduce DNA into plant cells is well known in the art. See, for example, the methods described by Fraley et ⁇ l., (1985), Rogers et al, (1987) and U.S. Patent No. 5,563,055, specifically incorporated herein by reference in its entirety.
  • Agrobacterium-mediated transformation is most efficient in dicotyledonous plants and is the preferable method for transformation of dicots, including Arabidopsis, tobacco, tomato, and potato. Indeed, while Agrobacterium-mediated transformation has been routinely used with dicotyledonous plants for a number of years, it has only recently become applicable to monocotyledonous plants. Advances in Agrobacterium-mediated transformation techniques have now made the technique applicable to nearly all monocotyledonous plants. For example, Agrobacterium-mediated transformation techniques have now been applied to rice (Hiei et ⁇ l, 1997; U.S. Patent No.
  • Krzyzek et al U.S. Patent No. 5,384,253, incorporated herein by reference in its entirety
  • certain cell wall-degrading enzymes such as pectin-degrading enzymes, are employed to render the target recipient cells more susceptible to transformation by electroporation than untreated cells.
  • recipient cells are made more susceptible to transformation by mechanical wounding.
  • friable tissues such as a suspension culture of cells or embryogenic callus or alternatively one may transform immature embryos or other organized tissue directly.
  • pectolyases pectolyases
  • mechanically wounding in a controlled manner.
  • some species which have been transformed by electroporation of intact cells include maize (U.S. Patent No.
  • One also may employ protoplasts for electroporation transformation of plants (Bates, 1994; Lazzeri, 1995).
  • protoplasts for electroporation transformation of plants
  • the generation of transgenic soybean plants by electroporation of cotyledon-derived protoplasts is described by Dhir and Widholm in Intl. Patent Appl. Publ. No. WO 9217598 (specifically incorporated herein by reference).
  • Other examples of species for which protoplast transformation has been described include barley (Lazerri, 1995), sorghum (Battraw et al, 1991), maize (Bhattacharjee et al, 1997), wheat (He et al, 1994) and tomato (Tsukada, 1989).
  • microprojectile bombardment U.S. Patent No. 5,550,318; U.S. Patent No. 5,538,880; U.S. Patent No. 5,610,042; and PCT Application WO 94/09699; each of which is specifically incorporated herein by reference in its entirety.
  • particles may be coated with nucleic acids and delivered into cells by a propelling force.
  • Exemplary particles include those comprised of tungsten, platinum, and preferably, gold. It is contemplated that in some instances DNA precipitation onto metal particles would not be necessary for DNA delivery to a recipient cell using microprojectile bombardment. However, it is contemplated that particles may contain DNA rather than be coated with DNA. Hence, it is proposed that DNA-coated particles may increase the level of DNA delivery via particle bombardment but are not, in and of themselves, necessary.
  • cells in suspension are concentrated on filters or solid culture medium.
  • immature embryos or other target cells may be arranged on solid culture medium.
  • the cells to be bombarded are positioned at an appropriate distance below the macroprojectile stopping plate.
  • An illustrative embodiment of a method for delivering DNA into plant cells by acceleration is the Biolistics Particle Delivery System, which can be used to propel particles coated with DNA or cells through a screen, such as a stainless steel or Nytex screen, onto a filter surface covered with monocot plant cells cultured in suspension.
  • the screen disperses the particles so that they are not delivered to the recipient cells in large aggregates. It is believed that a screen intervening between the projectile apparatus and the cells to be bombarded reduces the size of projectiles aggregate and may contribute to a higher frequency of transformation by reducing the damage inflicted on the recipient cells by projectiles that are too large.
  • Microprojectile bombardment techniques are widely applicable, and may be used to transform virtually any plant species.
  • species for which have been transformed by microprojectile bombardment include monocot species such as maize (PCT Application WO 95/06128), barley (Ritala et al, 1994; Hensgens et al, 1993), wheat (U.S. Patent No.
  • Transformation of plant protoplasts can be achieved using methods based on calcium phosphate precipitation, polyethylene glycol treatment, electroporation, and combinations of these treatments (see, e.g., Potrykus et al, 1985; Lorz et al, 1985; Omirulleh et al, 1993; Fromm et al, 1986; Uchimiya et al, 1986; Callis et al, 1987; Marcotte et al, 1988).
  • Examples of the use of direct uptake transformation of cereal protoplasts include transformation of rice (Ghosh-Biswas et al, 1994), sorghum (Battraw and Hall, 1991), barley (Lazerri, 1995), oat (Zheng and Edwards, 1990) and maize (Omirulleh et al, 1993).
  • site-specific integration techniques could be used to insertionally mutagenize or replace a native NOR gene sequence.
  • An advantage of site- specific integration or excision is that it can be used to overcome problems associated with conventional transformation techniques, in which transformation constructs typically randomly integrate into a host genome in multiple copies. This random insertion of introduced D ⁇ A into the genome of host cells can be lethal if the foreign D ⁇ A inserts into an essential gene.
  • the expression of a transgene may be influenced by "position effects" caused by the surrounding genomic DNA.
  • Homologous recombination is a reaction between any pair of DNA sequences having a similar sequence of nucleotides, where the two sequences interact (recombine) to form a new recombinant DNA species.
  • the frequency of homologous recombination increases as the length of the shared nucleotide DNA sequences increases, and is higher with linearized plasmid molecules than with circularized plasmid molecules.
  • Homologous recombination can occur between two DNA sequences that are less than identical, but the recombination frequency declines as the divergence between the two sequences increases.
  • Introduced DNA sequences can be targeted via homologous recombination by linking a DNA molecule of interest to sequences sharing homology with endogenous sequences of the host cell.
  • conserved NOR sequences could be used to replace a native NOR sequence with one of the NOR sequences provided herein.
  • the two homologous sequences can interact to insert the introduced D ⁇ A at the site where the homologous genomic D ⁇ A sequences were located. Therefore, the choice of homologous sequences contained on the introduced D ⁇ A will determine the site where the introduced D ⁇ A is integrated via homologous recombination.
  • the D ⁇ A sequence of interest is linked to D ⁇ A sequences sharing homology to a single copy gene of a host plant cell, the D ⁇ A sequence of interest will be inserted via homologous recombination at only that single specific site.
  • the DNA sequence of interest can be inserted via homologous recombination at each of the specific sites where a copy of the gene is located.
  • DNA can be inserted into the host genome by a homologous recombination reaction involving either a single reciprocal recombination (resulting in the insertion of the entire length of the introduced DNA) or through a double reciprocal recombination (resulting in the insertion of only the DNA located between the two recombination events).
  • a homologous recombination reaction involving either a single reciprocal recombination (resulting in the insertion of the entire length of the introduced DNA) or through a double reciprocal recombination (resulting in the insertion of only the DNA located between the two recombination events).
  • a homologous recombination reaction involving either a single reciprocal recombination (resulting in the insertion of the entire length of the introduced DNA) or through a double reciprocal recombination (resulting in the insertion of only the DNA located between the two recombination events).
  • the introduced DNA should contain sequences homologous to the selected gene.
  • a double recombination event can be achieved by flanking each end of the DNA sequence of interest (the sequence intended to be inserted into the genome) with DNA sequences homologous to the selected gene.
  • a homologous recombination event involving each of the homologous flanking regions will result in the insertion of the foreign DNA.
  • only those DNA sequences located between the two regions sharing genomic homology become integrated into the genome.
  • homologous recombination is a relatively rare event compared to random insertion events.
  • foreign DNA molecules find homologous sequences in the cell's genome and recombine at a frequency of approximately 0.5-4.2X10 "4 .
  • any transformed cell that contains an introduced DNA sequence integrated via homologous recombination will also likely contain numerous copies of randomly integrated introduced DNA sequences. Therefore, to maintain control over the copy number and the location of the inserted DNA, these randomly inserted DNA sequences can be removed.
  • One manner of removing these random insertions is to utilize a site-specific recombinase system.
  • a site specific recombinase system consists of three elements: two pairs of DNA sequence (the site - specific recombination sequences) and a specific enzyme (the site-specific recombinase).
  • the site-specific recombinase will catalyze a recombination reaction only between two site -specific recombination sequences.
  • a number of different site specific recombinase systems could be employed in accordance with the instant invention, including, but not limited to, the Cre/lox system of bacteriophage PI (U.S. Patent No. 5,658,772, specifically incorporated herein by reference in its entirety), the FLP/FRT system of yeast (Golic and Lindquist, 1989), the Gin recombinase of phage Mu (Maeser et al, 1991), the Pin recombinase of E. coli (Enomoto et al, 1983), and the R/RS system of the pSRl plasmid (Araki et al, 1992).
  • the bacteriophage PI Cre/lox and the yeast FLP/FRT systems constitute two particularly useful systems for site specific integration or excision of transgenes.
  • a recombinase (Cre or FLP) will interact specifically with its respective site -specific recombination sequence (lox or FRT, respectively) to invert or excise the intervening sequences.
  • the sequence for each of these two systems is relatively short (34 bp for lox and 47 bp for FRT) and therefore, convenient for use with transformation vectors.
  • Cre-lox In the Cre-lox system, discovered in bacteriophage PI, recombination between loxP sites occurs in the presence of the Cre recombinase (see, e.g., U.S. Patent No. 5,658,772, specifically incorporated herein by reference in its entirety). This system has been utilized to excise a gene located between two lox sites which had been introduced into a yeast genome (Sauer, 1987). Cre was expressed from an inducible yeast GAL1 promoter and this Cre gene was located on an autonomously replicating yeast vector.
  • lox sites on the same DNA molecule can have the same or opposite orientation with respect to each other. Recombination between lox sites in the same orientation results in a deletion of the DNA segment located between the two lox sites and a connection between the resulting ends of the original DNA molecule.
  • the deleted DNA segment forms a circular molecule of DNA.
  • the original DNA molecule and the resulting circular molecule each contain a single lox site. Recombination between lox sites in opposite orientations on the same DNA molecule results in an inversion of the nucleotide sequence of the DNA segment located between the two lox sites.
  • reciprocal exchange of DNA segments proximate to lox sites located on two different DNA molecules can occur. All of these recombination events are catalyzed by the product of the Cre coding region.
  • Modification and changes may be made in the nucleic acids provided by the present invention and accordingly the structure of the polypeptides encoded thereby, and still obtain functional molecules that encode a NOR polypeptide.
  • the following is a discussion based upon alerting nucleic acids in the NOR sequences to result in a changing of the amino acids of a NOR polypeptide to create an equivalent, or even an improved, second-generation molecule.
  • mutated NOR proteins are contemplated to be useful for increasing the activity of the protein.
  • the amino acid changes may be achieved by changing the codons of the D ⁇ A sequence, according to the codons given in Table 1.
  • Tyrosine Tyr Y UAC UAU For example, certain amino acids may be substituted for other amino acids in a protein structure without appreciable loss of interactive binding capacity with structures such as, for example, antigen-binding regions of antibodies or binding sites on substrate molecules. Since it is the interactive capacity and nature of a protein that defines that protein's biological functional activity, certain amino acid sequence substitutions can be made in a protein sequence, and, of course, its underlying DNA coding sequence, and nevertheless obtain a protein with like properties. It is thus contemplated by the inventors that various changes may be made in the peptide sequences of the disclosed compositions, or corresponding DNA sequences which encode said peptides without appreciable loss of their biological utility or activity.
  • the hydropathic index of amino acids may be considered.
  • the importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte et al, 1982, incorporate herein by reference). It is accepted that the relative hydropathic character of the amino acid contributes to the secondary structure of the resultant protein, which in turn defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA, antibodies, antigens, and the like.
  • Each amino acid has been assigned a hydropathic index on the basis of their hydrophobicity and charge characteristics (Kyte et al, 1982), these are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenyialanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (-0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate (-3.5); glutamine (-3.5); aspartate (-3.5); asparagine (-3.5); lysine (-3.9); and arginine (-4.5).
  • amino acids may be substituted by other amino acids having a similar hydropathic index or score and still result in a protein with similar biological activity, i.e., still obtain a biological functionally equivalent protein.
  • substitution of amino acids whose hydropathic indices are within ⁇ 2 is preferred, those which are within ⁇ 1 are particularly preferred, and those within ⁇ 0.5 are even more particularly preferred.
  • hydrophihcity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0 ⁇ 1); glutamate (+3.0 ⁇ 1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5 ⁇ 1); alanine (-0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3); phenyialanine (-2.5); tryptophan (-3.4).
  • an amino acid can be substituted for another having a similar hydrophihcity value and still obtain a biologically equivalent, and in particular, an immunologically equivalent protein.
  • substitution of amino acids whose hydrophihcity values are within ⁇ 2 is preferred, those which are within ⁇ 1 are particularly preferred, and those within ⁇ 0.5 are even more particularly preferred.
  • amino acid substitutions are generally therefore based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophihcity, charge, size, and the like.
  • Exemplary substitutions which take various of the foregoing characteristics into consideration are well known to those of skill in the art and include: arginine and lysine; glutamate and aspartate; serine and threonine; glutamine and asparagine; and valine, leucine and isoleucine.
  • peptide mimetics are peptide-containing molecules that mimic elements of protein secondary structure. See, for example, Johnson et al, "Peptide Turn Mimetics” in BIOTECHNOLOGY AND PHARMACY, Pezzuto et al, Eds., Chapman and Hall, New York (1993).
  • the underlying rationale behind the use of peptide mimetics is that the peptide backbone of proteins exists chiefly to orient amino acid side chains in such a way as to facilitate molecular interactions, such as those of antibody and antigen.
  • a peptide mimetic is expected to permit molecular interactions similar to the natural molecule.
  • the next steps generally concern identifying the transformed cells for further culturing and plant regeneration.
  • identifying the transformed cells for further culturing and plant regeneration.
  • one may desire to employ a selectable or screenable marker gene with a transformation vector prepared in accordance with the invention.
  • DNA is introduced into only a small percentage of target cells in any one experiment.
  • a means for selecting those cells that are stably transformed is to introduce into the host cell, a marker gene which confers resistance to some normally inhibitory agent, such as an antibiotic or herbicide.
  • antibiotics which may be used include the aminoglycoside antibiotics neomycin, kanamycin and paromomycin, or the antibiotic hygromycin.
  • aminoglycoside antibiotics Resistance to the aminoglycoside antibiotics is conferred by aminoglycoside phosphostransferase enzymes such as neomycin phosphotransferase II (NPT IT) or NPT I, whereas resistance to hygromycin is conferred by hygromycin phosphotransferase.
  • aminoglycoside phosphostransferase enzymes such as neomycin phosphotransferase II (NPT IT) or NPT I
  • hygromycin phosphotransferase Resistance to the aminoglycoside antibiotics is conferred by aminoglycoside phosphostransferase enzymes such as neomycin phosphotransferase II (NPT IT) or NPT I
  • NPT IT neomycin phosphotransferase II
  • hygromycin phosphotransferase Resistance to the aminoglycoside antibiotics is conferred by aminoglycoside phosphostransferase
  • surviving cells are those cells where, generally, the resistance-conferring gene has been integrated and expressed at sufficient levels to permit cell survival. Cells may be tested further to confirm stable integration of the exogenous DNA.
  • Bialaphos is a tripeptide antibiotic produced by Streptomyces hygroscopicus and is composed of phosphinothricin (PPT), an analogue of L-glutamic acid, and two L-alanine residues. Upon removal of the L-alanine residues by intracellular peptidases, the PPT is released and is a potent inhibitor of glutamine synthetase (GS), a pivotal enzyme involved in ammonia assimilation and nitrogen metabolism (Ogawa et al, 1973). Synthetic PPT, the active ingredient in the herbicide LibertyTM also is effective as a selection agent.
  • PPT phosphinothricin
  • GS glutamine synthetase
  • Synthetic PPT the active ingredient in the herbicide LibertyTM also is effective as a selection agent.
  • PPT phosphinothricin acetyl transferase
  • this enzyme acetylates the free amino group of PPT preventing auto-toxicity (Thompson et al, 1987).
  • the bar gene has been cloned (Murakami et al, 1986; Thompson et al, 1987) and expressed in transgenic tobacco, tomato, potato (De Block et al, 1987) Brassica (De Block et al, 1989) and maize (U.S. Patent No. 5,550,318).
  • some transgenic plants which expressed the resistance gene were completely resistant to commercial formulations of PPT and bialaphos in greenhouses.
  • Glyphosate inhibits the action of the enzyme EPSPS which is active in the aromatic amino acid biosynthetic pathway. Inhibition of this enzyme leads to starvation for the amino acids phenyialanine, tyrosine, and tryptophan and secondary metabolites derived thereof.
  • U.S. Patent No. 4,535,060 describes the isolation of EPSPS mutations which confer glyphosate resistance on the Salmonella typhimurium gene for EPSPS, aroA.
  • the EPSPS gene was cloned from Zea mays and mutations similar to those found in a glyphosate resistant aroA gene were introduced in vitro. Mutant genes encoding glyphosate resistant EPSPS enzymes are described in, for example, International Patent WO 97/4103. The best characterized mutant EPSPS gene conferring glyphosate resistance comprises amino acid changes at residues 102 and 106, although it is anticipated that other mutations will also be useful (PCT/WO97/4103).
  • bombarded tissue is cultured for 0 - 28 days on nonselective medium and subsequently transferred to medium containing from 1-3 mg/1 bialaphos or 1-3 mM glyphosate as appropriate. While ranges of 1- 3 mg/1 bialaphos or 1-3 mM glyphosate will typically be preferred, it is proposed that ranges of 0.1-50 mg/1 bialaphos or 0.1-50 mM glyphosate will find utility in the practice of the invention.
  • Tissue can be placed on any porous, inert, solid or semi-solid support for bombardment, including but not limited to filters and solid culture medium.
  • Bialaphos and glyphosate are provided as examples of agents suitable for selection of transformants, but the technique of this invention is not limited to them.
  • the herbicide DALAPON 2,2-dichloropropionic acid
  • the enzyme 2,2-dichloropropionic acid dehalogenase inactivates the herbicidal activity of 2,2-dichloropropionic acid and therefore confers herbicidal resistance on cells or plants expressing a gene encoding the dehalogenase enzyme (Buchanan- Wollaston et al, 1992; U.S. Patent Appl. No. 08/113,561, filed August 25, 1993; U.S. Patent No. 5,508,468; and U.S. Patent No. 5,508,468; each of the disclosures of which is specifically incorporated herein by reference in its entirety).
  • anthranilate synthase which confers resistance to certain amino acid analogs, e.g., 5-methyltryptophan or 6-methyl anthranilate, may be useful as a selectable marker gene.
  • an anthranilate synthase gene as a selectable marker was described in U.S. Patent No. 5,508,468; and U.S. Patent Application 08/604,789.
  • a screenable marker trait is the red pigment produced under the control of the R-locus in maize. This pigment may be detected by culturing cells on a solid support containing nutrient media capable of supporting growth at this stage and selecting cells from colonies (visible aggregates of cells) that are pigmented. These cells may be cultured further, either in suspension or on solid media.
  • the R-locus is useful for selection of transformants from bombarded immature embryos. In a similar fashion, the introduction of the Cl and B genes will result in pigmented cells and/or tissues.
  • the enzyme luciferase may be used as a screenable marker in the context of the present invention.
  • cells expressing luciferase emit light which can be detected on photographic or x-ray film, in a luminometer (or liquid scintillation counter), by devices that enhance night vision, or by a highly light sensitive video camera, such as a photon counting camera. All of these assays are nondestructive and transformed cells may be cultured further following identification.
  • the photon counting camera is especially valuable as it allows one to identify specific cells or groups of cells which are expressing luciferase and manipulate those in real time.
  • Another screenable marker which may be used in a similar fashion is the gene coding for green fluorescent protein.
  • a selection agent such as bialaphos or glyphosate
  • selection with a growth inhibiting compound, such as bialaphos or glyphosate at concentrations below those that cause 100% inhibition followed by screening of growing tissue for expression of a screenable marker gene such as luciferase would allow one to recover transformants from cell or tissue types that are not amenable to selection alone.
  • combinations of selection and screening may enable one to identify transformants in a wider variety of cell and tissue types. This may be efficiently achieved using a gene fusion between a selectable marker gene and a screenable marker gene, for example, between an NPTII gene and a GFP gene.
  • Cells that survive the exposure to the selective agent, or cells that have been scored positive in a screening assay may be cultured in media that supports regeneration of plants.
  • MS and N6 media may be modified by including further substances such as growth regulators.
  • a preferred growth regulator for such purposes is dicamba or 2,4-D.
  • other growth regulators may be employed, including NAA, NAA + 2,4-D or perhaps even picloram. Media improvement in these and like ways has been found to facilitate the growth of cells at specific developmental stages.
  • Tissue may be maintained on a basic media with growth regulators until sufficient tissue is available to begin plant regeneration efforts, or following repeated rounds of manual selection, until the morphology of the tissue is suitable for regeneration, at least 2 wk, then transferred to media conducive to maturation of embryoids. Cultures are transferred every 2 wk on this medium. Shoot development will signal the time to transfer to medium lacking growth regulators.
  • the transformed cells identified by selection or screening and cultured in an appropriate medium that supports regeneration, will then be allowed to mature into plants.
  • Developing plantlets are transferred to soiless plant growth mix, and hardened, e.g., in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO , and 25- 1
  • Plants are preferably matured either in a growth chamber or greenhouse. Plants are regenerated from about 6 wk to 10 months after a transformant is identified, depending on the initial tissue. During regeneration, cells are grown on solid media in tissue culture vessels. Illustrative embodiments of such vessels are petri dishes and Plant Cons. Regenerating plants are preferably grown at about 19 to 28°C. After the regenerating plants have reached the stage of shoot and root development, they may be transferred to a greenhouse for further growth and testing.
  • seeds on transformed plants may occasionally require embryo rescue due to cessation of seed development and premature senescence of plants.
  • To rescue developing embryos they are excised from surface-disinfected seeds 10-20 days post- pollination and cultured.
  • An embodiment of media used for culture at this stage comprises MS salts, 2% sucrose, and 5.5 g/1 agarose.
  • embryo rescue large embryos (defined as greater than 3 mm in length) are germinated directly on an appropriate media. Embryos smaller than that may be cultured for 1 wk on media containing the above ingredients along with 10 '5 M abscisic acid and then transferred to growth regulator-free medium for germination.
  • Progeny may be recovered from transformed plants and tested for expression of the exogenous expressible gene by localized application of an appropriate substrate to plant parts such as leaves.
  • an appropriate substrate such as leaves.
  • transformed parental plants (Ro) and their progeny of any generation tested exhibited no bialaphos-related necrosis after localized application of the herbicide Basta to leaves, if there was functional PAT activity in the plants as assessed by an in vitro enzymatic assay. All PAT positive progeny tested contained bar, confirming that the presence of the enzyme and the resistance to bialaphos were associated with the transmission through the germline of the marker gene.
  • assays include, for example, “molecular biological” assays, such as Southern and Northern blotting and PCRTM; “biochemical” assays, such as detecting the presence of a protein product, e.g., by immunological means (ELISAs and Western blots) or by enzymatic function; plant part assays, such as leaf or root assays; and also, by analyzing the phenotype of the whole regenerated plant.
  • Genomic DNA may be isolated from callus cell lines or any plant parts to determine the presence of the exogenous gene through the use of techniques well known to those skilled in the art. Note, that intact sequences will not always be present, presumably due to rearrangement or deletion of sequences in the cell.
  • PCRTM polymerase chain reaction
  • Positive proof of DNA integration into the host genome and the independent identities of transformants may be determined using the technique of Southern hybridization. Using this technique specific DNA sequences that were introduced into the host genome and flanking host DNA sequences can be identified. Hence the Southern hybridization pattern of a given transformant serves as an identifying characteristic of that transformant. In addition it is possible through Southern hybridization to demonstrate the presence of introduced genes in high molecular weight DNA, i.e., confirm that the introduced gene has been integrated into the host cell genome.
  • the technique of Southern hybridization provides information that is obtained using PCRTM, e.g., the presence of a gene, but also demonstrates integration into the genome and characterizes each individual transformant.
  • RNA will only be expressed in particular cells or tissue types and hence it will be necessary to prepare RNA for analysis from these tissues.
  • PCRTM techniques also may be used for detection and quantitation of RNA produced from introduced genes. In this application of PCRTM it is first necessary to reverse transcribe RNA into DNA, using enzymes such as reverse transcriptase, and then through the use of conventional PCRTM techniques amplify the DNA. In most instances PCRTM techniques, while useful, will not demonstrate integrity of the RNA product. Further information about the nature of the RNA product may be obtained by Northern blotting. This technique will demonstrate the presence of an RNA species and give information about the integrity of that RNA. The presence or absence of an RNA species also can be determined using dot or slot blot Northern hybridizations. These techniques are modifications of Northern blotting and will only demonstrate the presence or absence of an RNA species.
  • Southern blotting and PCRTM may be used to detect the gene(s) in question, they do not provide information as to whether the corresponding protein is being expressed. Expression may be evaluated by specifically identifying the protein products of the introduced genes or evaluating the phenotypic changes brought about by their expression.
  • Assays for the production and identification of specific proteins may make use of physical-chemical, structural, functional, or other properties of the proteins.
  • Unique physical- chemical or structural properties allow the proteins to be separated and identified by electrophoretic procedures, such as native or denaturing gel electrophoresis or isoelectric focusing, or by chromatographic techniques such as ion exchange or gel exclusion chromatography.
  • the unique structures of individual proteins offer opportunities for use of specific antibodies to detect their presence in formats such as an ELISA assay. Combinations of approaches may be employed with even greater specificity such as western blotting in which antibodies are used to locate individual gene products that have been separated by electrophoretic techniques. Additional techniques may be employed to absolutely confirm the identity of the product of interest such as evaluation by amino acid sequencing following purification. Although these are among the most commonly employed, other procedures may be additionally used.
  • Assay procedures also may be used to identify the expression of proteins by their functionality, especially the ability of enzymes to catalyze specific chemical reactions involving specific substrates and products. These reactions may be followed by providing and quantifying the loss of substrates or the generation of products of the reactions by physical or chemical procedures. Examples are as varied as the enzyme to be analyzed and may include assays for PAT enzymatic activity by following production of radiolabeled acetylated phosphinothricin from phosphinothricin and l4 C-acetyl Co A or for anthranilate synthase activity by following loss of fluorescence of anthranilate, to name two.
  • bioassays Very frequently the expression of a gene product is determined by evaluating the phenotypic results of its expression. These assays also may take many forms including but not limited to analyzing changes in the chemical composition, morphology, or physiological properties of the plant. Chemical composition may be altered by expression of genes encoding enzymes or storage proteins which change amino acid composition and may be detected by amino acid analysis, or by enzymes which change starch quantity which may be analyzed by near infrared reflectance spectrometry. Morphological changes may include greater stature or thicker stalks. Most often changes in response of plants or plant parts to imposed treatments are evaluated under carefully controlled conditions termed bioassays.
  • Assays may be employed with the instant invention for determination of the relative efficiency of transgene expression. Such methods would also be useful in evaluating, for example, random or site-specific mutants of the NOR sequences provided herein. Alternatively, assays could be used to determine the efficacy of expression when various different enhancers, terminators or other types of elements potentially used in the preparation of transformation constructs.
  • expression assays may comprise a system utilizing embryogenic or non- embryogenic cells, or alternatively, whole plants.
  • An advantage of using cellular assays is that regeneration of large numbers of plants is not required.
  • the systems are limited in that promoter activity in the non-regenerated cells may not directly correlate with expression in a plant. Additionally, assays of tissue or developmental specific promoters are generally not feasible.
  • the biological sample to be assayed may comprise nucleic acids isolated from the cells of any plant material according to standard methodologies (Sambrook et al, 1989).
  • the nucleic acid may be genomic DNA or fractionated or whole cell RNA. Where RNA is used, it may be desired to convert the RNA to a complementary DNA.
  • the RNA is whole cell RNA; in another, it is poly-A RNA. Normally, the nucleic acid is amplified.
  • the specific nucleic acid of interest is identified in the sample directly using amplification or with a second, known nucleic acid following amplification.
  • the identified product is detected.
  • the detection may be performed by visual means (e.g., ethidium bromide staining of a gel).
  • the detection may involve indirect identification of the product via chemiluminescence, radioactive scintigraphy of radiolabel or fluorescent label or even via a system using electrical or thermal impulse signals (Affymax Technology; Bellus, 1994).
  • the non- transformed control plants will be of a genetic background similar to the transformed plants. In this way, it is possible to detect differences in the amount or kind of protein detected in various transformed plants.
  • clonal cultures of cells for example, callus or an immature embryo, may be compared to other cells samples.
  • assays are contemplated in the screening of cells or plants of the current invention and associated promoters. These techniques may in cases be used to detect for both the presence and expression of the particular genes as well as rearrangements that may have occurred in the gene construct.
  • FISH fluorescent in situ hybridization
  • PFGE pulsed field gel electrophoresis
  • SSCA single-stranded conformation analysis
  • ASO allele-specific oligonucleotide
  • FISH fluorescent in situ hybridization
  • PFGE pulsed field gel electrophoresis
  • SSCA single-stranded conformation analysis
  • ASO allele-specific oligonucleotide
  • dot blot analysis denaturing gradient gel electrophoresis
  • RFLP PCRTM-SSCP.
  • RT Reverse transcription
  • RT-PCRTM relative quantitative PCRTM
  • PCRTM the number of molecules of the amplified target DNA increase by a factor approaching two with every cycle of the reaction until some reagent becomes limiting. Thereafter, the rate of amplification becomes increasingly diminished until there is no increase in the amplified target between cycles.
  • a graph is plotted in which the cycle number is on the X axis and the log of the concentration of the amplified target DNA is on the Y axis, a curved line of characteristic shape is formed by connecting the plotted points. Beginning with the first cycle, the slope of the line is positive and constant. This is said to be the linear portion of the curve. After a reagent becomes limiting, the slope of the line begins to decrease and eventually becomes zero. At this point the concentration of the amplified target DNA becomes asymptotic to some fixed value. This is said to be the plateau portion of the curve.
  • the concentration of the target DNA in the linear portion of the PCRTM amplification is directly proportional to the starting concentration of the target before the reaction began.
  • concentration of the amplified products of the target DNA in PCRTM reactions that have completed the same number of cycles and are in their linear ranges, it is possible to determine the relative concentrations of the specific target sequence in the original DNA mixture. If the DNA mixtures are cDNAs synthesized from RNAs isolated from different tissues or cells, the relative abundances of the specific mRNA from which the target sequence was derived can be determined for the respective tissues or cells. This direct proportionality between the concentration of the PCRTM products and the relative mRNA abundances is only true in the linear range of the PCRTM reaction.
  • the final concentration of the target DNA in the plateau portion of the curve is determined by the availability of reagents in the reaction mix and is independent of the original concentration of target DNA. Therefore, the first condition that must be met before the relative abundances of a mRNA species can be determined by RT-PCRTM for a collection of RNA populations is that the concentrations of the amplified PCRTM products must be sampled when the PCRTM reactions are in the linear portion of their curves.
  • the second condition that must be met for an RT-PCRTM study to successfully determine the relative abundances of a particular mRNA species is that relative concentrations of the amplifiable cDNAs must be normalized to some independent standard.
  • the goal of an RT-PCRTM study is to determine the abundance of a particular mRNA species relative to the average abundance of all mRNA species in the sample.
  • Most protocols for competitive PCRTM utilize internal PCRTM standards that are approximately as abundant as the target. These strategies are effective if the products of the PCRTM amplifications are sampled during their linear phases. If the products are sampled when the reactions are approaching the plateau phase, then the less abundant product becomes relatively over represented.
  • Comparisons of relative abundances made for many different RNA samples become distorted in such a way as to make differences in relative abundances of RNAs appear less than they actually are. This is not a significant problem if the internal standard is much more abundant than the target. If the internal standard is more abundant than the target, then direct linear comparisons can be made between RNA samples.
  • RT-PCRTM assay for plant tissue.
  • the problems inherent in plant tissue samples are that they are of variable quantity (making normalization problematic), and that they are of variable quality (necessitating the co-amplification of a reliable internal control, preferably of larger size than the target). Both of these problems are overcome if the RT-PCRTM is performed as a relative quantitative RT-PCRTM with an internal standard in which the internal standard is an amplifiable cDNA fragment that is larger than the target cDNA fragment and in which the abundance of the mRNA encoding the internal standard is roughly 5-100 fold higher than the mRNA encoding the target.
  • This assay measures relative abundance, not absolute abundance of the respective mRNA species.
  • RT-PCRTM assays can be superior to those derived from the relative quantitative RT-PCRTM assay with an internal standard.
  • Markers represent an efficient means for assaying the expression of transgenes.
  • a selectable marker one could quantitatively determine the resistance conferred upon a plant or plant cell by a construct comprising the selectable marker coding region operably linked to the promoter to be assayed, e.g., an RS324 promoter.
  • various plant parts could be exposed to a selective agent and the relative resistance provided in these parts quantified, thereby providing an estimate of the tissue specific expression of the promoter.
  • Screenable markers constitute another efficient means for quantifying the expression of a given transgene. Potentially any screenable marker could be expressed and the marker gene product quantified, thereby providing an estimate of the efficiency with which the promoter directs expression of the transgene. Quantification can readily be carried out using either visual means, or, for example, a photon counting device.
  • a preferred screenable marker gene assay for use with the current invention constitutes the use of the screenable marker gene ⁇ -glucuronidase (GUS). Detection of GUS activity can be performed histochemically using 5-bromo-4-chloro-3-indolyl glucuronide (X- gluc) as the substrate for the GUS enzyme, yielding a blue precipitate inside of cells containing GUS activity. This assay has been described in detail (Jefferson, 1987). The blue coloration can then be visually scored, and estimates of expression efficiency thereby provided. GUS activity also can be determined by immunoblot analysis or a fluorometric GUS specific activity assay (Jefferson, 1987).
  • Protein purification techniques are well known to those of skill in the art. These techniques involve, at one level, the crude fractionation of the cellular milieu to polypeptide and non-polypeptide fractions. Having separated the polypeptide from other proteins, the polypeptide of interest may be further purified using chromatographic and electrophoretic techniques to achieve partial or complete purification (or purification to homogeneity). Analytical methods particularly suited to the preparation of a pure peptide are ion-exchange chromatography, exclusion chromatography; polyacrylamide gel electrophoresis; and isoelectric focusing. A particularly efficient method of purifying peptides is fast protein liquid chromatography or even HPLC.
  • Partial purification may be accomplished by using fewer purification steps in combination, or by utilizing different forms of the same general purification scheme. For example, it is appreciated that a cation-exchange column chromatography performed utilizing an HPLC apparatus will generally result in a greater "- fold" purification than the same technique utilizing a low pressure chromatography system. Methods exhibiting a lower degree of relative purification may have advantages in total recovery of protein product, or in maintaining the activity of an expressed protein.
  • High Performance Liquid Chromatography is characterized by a very rapid separation with extraordinary resolution of peaks. This is achieved by the use of very fine particles and high pressure to maintain an adequate flow rate. Separation can be accomplished in a matter of minutes, or at most an hour. Moreover, only a very small volume of the sample is needed because the particles are so small and close-packed that the void volume is a very small fraction of the bed volume. Also, the concentration of the sample need not be very great because the bands are so narrow that there is very little dilution of the sample.
  • Gel chromatography is a special type of partition chromatography that is based on molecular size.
  • the theory behind gel chromatography is that the column, which is prepared with tiny particles of an inert substance that contain small pores, separates larger molecules from smaller molecules as they pass through or around the pores, depending on their size.
  • the sole factor determining rate of flow is the size.
  • molecules are eluted from the column in decreasing size, so long as the shape is relatively constant.
  • Gel chromatography is unsurpassed for separating molecules of different size because separation is independent of all other factors such as pH, ionic strength, temperature, etc. There also is virtually no adsorption, less zone spreading and the elution volume is related in a simple matter to molecular weight.
  • Affinity Chromatography is a chromatographic procedure that relies on the specific affinity between a substance to be isolated and a molecule that it can specifically bind to. This is a receptor-ligand type interaction.
  • the column material is synthesized by covalently coupling one of the binding partners to an insoluble matrix. The column material is then able to specifically adsorb the substance from the solution. Elution occurs by changing the conditions to those in which binding will not occur (alter pH, ionic strength, temperature, etc.).
  • Lectins are a class of substances that bind to a variety of polysaccharides and glycoproteins. Lectins are usually coupled to agarose by cyanogen bromide. Conconavalin A coupled to Sepharose was the first material of this sort to be used and has been widely used in the isolation of polysaccharides and glycoproteins other lectins that have been include lentil lectin, wheat germ agglutinin which has been useful in the purification of N-acetyl glucosaminyl residues and Helix pomatia lectin.
  • Lectins themselves are purified using affinity chromatography with carbohydrate ligands. Lactose has been used to purify lectins from castor bean and peanuts; maltose has been useful in extracting lectins from lentils and jack bean; N-acetyl-D galactosamine is used for purifying lectins from soybean; N-acetyl glucosaminyl binds to lectins from wheat germ; D-galactosamine has been used in obtaining lectins from clams and L-fucose will bind to lectins from lotus.
  • the matrix should be a substance that itself does not adsorb molecules to any significant extent and that has a broad range of chemical, physical and thermal stability.
  • the ligand should be coupled in such a way as to not affect its binding properties.
  • the ligand should also provide relatively tight binding. And it should be possible to elute the substance without destroying the sample or the ligand.
  • affinity chromatography One of the most common forms of affinity chromatography is immunoaffinity chromatography. The generation of antibodies that would be suitable for use in accord with the present invention is discussed below.
  • the present invention also encompasses DNA segments that are complementary, or essentially complementary, to the sequences set forth in SEQ ID NO:l, SEQ ID NO:6, and SEQ ID NO:7.
  • Nucleic acid sequences that are "complementary” are those that are capable of base-pairing according to the standard Watson-Crick complementary rules.
  • the term “complementary sequences” means nucleic acid sequences that are substantially complementary, as may be assessed by the same nucleotide comparison set forth above, or as defined as being capable of hybridizing to the nucleic acid segment of SEQ ID NO:l, SEQ ID NO:6, or SEQ ID NO:7 under relatively stringent conditions such as those described herein. Such sequences may encode the entire NOR protein or functional or non-functional fragments thereof.
  • the hybridizing segments may be shorter oligonucleotides. Sequences of 17 bases long should occur only once in the genome of most plant species and, therefore, suffice to specify a unique target sequence. Although shorter oligomers are easier to make, numerous other factors are involved in determining the specificity of hybridization. Both binding affinity and sequence specificity of an oligonucleotide to its complementary target increases with increasing length.
  • exemplary oligonucleotides of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more base pairs will be used, although others are contemplated. Longer polynucleotides encoding 250, 500, 1000, 1212, 1500, 2000, 2500, or 3000 bases and longer are contemplated as well. Such oligonucleotides will find use, for example, as probes in Southern and Northern blots and as primers in amplification reactions.
  • hybridization conditions will be well known to those of skill in the art. In certain applications, for example, substitution of amino acids by site-directed mutagenesis, it is appreciated that lower stringency conditions are required. Under these conditions, hybridization may occur even though the sequences of probe and target strand are not perfectly complementary, but are mismatched at one or more positions. Conditions may be rendered less stringent by increasing salt concentration and decreasing temperature. For example, a medium stringency condition could be provided by about 0.1 to 0.25 M NaCl at temperatures of about 37°C to about 55°C, while a low stringency condition could be provided by about 0.15 M to about 0.9 M salt, at temperatures ranging from about 20°C to about 55°C. Thus, hybridization conditions can be readily manipulated, and thus will generally be a method of choice depending on the desired results.
  • hybridization may be achieved under conditions of, for example, 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl 2 , 10 mM dithiothreitol, at temperatures between approximately 20°C to about 37°C.
  • Other hybridization conditions utilized could include approximately 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM MgCl 2 , at temperatures ranging from approximately 40°C to about 72°C.
  • Formamide and SDS also may be used to alter the hybridization conditions.
  • One method of using probes and primers of the present invention is in the search for genes related to NOR from other species.
  • the target DNA will be a genomic or cDNA library, although screening may involve analysis of RNA molecules.
  • screening may involve analysis of RNA molecules.
  • Site-specific mutagenesis is a technique useful in the preparation of individual peptides, or biologically functional equivalent proteins or peptides, through specific mutagenesis of the underlying DNA.
  • the technique further provides a ready ability to prepare and test sequence variants, incorporating one or more of the foregoing considerations, by introducing one or more nucleotide sequence changes into the DNA.
  • Site- specific mutagenesis allows the production of mutants through the use of specific oligonucleotide sequences which encode the DNA sequence of the desired mutation, as well as a sufficient number of adjacent nucleotides, to provide a primer sequence of sufficient size and sequence complexity to form a stable duplex on both sides of the deletion junction being traversed.
  • a primer of about 17 to 25 nucleotides in length is preferred, with about 5 to 10 residues on both sides of the junction of the sequence being altered.
  • the technique typically employs a bacteriophage vector that exists in both a single stranded and double stranded form.
  • Typical vectors useful in site-directed mutagenesis include vectors such as the Ml 3 phage. These phage vectors are commercially available and their use is generally well known to those skilled in the art.
  • Double stranded plasmids are also routinely employed in site directed mutagenesis, which eliminates the step of transferring the gene of interest from a phage to a plasmid.
  • site-directed mutagenesis is performed by first obtaining a single-stranded vector, or melting of two strands of a double stranded vector which includes within its sequence a DNA sequence encoding the desired protein.
  • An oligonucleotide primer bearing the desired mutated sequence is synthetically prepared.
  • This primer is then annealed with the single-stranded DNA preparation, taking into account the degree of mismatch when selecting hybridization conditions, and subjected to DNA polymerizing enzymes such as E. coli polymerase I Klenow fragment, in order to complete the synthesis of the mutation-bearing strand.
  • E. coli polymerase I Klenow fragment DNA polymerizing enzymes
  • a heteroduplex is formed wherein one strand encodes the original non-mutated sequence and the second strand bears the desired mutation.
  • This heteroduplex vector is then used to transform appropriate cells, such as E. coli cells, and clones are selected that include recombinant vectors bearing the mutated sequence arrangement.
  • sequence variants of the selected gene using site-directed mutagenesis is provided as a means of producing potentially useful species and is not meant to be limiting, as there are other ways in which sequence variants of genes may be obtained.
  • recombinant vectors encoding the desired gene may be treated with mutagenic agents, such as hydroxylamine, to obtain sequence variants.
  • mutagenic agents such as hydroxylamine
  • transgenic plants may be made by crossing a plant having a construct of the invention to a second plant lacking the construct.
  • a nucleic acid sequence encoding a NOR coding sequence can be introduced into a particular plant variety by crossing, without the need for ever directly transforming a plant of that given variety. Therefore, the current invention not only encompasses a plant directly created from cells which have been transformed in accordance with the current invention, but also the progeny of such plants.
  • progeny denotes the offspring of any generation of a parent plant prepared in accordance with the instant invention, wherein the progeny comprises a construct prepared in accordance with the invention.
  • Crossing a plant to provide a plant line having one or more added transgenes relative to a starting plant line, as disclosed herein, is defined as the techniques that result in a transgene of the invention being introduced into a plant line by crossing a starting line with a donor plant line that comprises a transgene of the invention. To achieve this one could, for example, perform the following steps:
  • backcrossing is herein defined as the process including the steps of: (a) crossing a plant of a first genotype containing a desired gene, DNA sequence or element to a plant of a second genotype lacking said desired gene, DNA sequence or element;
  • step (d) repeating steps (b) and (c) for the purpose of transferring said desired gene, DNA sequence or element from a plant of a first genotype to a plant of a second genotype.
  • Introgression of a DNA element into a plant genotype is defined as the result of the process of backcross conversion.
  • a plant genotype into which a DNA sequence has been introgressed may be referred to as a backcross converted genotype, line, inbred, or hybrid.
  • a plant genotype lacking said desired DNA sequence may be referred to as an unconverted genotype, line, inbred, or hybrid.
  • Exogenous gene A gene which is not normally present in a given host genome in the exogenous gene's present form In this respect, the gene itself may be native to the host genome, however, the exogenous gene will comprise the native gene altered by the addition or deletion of one or more different regulatory elements.
  • Expression The combination of intracellular processes, including transcription and translation undergone by a coding DNA molecule such as a structural gene to produce a polypeptide.
  • Expression vector A nucleic acid comprising one or more coding sequences which one desires to have expressed in a transgenic organism.
  • Progeny Any subsequent generation, including the seeds and plants therefrom, which is derived from a particular parental plant or set of parental plants.
  • Promoter A recognition site on a DNA sequence or group of DNA sequences that provide an expression control element for a structural gene and to which RNA polymerase specifically binds and initiates RNA synthesis (transcription) of that gene.
  • Ro Transgenic Plant A plant which has been directly transformed with a selected DNA or has been regenerated from a cell or cell cluster which has been transformed with a selected DNA.
  • Regeneration The process of growing a plant from a plant cell (e.g., plant protoplast, callus or explant).
  • a plant cell e.g., plant protoplast, callus or explant.
  • Selected DNA A DNA which one desires to have expressed in a transgenic plant, plant cell or plant part.
  • a selected DNA may be native or foreign to a host genome, but where the selected DNA is present in the host genome, may include one or more regulatory or functional elements which alter the expression profile of the selected gene relative to native copies of the gene.
  • Selected Gene A gene which one desires to have expressed in a transgenic plant, plant cell or plant part.
  • a selected gene may be native or foreign to a host genome, but where the selected gene is present in the host genome, will include one or more regulatory or functional elements which differ from native copies of the gene.
  • Transformation construct A chimeric DNA molecule which is designed for introduction into a host genome by genetic transformation.
  • Preferred transformation constructs will comprise all of the genetic elements necessary to direct the expression of one or more exogenous genes, for example, NOR genes. Included within in this term are, for example, expression cassettes isolated from a starting vector molecule.
  • Transformed cell A cell the DNA complement of which has been altered by the introduction of an exogenous DNA molecule into that cell.
  • Transgene A segment of DNA which has been incorporated into a host genome or is capable of autonomous replication in a host cell and is capable of causing the expression of one or more cellular products. Exemplary transgenes will provide the host cell, or plants regenerated therefrom, with a novel phenotype relative to the corresponding non-transformed cell or plant. Transgenes may be directly introduced into a plant by genetic transformation, or may be inherited from a plant of any previous generation which was transformed with the
  • Transgenic plant A plant or progeny plant of any subsequent generation derived therefrom, wherein the DNA of the plant or progeny thereof contains an introduced exogenous DNA segment not originally present in a non-transgenic plant of the same strain.
  • the transgenic plant may additionally contain sequences which are native to the plant being transformed, but wherein the "exogenous" gene has been altered in order to alter the level or pattern of expression of the gene.
  • Transit peptide A polypeptide sequence which is capable of directing a polypeptide to a particular organelle or other location within a cell.
  • rin locus was initially mapped to a 10 cM region of chromosome 5 flanked by RFLP markers CT93 and TG448.
  • Sample results from gel blot hybridization of pooled D ⁇ A samples with RFLP probes are shown for TG448 (tightly linked) and TGI 85 (unlinked - greater than 50 cM away).
  • C represents a D ⁇ A pool derived from 5 individuals with ripening fruit, "e” and "c” designate the L. esculentum (mutant) and L. cheesmannii (normal) alleles of the RFLP probes employed, respectively.
  • Hybridization to the "c" allele of TG448 in pools 1 , 3 and 6 represents individuals within these pools which have undergone recombination between the TG448 and rin loci.
  • the entire set of 45 pools was used to generate an RFLP map of the rin region of chromosome 5.
  • pairs of DNA pools nearly isogenic for all three ripening locus regions were generated and screened for polymorphic RAPD products.
  • Random primers will be purchased from Operon Technologies and the population used for the generation of isogenic DNA pools is the L. esculentum X L. pennellli F2 mapping population used to generate the tomato RFLP map. This population will be used rather than the actual ripening gene mapping populations because of the higher degree of polymorphism between the parents (Miller and Tanksley, 1990). The purpose of this effort will be to identify tightly linked molecular probes to be utilized in chromosome walks.
  • 500 primers should result in approximately 2,500 amplified loci of the tomato genome. Given the estimated map size of 1500 cM for the tomato genome, 500 primers should yield approximately 1-2 markers within 1 cM on either side of a target locus. In the event that sufficient polymorphic markers are not identified for one or more of the target loci, additional primers will be acquired through mutual primer exchanges. Also, the use of random primer pairs has recently been demonstrated to yield significant numbers of unique amplification products from tomato genomic DNA.
  • a total of 100 random 10 base primers were utilized for amplification of nearly isogenic DNA pools resulting in one polymorphic PCR product, P76.
  • the 0.5 kb P76 amplification product was gel-purified, labeled and mapped via an EcoRI RFLP to the target region.
  • CT93 which are 1.24 cM and 2.9 cM from rin, respectively.
  • CT63 although only 0.24 cM from RIN on the TG503 side, was not employed as a probe because it is a member of a small gene family and unlinked YAC clones would likely be recovered.
  • Yrin2 demonstrated hybridization to both TG503 and CT63 suggesting that 1) it contained sequences closer to the target locus than any of the other clones, and 2) the estimated 191 kb/cM ratio in the region of RIN was within two fold of accurate (i.e. TG503 and CT63 are separated by 1 cM and reside on a 360 kb YAC).
  • a single copy end of Yr «2 (Yr/ " «2R) was isolated by inverse PCR and mapped, in a population of 670 F2 progeny, on the RIN side of CT63 0.2 cM from rin. This end was subsequently utilized to take a "step" toward RIN in the tomato YAC library resulting in the isolation of 4 additional YAC clones, YrinS, Yrin9, Yrinl l, and Yrml2. 7 of the 8 possible YAC ends were isolated through inverse PCR and/or plasmid rescue for generation of a YAC contig via cross-hybridization of ends with RIN region YACs, and RFLP mapping.
  • Two YAC clones were determined to be chimeric based on RFLP mapping (Y ⁇ ' «9R) and sequencing of YAC ends (Yr «8R - greater than 95% homology with tobacco chloroplast DNA).
  • Yr «8R One YAC end, Yr «8L, cosegregated with RIN and hybridized to none of the other YAC clones, suggesting that it extended the furthest toward RIN and may harbor the target gene.
  • cDNA libraries in the vector lambda gtlO and made from Mature Green, Breaker, and Red Ripe stage fruit are all available in the laboratory (lambda gtlO does not cross hybridize with the YAC vector pYAC4). All 3 libraries will be screened because it is not known which stage will express the highest levels of target gene product. Construction of a fourth cDNA library may also be used in lambda gtlO made from mRNA derived from several stages of immature fruit development. Specifically, mRNA will be combined from ovaries prior to pollination, 2 days post pollination, and every 10 days post-pollination up to the Mature Green stage (approximately 30 days in cultivar Ailsa Craig). This library will help to minimize the problem of not knowing when during fruit development the RIN or NOR gene is expressed. Tissue for all but the unpollinated ovaries are stored in a -80°C freezer.
  • High molecular weight D ⁇ A gel-blot analysis was also utilized to estimate the kb/cM ratio in the region of the NOR locus.
  • a 1000 kb Cspl fragment hybridized to both CT16 and TG313 which flank the NOR locus and are separated by approximately 5 cM. Based on this observation, it was estimated that 1 cM in the region of the NOR locus corresponds to approximately 200 kb.
  • CT16 Prior to initiation of the chromosome walk to nor, the closest known flanking markers were CT16 (0.9 cM) and CT41 (2.3 cM). Based on the published tomato RFLP map (Tanksley et al, 1992), it was known that TG395 resided in the interval between CT41 and CT16 and thus represented a closer marker to NOR than at least one of the two. TG395 was mapped as a sequence tagged site (due to lack of RFLPs between the two parents of the mapping population) to 1.4 cM from NOR on the CT41 side. PCR screening of the tomato YAC library with TG395 specific primers resulted in the identification of 7 YAC clones ranging in size from 50 kb - 490 kb. CT16 was not used for library screening because of difficulty in generating reliable PCR primers.
  • YAC end and RFLP marker cross hybridizations yielded a YAC contig.
  • TG395 which was used to retrieve this clone from the library
  • CT16 CT16
  • a high titer cosmid library (>500,000 clones) was then prepared of the yeast containing Ynor3 to use in fine mapping and walking to NOR within the Ynor3 clone.
  • The, cosmid vector employed, 04541 contains T-D ⁇ A borders to permit direct Agrobacterium transfer into plants. Random Ynor3 Pstl and Haelll subclones were also isolated to use as fine mapping probes.
  • a "breaker" stage tomato fruit cD ⁇ A library was also screened with Ynor3 as probe, yielding numerous clones for characterization for linkage to nor. EXAMPLE 4 Characterization of YAC clones harboring the rin and nor loci.
  • Yrinl 1 a YAC termed Yrinl 1 was identified which harbored the rin locus as determined by random subcloning of Yrinl 1 restriction fragments and RFLP mapping to determine that sequences flanking the target locus were contained on this YAC.
  • This YAC also contained sequences that were absent from the YAC descried above with an internal deletion (thus confirming the integrity of Yrinl 1), and said fragments were tightly linked to the rin locus.
  • EXAMPLE 5 cDNA library screening
  • cDNAs hybridizing to the two candidate gene YACs, and thus potentially representing target gene transcripts, were verified for homology via hybridization as probes back to the respective Yrinl 1 and Ynor3 YACs. Positives were mapped as RFLPs and sequenced.
  • CDl 1 Ynor3 hybridizing cDNA, CDl 1, was one of two clones found to cosegregate with the nor locus and to hybridize to the BAC clone most likely (via hybridization to wor-linked markers) to harbor the target locus. Both CD11 and the other co-segregating cDNA (CD5) were hybridized to RNA gel-blots of normal and mutant fruit RNAs. CD5 was constitutively expressed throughout fruit development while CD11 was induced during ripening and by ethylene. CDl 1 was also greatly reduced in expression in fruit of the nor mutant. CDl 1 was sequenced and found to have homology to the CUC (cup-shaped-cotyledon) gene of Arabidopsis.
  • CUC cup-shaped-cotyledon
  • This gene also has homology to two functionally defined Arabidopsis transcription factors of otherwise unknown function.
  • primers were generated for RT-PCR of CD 11 mRNA.
  • CD11 alleles from normal (Nor/Nor) and mutant (nor/nor) tomato lines were generated by RT-PCR and sequenced.
  • the mutant allele harbors a 2 bp deletion relative to the normal CD11 allele resulting in a stop codon approximately mid- way through the CDl 1 open reading frame.
  • the CDl 1 sequence represents the tomato NOR gene.
  • An original sequence obtained of the clone is indicated in SEQ ID ⁇ :l and a corrected version of the sequence in SEQ ID N ⁇ :6.
  • the cDNA identified as representing NOR was be tested for function in ripening through the use of antisense and sense expression constructs in normal and mutant tomatoes, respectively. Antisense gene suppression has proven an effective tool for determining gene function during tomato fruit ripening (reviewed in Gray et al, 1994).
  • D ⁇ A constructs were prepared for delivery of sense or antisense NOR gene cD ⁇ A (CD-I 1) sequences into plant genomes (FIG. 1).
  • ⁇ R-pBI121 sense and antisense constructs were made by replacing the GUS gene of T-DNA binary vector pBI121 with the full-length
  • NOR cD ⁇ A referred to as CD-11 (1180 bp) in sense and antisense orientations, respectively, relative to the CaMV35S promoter (35S-P) of pBI121 (FIG. 1).
  • the NOR cD ⁇ A (CD-11 insert) was subcloned between Smal and Sacl restriction sites resulting from removal of the GUS gene from pBI121.
  • EcoRV and Sacl sites of the pBluescript vector containing the NOR cD ⁇ A were employed due to the fact that Smal and
  • EcoRV (blunt) ends are compatible for ligation.
  • the resulting ligated sequence no longer can be digested with Smal or EcoRV.
  • Completed sense and antisense constructs were initially transformed into E. coli DH 10B cells and then resulting plasmid D ⁇ A was isolated and transformed into Agrobacterium tumefaciens strain LBA 4404 for use in transfer into the tomato gene as described herein.
  • the sense and antisense orientations of the NOR cD ⁇ A sequence relative to the EcoRV and Sacl restriction sites were obtained by subcloning the original NOR cD ⁇ A bound by EcoRI sites from the original cD ⁇ A library vector (lambda gtlO) into the EcoRI site of plasmid vector pBluescript. Due to the fact that the cD ⁇ A sequence was flanked by identical restriction sites (EcoRI), the insert could insert in either direction essentially at random.
  • NOR cD ⁇ A 3 bp of pBluescript polyhnker was included on the Smal side of the cD ⁇ A and 51 bp of pBluescript polyhnker was included on the Sacl side of the insert (including the following restriction sites: SacII, ⁇ otI, Xbal, Spel, BamHI, Smal, Pstl, EcoRI).
  • Transgenic tomato plant were prepared as follows. First, the explant was prepared by sterilizing seeds with soaking in 20% bleach + 0.1% Tween-20 for 15 minutes. The seeds were rinses 4 times in sterile distilled H20 and the seeds sown on MSO medium ( (1 Liter): 4.0 g MS Salts (Gibco), 5.0 ml B5 Vitamins, 5.0 ml MS Iron/EDTA, 20.0 g sucrose, 7.0 g agar (phytagar), pH medium to 6.0 with KOH, autoclave) in sterile glass jars, grow in growth chamber. Agrobacterium was then prepared by streaking selective fresh plates with Agrobacterium containing the desired construct for 2-3 days before it was needed.
  • MSO medium (1 Liter): 4.0 g MS Salts (Gibco), 5.0 ml B5 Vitamins, 5.0 ml MS Iron/EDTA, 20.0 g sucrose, 7.0 g agar (phytagar), pH medium to 6.0 with KOH, autoclave) in
  • a single colony was picked from the plate and grown in tubes containing 2 ml YEP medium (YEP Rich Medium (500 ml): 5.0 g Bacto-peptone, 2.5 g ⁇ aCl, 5.0 g Bacto Yeast Extract, 7.5 g Bacto agar, autoclave) with appropriate antibiotics, followed by incubation on a shaker at 28°C overnight. Explants were precultured two days before infection takes place, and 8-10 day old cotyledons were excised. With sterile forceps, cotyledons were removed and placed onto an MSO plate. Using forceps and a blade, the cotyledons were cut in 1-2 pieces.
  • YEP medium YEP Rich Medium (500 ml): 5.0 g Bacto-peptone, 2.5 g ⁇ aCl, 5.0 g Bacto Yeast Extract, 7.5 g Bacto agar, autoclave
  • Explants were precultured two days before infection takes
  • cotyledon pieces were placed on co-cultivation media ((500 ml): 500 ml MSO Medium, 1 ml KH2PO4 (100 mg/ml), 250 (1 Kinetin (0.2 mg/ml), 100 (1 2,4 D (1 mg/ml), 735 (1 acetosyringone)), wrapped in parafilm and placed in growth chamber for 2-3 days.
  • co-cultivation media ((500 ml): 500 ml MSO Medium, 1 ml KH2PO4 (100 mg/ml), 250 (1 Kinetin (0.2 mg/ml), 100 (1 2,4 D (1 mg/ml), 735 (1 acetosyringone)
  • Regeneration Medium (1Z) 500 ml MSO Medium, 5.0 ml Carbenicillin stock, 1.0 ml Kanamycin stock, 0.5 ml Zeatin (1 mg/ml), 0.1 ml IAA
  • Regeneration Medium (1Z) 500 ml MSO Medium, 5.0 ml Carbenicillin stock, 1.0 ml Kanamycin stock, 0.5 ml Zeatin (1 mg/ml), 0.1 ml IAA
  • YEB Rich Medium 500 ml: 2.75g Beef Extract, 0.55g Yeast Extract, 2.75g peptone, 2.75g sucrose, 1 ml MgSO4 (1M) pH 7.2, 7.5 g Bactoagar, autoclave.
  • B5 vitamins 100 ml: 2.0 g myo-inositol, 0.2 g thiamine-HCl, 20.0 mg nicotinic acid, 20.0 mg pyridoxine-HCl, mix, then put in autoclaved bottle.
  • MS Iron/EDTA 100 ml: 556.0 mg FeSO4-7H2O, 746.0 mg Na2EDTA-2H2O, mix, then put in autoclaved bottle.
  • Benzylamino-purine (BAP): 1 mg BAP/ 1 ml H2O, dissolve BAP with 5N KOH dropwise, bring up to volume with ddH2O, filter sterilize in TC Hood, refrigerate.
  • Zeatin 1 mg Zeatin/1 ml H20, dissolve with 4N NaOH dropwise, bring up to volume with ddH2O, filter sterilize in TC Hood, refrigerate.
  • Indoleacetic acid (IAA) 1 mg IAA / 1 ml ethanol, dissolve with 100% ethanol, filter sterilize in TC Hood, refrigerate in foil (light sensitive, Good 1 week).
  • Acetosyringone stock (ACE) (lOmg/ml): weigh out 100 mg of acetosyringone, add 10 ml 70% ethanol, filter sterilize, put in 1.5 ml tubes, place in -20C freezer.
  • Carbenicillin Stock (50mg/ml): weigh out 5 grams Carbenicillin, add 100 ml ddH20, filter sterilize, put in 12 ml tubes, place in -20°C freezer.
  • Kanamycin Stock (50mg/ml): weigh out 5 grams Kanamycin, add 100 ml ddH20, filter sterilize, put in 12 ml tubes, place in -20C freezer.
  • Tetracycline Stock (3mg/ml): dissolve 3 mg tetracycline in 1 ml ddH20, filter sterlize, refrigerate in foil (light sensitive), good 1 day.
  • FIG. 2 Shown in FIG. 2 are representative control and transformed fruit from tomato a line of the genotype nor/nor in the cultivar MHl and transformed with ⁇ R-pBI121 Sense (FIG. 1). Primary transformants (T0) were confirmed for transgene integration via DNA gel-blot analysis and subsequently self-pollinated. Resulting seed were harvested and grown (TI generation) and analyzed for transgene segregation. Representative fully mature fruit from TI nor/nor individuals that either harbor the sense NOR transgene (+) or have segregated it out (-) are shown.
  • transgene expression in the mutant background was shown to partially recover the non-ripening phenotype and confer ripening.
  • relatively low expression of the transgene was observed as compared to expression of NOR in normally ripening (Nor/Nor) fruit.
  • Representative normal ( ⁇ or/ ⁇ or) and nearly isogenic mutant (nor/nor) cultivar MHl tomato fruit are shown as controls.
  • the partial recovery of ripening in the nor/nor fruit harboring the ⁇ OR-pBI121 (+) transgene verified the isolation of the NOR gene.
  • partial ripening phenotype observed in this line demonstrated that regulated expression of the NOR gene can be used to create a range of degrees of ripening and ripening-associated characteristics (e.g., carotenoid accumulation, ripe flavor, nutrient composition, softness, pathogen susceptibility).
  • degrees of ripening and ripening-associated characteristics e.g., carotenoid accumulation, ripe flavor, nutrient composition, softness, pathogen susceptibility
  • Genomic DNA sequences corresponding to the NOR cD ⁇ A were isolated from the tomato genomic library whose construction is described below (FIG. 5). Full length cD ⁇ As were sequenced at their termini, and oligonucleotide primers were be synthesized corresponding to the 5' and 3' ends. Candidate genomic clones were then utilized as a template in sequencing reactions with these end primers. Those genomic clones harboring DNA sequences from both ends of the corresponding full length cDNA, as determined by sequencing, were restriction mapped to identify location of the transcribed region within the genomic clone insert.
  • D) Construction of target gene containing libraries in the cosmid/plant transformation vector In order to facilitate generation of a contig spanning a target locus, libraries of genomic D ⁇ A from yeast containing YAC clones harboring the desired sequence were constructed using the cosmid/plant transformation vector 04541. The much smaller size of the yeast genome relative to tomato simplified the screening and contig construction. Libraries in 04541 were generated from yeast harboring Yrin8 and Ynor3. Test screening of the Yrin8 library with CT63, Yrin2R, and Yrin8L demonstrated the presence of clones containing all three probed sequences. In addition, clones hybridizing to TG395, CT16, CDnorl and CDnor2 (the only 4 probes tested) were retrieved from the Ynor3 library as well.
  • the walk from CDnor2 was initiated in the Ynor3 yeast cosmid library, while that from Yrin8L was performed in the tomato genomic cosmid library described above because RIN may have been off the end of Yr «8.
  • a DNA sequence surrounding the 04541 cloning site was generated as were nested primers for IPCR of insert ends.
  • Backcrossing can be used to improve a starting plant.
  • Backcrossing transfers a specific desirable trait from one source to an inbred or other plant that lacks that trait. This can be accomplished, for example, by first crossing a superior inbred (A) (recurrent parent) to a donor inbred (non-recurrent parent), which carries the appropriate gene(s) for the trait in question, for example, a construct prepared in accordance with the current invention.
  • the progeny of this cross first are selected in the resultant progeny for the desired trait to be transferred from the non-recurrent parent, then the selected progeny are mated back to the superior recurrent parent (A).
  • the progeny are hemizygous for loci controlling the characteristic being transferred, but are like the superior parent for most or almost all other genes.
  • the last backcross generation would be selfed to give progeny which are pure breeding for the gene(s) being transferred, i.e. one or more transformation events.
  • transgenes are valuable in that they typically behave genetically as any other gene and can be manipulated by breeding techniques in a manner identical to any other gene. Therefore, one may produce inbred plants which are true breeding for one or more transgenes. By crossing different inbred plants, one may produce a large number of different hybrids with different combinations of transgenes. In this way, plants may be produced which have the desirable agronomic properties frequently associated with hybrids ("hybrid vigor"), as well as the desirable characteristics imparted by one or more transgene(s).
  • Genetic markers may be used to assist in the introgression of one or more transgenes of the invention from one genetic background into another. Marker assisted selection offers advantages relative to conventional breeding in that it can be used to avoid errors caused by phenotypic variations. Further, genetic markers may provide data regarding the relative degree of elite germplasm in the individual progeny of a particular cross. For example, when a plant with a desired trait which otherwise has a non-agronomically desirable genetic background is crossed to an elite parent, genetic markers may be used to select progeny which not only possess the trait of interest, but also have a relatively large proportion of the desired germplasm. In this way, the number of generations required to introgress one or more traits into a particular genetic background is minimized.
  • Marker assisted breeding may be undertaken as follows. Seed of plants with the desired trait are planted in soil in the greenhouse or in the field. Leaf tissue is harvested from the plant for preparation of DNA at any point in growth at which approximately one gram of leaf tissue can be removed from the plant without compromising the viability of the plant. Genomic DNA is isolated using a procedure modified from Shure et al. (1983). Approximately one gram of leaf tissue from a seedling is lypholyzed overnight in 15 ml polypropylene tubes. Freeze-dried tissue is ground to a powder in the tube using a glass rod.
  • Powdered tissue is mixed thoroughly with 3 ml extraction buffer (7.0 urea, 0.35 M NaCl, 0.05 M Tris-HCl pH 8.0, 0.01 M EDTA, 1% sarcosine).
  • Tissue/buffer homogenate is extracted with 3 ml phenol/chloroform.
  • the aqueous phase is separated by centrifugation, and precipitated twice using 1/10 volume of 4.4 M ammonium acetate pH 5.2, and an equal volume of isopropanol.
  • the precipitate is washed with 75%) ethanol and resuspended in 100-500 ⁇ l TE (0.01 M Tris- HCl, 0.001 M EDTA, pH 8.0).
  • Genomic DNA is then digested with a 3 -fold excess of restriction enzymes, electrophoresed through 0.8% agarose (FMC), and transferred (Southern, 1975) to Nytran (Schleicher and Schuell) using 10X SCP (20 SCP: 2M NaCl, 0.6 M disodium phosphate, 0.02 M disodium EDTA).
  • 10X SCP 20 SCP: 2M NaCl, 0.6 M disodium phosphate, 0.02 M disodium EDTA.
  • the filters are prehybridized in 6X SCP, 10% dextran sulfate, 2% sarcosine, and 500 ⁇ g/ml denatured salmon sperm DNA and 32 P-labeled probe generated by random priming (Feinberg & Vogelstein, 1983).
  • Hybridized filters are washed in 2X SCP, 1% SDS at 65° for 30 minutes and visualized by autoradiography using Kodak XAR5 film. Genetic polymorphisms which are genetically linked to traits of interest are thereby used to predict the presence or absence of the traits of interest.
  • Each lane of a Southern blot represents DNA isolated from one plant.
  • the integration event composition of each plant may be determined. Correlations may be established between the contributions of particular integration events to the phenotype of the plant. Only those plants that contain a desired combination of integration events may be advanced to maturity and used for pollination. DNA probes corresponding to particular transgene integration events are useful markers during the course of plant breeding to identify and combine particular integration events without having to grow the plants and assay the plants for agronomic performance.
  • restriction enzymes will be used to digest genomic DNA, either singly or in combinations.
  • One of skill in the art will recognize that many different restriction enzymes will be useful and the choice of restriction enzyme will depend on the DNA sequence of the transgene integration event that is used as a probe and the DNA sequences in the genome surrounding the transgene. For a probe, one will want to use DNA or RNA sequences which will hybridize to the DNA used for transformation. One will select a restriction enzyme that produces a DNA fragment following hybridization that is identifiable as the transgene integration event. Thus, particularly useful restriction enzymes will be those which reveal polymorphisms that are genetically linked to specific transgenes or traits of interest.
  • Genomic DNA is isolated using a procedure modified from Shure, et al, 1983. Approximately 1 gm callus or leaf tissue is ground to a fine powder in liquid nitrogen using a mortar and pestle. Powdered tissue is mixed thoroughly with 4 ml extraction buffer (7.0 M urea, 0.35 M NaCl, 0.05 M Tris-HCl pH 8.0, 0.01 M EDTA, 1% sarcosine). Tissue/buffer homogenate is extracted with 4 ml phenol/ chloroform. The aqueous phase is separated by centrifugation, passed through Miracloth, and precipitated twice using 1/10 volume of 4.4 M ammonium acetate, pH 5.2 and an equal volume of isopropanol. The precipitate is washed with 70% ethanol and resuspended in 200-500 ⁇ l TE (0.01 M Tris-HCl, 0.001 M EDTA, pH 8.0).
  • PCR polymerase chain reaction
  • the reaction is run in a thermal cycling machine as follows: 3 minutes at 94°C, 39 repeats of the cycle 1 minute at 94°C, 1 minute at 50°C, 30 seconds at 72°C, followed by 5 minutes at 72°C. Twenty ⁇ l of each reaction mix is run on a 3.5% NuSieve gel in TBE buffer (90 mM Tris-borate, 2 mM EDTA) at 50V for two to four hours.
  • genomic DNA is digested with a 3-fold excess of restriction enzymes, electrophoresed through 0.8% agarose (FMC), and transferred (Southern, 1975) to Nytran (Schleicher and Schuell) using 10X SCP (20X SCP: 2 M NaCl, 0.6 M disodium phosphate, 0.02 M disodium EDTA).
  • 10X SCP 20X SCP: 2 M NaCl, 0.6 M disodium phosphate, 0.02 M disodium EDTA.
  • Probes are labeled with 32 P using the random priming method (Boehringer Mannheim) and purified using Quik-Sep® spin columns (Isolab Inc., Akron, OH).
  • compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods and in the steps or in the sequence of steps of the methods described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.
  • Knittel Gruber; Hahne; Lenee, Plant Cell Reports, 14(2-3):81-86, 1994.
  • Van der Krol Mur, Beld, Mol, Stuitje, Plant Cell, 2:291-99, 1990. Van Eck; Blowers; Earle, Plant Cell Reports, 14(5):299-304, 1995.

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Abstract

L'invention porte sur des séquences d'acides nucléiques codant pour le gène NOR, sur des compositions comportant ces séquences, sur des plantes transformées à l'aide de ces compositions, et sur des procédés d'expression du gène NOR. Ces procédés incluent la création de plantes transgéniques à l'aide du gène NOR par transformation génétique ainsi que des procédés de sélection. Les séquences de cette invention constituent un nouvel outil important de création de plantes transgéniques, présentant de préférence une ou plusieurs caractéristiques bénéfiques additionnelles.
PCT/US2000/019071 1999-07-12 2000-07-12 Compositions de gene nor et leurs procedes d'utilisation WO2001014561A1 (fr)

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WO2009112546A1 (fr) 2008-03-13 2009-09-17 Semillas Fitó, S.A. Procédé pour produire des plantes de tomate ayant des caractéristiques de longue durée de vie
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US9217164B2 (en) 2007-03-01 2015-12-22 Basf Enzymes Llc Nitrilases, nucleic acids encoding them and methods for making and using them
CN108580300A (zh) * 2018-05-31 2018-09-28 贵州楷丰农业科技有限公司 一种水稻种子筛选设备

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US7993901B2 (en) 1999-12-29 2011-08-09 Verenium Corporation Nitrilases and methods for making and using them
US7521216B2 (en) 1999-12-29 2009-04-21 Verenium Corporation Nitrilases and methods for making and using them
US7608445B1 (en) 1999-12-29 2009-10-27 Verenium Corporation Nitrilases, nucleic acids encoding them and methods for making and using them
US7651849B2 (en) 1999-12-29 2010-01-26 Darcy Madden, legal representative Nitrilases
US9315792B2 (en) 1999-12-29 2016-04-19 Basf Enzymes Llc Nitrilases, nucleic acids encoding them and methods for making and using them
US7811804B2 (en) 1999-12-29 2010-10-12 Verenium Corporation Nitrilases, nucleic acids encoding them and methods for making and using them
US9828594B2 (en) 1999-12-29 2017-11-28 Basf Enzymes Llc Nitrilases, nucleic acids encoding them and methods for making and using them
US8501451B2 (en) 1999-12-29 2013-08-06 Verenium Corporation Nitrilases and methods for making and using them
US8906663B2 (en) 1999-12-29 2014-12-09 Verenium Corporation Nitrilases
US8034595B2 (en) 1999-12-29 2011-10-11 Verenium Corporation Nitrilases and methods for making and using them
US8088613B2 (en) 1999-12-29 2012-01-03 Verenium Corporation Nitrilases, nucleic acids encoding them and methods for making and using them
US8778651B2 (en) 1999-12-29 2014-07-15 Verenium Corporation Nitrilases, nucleic acids encoding them and methods for making and using them
US8318471B2 (en) 1999-12-29 2012-11-27 Verenium Corporation Nitrilases, nucleic acids encoding them and methods for making and using them
US8334125B2 (en) 1999-12-29 2012-12-18 Verenium Corporation Nucleic acids encoding nitrilases
US7300775B2 (en) 1999-12-29 2007-11-27 Verenium Corporation Methods for producing α-substituted carboxylic acids using nitrilases and strecker reagents
US8372608B2 (en) 2002-06-13 2013-02-12 Verenium Corporation Processes for making [R]-ethyl 4-cyano-3 hydroxybutyric acid
US9217164B2 (en) 2007-03-01 2015-12-22 Basf Enzymes Llc Nitrilases, nucleic acids encoding them and methods for making and using them
ES2336180A1 (es) * 2008-03-13 2010-04-08 Semillas Fito, S.A. Procedimiento para producir plantas de tomate con caracteristicas de larga vida.
WO2009112546A1 (fr) 2008-03-13 2009-09-17 Semillas Fitó, S.A. Procédé pour produire des plantes de tomate ayant des caractéristiques de longue durée de vie
CN101935701B (zh) * 2010-08-10 2012-07-04 南京农业大学 检测转cp4-epsps基因大豆及其深加工产品中转基因成份的方法及试剂盒
CN101935701A (zh) * 2010-08-10 2011-01-05 南京农业大学 检测转cp4-epsps基因大豆及其深加工产品中转基因成份的方法及试剂盒
CN108580300A (zh) * 2018-05-31 2018-09-28 贵州楷丰农业科技有限公司 一种水稻种子筛选设备

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