Classifications

• • 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)
  • C12N15/8216—Methods for controlling, regulating or enhancing expression of transgenes in plant cells
• • 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

Definitions

• the invention relates to nucleic acid sequences isolated from sugarcane and to methods of using them.
• the inventions relates to nucleotide sequences which are derived from sugarcane polyubiquitin genes and which are capable of directing constitutive expression of a nucleic acid sequence of interest that is operably linked to the sugarcane polyubiquitin nucleotide sequences.
• the sugarcane polyubiquitin nucleotide sequences are useful in regulating expression of a nucleic acid sequence of interest in monocotyledonous and dicotyledonous plants.
• high levels of protein expression aid the generation of plants which exhibit commercially important phenotypic properties, such as pest and disease resistance, resistance to environmental stress ⁇ e.g., water- logging, drought, heat, cold, light- intensity, day-length, chemicals, etc.), improved qualities (e.g., high yield of fruit, extended shelf- life, uniform fruit shape and color, higher sugar content, higher vitamins C and A content, lower acidity, etc.).
• promoter sequences which are capable of driving expression of transgenes ⁇ e.g.. selectable marker genes) in plants are known in the art and are derived from a variety of sources such as bacteria, plant DNA viruses, and plants. Promoters of bacterial origin include the octopine synthase promoter, the nopaline synthase promoter and other promoters derived from native Ti plasmids. Promoters of viral origin include the 35S and 19S RNA promoters
• Plant promoters include the ribulose-1.3-diphosphate carboxvlase small subunit promoter, the phaseolin promoter, and the maize polyubiquitin promoter.
• promoter sequences which function in plant cells are available, expression of more than one gene (e.g., a selectable marker gene and an agronomically relevant gene) which is operably linked to the same promoter sequence is likely to be hampered by homology dependent silencing of transgenes in plants.
• additional promoter sequences which are capable of driving transgene expression.
• promoter sequences which drive transgene expression in both monocotyledonous and dicotyledonous plant cells are examples of driving transgene expression in both monocotyledonous and dicotyledonous plant cells.
• the present invention provides nucleic acid sequences having promoter activity.
• the nucleic acid sequences provided herein direct expression of operably linked nucleotide sequences in cells, tissues and organs of monocotyledonous and dicotyledonous plants.
• the invention provides a substantially purified nucleic acid sequence comprising a nucleotide sequence selected from the group consisting of SEQ ID NO:l, the complement of SEQ ID NO:l, homologs of SEQ ID NO:l, homologs of the complement of SEQ ID NO:l ; SEQ ID NO:3, the complement of SEQ ID NO:3, homologs of SEQ ID NO:3, and homologs of the complement of SEQ ID NO:3.
• the nucleotide sequence is characterized by having promoter activity. In a more preferred embodiment, the promoter activity is constitutive. In another embodiment, nucleotide sequence is double- stranded. In yet another embodiment, the nucleotide sequence is single-stranded. In yet another alternative embodiment, the nucleic acid sequence is contained in a plant cell. In a preferred embodiment, the plant cell is derived from a monocotyledonous plant. In a more preferred embodiment, the monocotyledonous plant is selected from the group consisting of sugarcane, maize, sorghum, pineapple, rice, barley, oat, wheat, rye, yam, onion, banana, coconut, date, and hop.
• the plant cell is derived from a dicotyledonous plant.
• the dicotyledonous plant is selected from the group consisting of tobacco, tomato, soybean, and papaya.
• the invention also provides a substantially purified nucleic acid sequence comprising a portion of a nucleotide sequence selected from the group consisting of SEQ ID NO:l and the complement thereof.
• the portion is characterized by having promoter activity.
• the promoter activity is constitutive.
• the portion is double-stranded.
• the portion is single-stranded.
• the portion comprises the nucleotide sequence selected from the group consisting of the nucleotides from 1 to 242 of SEQ ID NO:7, from 245 to 787 of SEQ ID NO:7, from 788 to 1020 of SEQ ID NO:7, from 1021 to 1084 of SEQ ID NO:7, from 1085 to 1 168 of
• nucleic acid sequence is contained in a plant cell.
• the plant cell is derived from a monocotyledonous plant.
• the monocotyledonous plant is selected from the group consisting of sugarcane, maize, sorghum, pineapple, rice, barley, oat, wheat, rye, yam, onion, banana, coconut, date, and hop.
• the plant cell is derived from a dicotyledonous plant.
• the dicotyledonous plant is selected from the group consisting of tobacco, tomato, soybean, and papaya.
• a substantially purified nucleic acid sequence comprising a portion of a nucleotide sequence selected from the group consisting of SEQ ID NO: 3 and the complement thereof.
• the portion is characterized by having promoter activity.
• the promoter activity is constitutive.
• the portion is double-stranded.
• the portion is single-stranded.
• the portion comprises the nucleotide sequence selected from the group consisting of the nucleotides 1 to 3600 of SEQ ID NO: 10, from 3602 to 3612 of SEQ ID NO:10, from 3614 to 3691 of SEQ ID NO:3, from 1 to 2248 of SEQ ID NO:3, from 2249 to 2313 of SEQ ID NO:3, from 2314 to 3688 of SEQ ID NO:3, and from 1671 to 2248 of SEQ ID NO:3.
• the nucleic acid sequence is contained in a plant cell.
• the plant cell is derived from a monocotyledonous plant.
• the monocotyledonous plant is selected from the group consisting of sugarcane, maize, sorghum, pineapple, rice, barley, oat, wheat, rye, yam, onion, banana, coconut, date, and hop.
• the plant cell is derived from a dicotyledonous plant.
• the dicotyledonous plant is selected from the group consisting of tobacco, tomato, soybean, and papaya.
• the invention additionally provides a substantially purified nucleic acid sequence comprising the EcoRI/Xbal fragment isolated from plasmid pubi4-GUS contained in Escherichia coli cells deposited as NRRLB-301 15, the complement of the fragment, homologs of the fragment, and homologs of the complement of the fragment.
• the nucleotide sequence is SEQ ID NO:7.
• the nucleotide sequence is characterized by having promoter activity.
• the promoter activity is constitutive.
• the nucleotide sequence is double-stranded.
• the nucleotide sequence is single-stranded.
• the nucleic acid sequence is contained in a plant cell.
• the plant cell is derived from a monocotyledonous plant.
• the monocotyledonous plant is selected from the group consisting of sugarcane, maize, sorghum, pineapple, rice, barley, oat, wheat, rye, yam, onion, banana, coconut, date, and hop.
• the plant cell is derived from a dicotyledonous plant.
• the dicotyledonous plant is selected from the group consisting of tobacco, tomato, soybean, and papaya.
• nucleotide sequence is SEQ ID NO: 10.
• nucleotide sequence is characterized by having promoter activity. In a more preferred embodiment, the promoter activity is constitutive. In another alternative preferred embodiment, the nucleotide sequence is double-stranded. In yet another alternative preferred embodiment, the nucleotide sequence is single-stranded.
• the nucleic acid sequence is contained in a plant cell.
• the plant cell is derived from a monocotyledonous plant.
• the monocotyledonous plant is selected from the group consisting of sugarcane, maize, sorghum, pineapple, rice, barley, oat, wheat, rye, yam, onion, banana, coconut, date, and hop.
• the plant cell is derived from a dicotyledonous plant.
• the dicotyledonous plant is selected from the group consisting of tobacco, tomato, soybean, and papaya.
• the invention further provides a substantially purified nucleic acid sequence comprising a portion of the EcoRI/_Yb ⁇ I fragment isolated from plasmid pubi4-GUS contained in Escherichia coli cells deposited as NRRLB-30115, and the complement of the fragment.
• the portion is characterized by having promoter activity.
• the promoter activity is constitutive.
• the portion is double-stranded.
• the portion is single-stranded.
• the nucleic acid sequence is contained in a plant cell.
• the plant cell is derived from a monocotyledonous plant.
• the monocotyledonous plant is selected from the group consisting of sugarcane, maize, sorghum, pineapple, rice, barley, oat, wheat, rye, yam, onion, banana, coconut, date, and hop.
• the plant cell is derived from a dicotyledonous plant.
• the dicotyledonous plant is selected from the group consisting of tobacco, tomato, soybean, and papaya.
• a substantially purified nucleic acid sequence comprising a portion of the Hindlll/Xbal fragment isolated from plasmid pubi9-GUS contained in Escherichia coli cells deposited as NRRLB-301 16, and the complement of the fragment.
• the portion is characterized by having promoter activity.
• the promoter activity is constitutive.
• the portion is double-stranded.
• the portion is single-stranded.
• the nucleic acid sequence is contained in a plant cell.
• the plant cell is derived from a monocotyledonous plant.
• the monocotyledonous plant is selected from the group consisting of sugarcane, maize, sorghum, pineapple, rice, barley, oat, wheat, rye, yam, onion, banana, coconut, date, and hop.
• the plant cell is derived from a dicotyledonous plant.
• the dicotyledonous plant is selected from the group consisting of tobacco, tomato, soybean, and papaya.
• the invention additionally provides a recombinant expression vector comprising a nucleotide sequence selected from the group consisting of S ⁇ Q ID NO:l, the complement of
• - 5 - vector is selected from the group consisting of pubi4-GUS, pubi9-GUS, 4PI-GUS and 9PI- GUS.
• the invention also provides a recombinant expression vector comprising a portion of a nucleotide sequence selected from the group consisting of SEQ ID NO:l and the complement thereof.
• Also provided herein is a recombinant expression vector comprising a portion of a nucleotide sequence selected from the group consisting of SEQ ID NO:3 and the complement thereof.
• transgenic plant cell comprising a nucleic acid sequence comprising a nucleotide sequence selected from the group consisting of SEQ
• the transgenic plant cell expresses the nucleic acid sequence of interest.
• the expression is constitutive.
• the transgenic plant cell is derived from a monocotyledonous plant.
• the monocotyledonous plant is selected from the group consisting of sugarcane, maize, sorghum, pineapple, rice, barley, oat, wheat, rye, yam, onion, banana, coconut, date, and hop.
• the transgenic plant cell is derived from a dicotyledonous plant.
• the dicotyledonous plant is selected from the group consisting of tobacco, tomato, soybean, and papaya.
• the nucleic acid sequence of interest is a sense sequence.
• the sense sequence encodes a protein selected from the group consisting of ⁇ - glucuronidase, luciferase, ⁇ -galactosidase, 1-aminocyclopropane-l-carboxylic acid deaminase, sucrose phosphate synthase, 5-enolpyruvyl-3- phosphoshikimate synthase, acetolactate synthase. RNase, wheat germ agglutinin, sweetness protein, and Bacillus thuringiensis crystal toxin proteins.
• the nucleic acid sequence of interest is an antisense sequence.
• the antisense sequence is selected from the group consisting of an antisense sequence to ACC synthase, to ethylene inducible sequences, and to polyphenol oxidase.
• the invention further provides a transgenic plant cell comprising a nucleic acid sequence comprising a portion of a nucleotide sequence selected from the group consisting of SEQ ID NO: l and the complement thereof.
• transgenic plant cell comprising a nucleic acid sequence comprising a portion of a nucleotide sequence selected from the group consisting of SEQ ID NO: 1
• a method for expressing a nucleic acid sequence of interest in a plant cell comprising: a) providing: i) a plant cell; ii) a nucleic acid sequence of interest; and iii) a nucleotide sequence selected from the group consisting of SEQ ID NO: l, the complement of SEQ ID NO:l, homologs of SEQ ID NO: l.
• the method further comprises d) identifying the transgenic plant cell. In another preferred embodiment, the method further comprises d) regenerating transgenic plant tissue from the transgenic plant cell.
• the methods further comprises d) regenerating a transgenic plant from the transgenic plant cell.
• the plant cell is derived from a monocotyledonous plant.
• the monocotyledonous plant is selected from the group consisting of sugarcane, maize, sorghum, pineapple, rice, barley, oat. wheat, rye, yam, onion, banana, coconut, date, and hop.
• the plant cell is derived from a dicotyledonous plant.
• the dicotyledonous plant is selected from the group consisting of tobacco, tomato, soybean, and papaya.
• the invention further provides a method for expressing a nucleic acid sequence of interest in a plant cell, comprising: a) providing: i) a plant cell; ii) a nucleic acid sequence of interest; and iii) a portion of a nucleotide sequence selected from the group consisting of SEQ ID NO:l and the complement thereof; b) operably linking the nucleic acid sequence of interest to the portion of a nucleotide sequence to produce a transgene; and c) introducing the transgene into the plant cell to produce a transgenic plant cell under conditions such that the nucleic acid sequence of interest is expressed in the transgenic plant cell.
• a method for expressing a nucleic acid sequence of interest in a plant cell comprising: a) providing: i) a plant cell; ii) a nucleic acid sequence of interest; and iii) a portion of a nucleotide sequence selected from the group consisting of SEQ ID NO:l and the complement
• the portion comprises the nucleotide sequence selected from the group consisting of the nucleotides from 1 to 242 of SEQ ID NO:7, from 245 to 787 of SEQ ID NO:7, from 788 to 1020 of SEQ ID NO:7, from 1021 to 1084 of SEQ ID NO:7. from 1085 to 1 168 of SEQ ID NO:7, from 1 169 to 1 173 of SEQ ID NO:7, from 1 174 to 1648 of SEQ ID NO:7. from 1649 to 1805 of SEQ ID NO:l, from 1 to 378 of SEQ ID NO: l, from 379 to 444 of
• SEQ ID NO: l and from 445 to 1810 of SEQ ID NO:l .
• Also provided by the invention is a method for expressing a nucleic acid sequence of interest in a plant cell, comprising: a) providing: i) a plant cell; ii) a nucleic acid sequence of interest; and iii) a portion of a nucleotide sequence selected from the group consisting of SEQ ID NO:3 and the complement thereof; b) operably linking the nucleic acid sequence of interest to the portion of a nucleotide sequence to produce a transgene; and c) introducing the transgene into the plant cell to produce a transgenic plant cell under conditions such that the nucleic acid sequence of interest is expressed in the transgenic plant cell.
• the portion comprises the nucleotide sequence selected from the group consisting of the nucleotides 1 to 3600 of SEQ ID NO: 10, from 3602 to 3612 of SEQ ID NO: 10, from
• Figure 1 shows a RNA gel blot of sugarcane polyubiquitin mRNA pools hybridized to gene-specific probes for Scubi 221, Scubi 511, Scubi 241, Scubi561, and Scubi 5121.
• Figure 2 shows a "Reverse northern” blot of sugarcane polyubiquitin mRNA pools.
• Figure 3 shows the nucleotide sequence of the sugarcane polyubiquitin ubi4 gene.
• Figure 3 A shows the nucleotide sequence (SEQ ID NO:l) including the translation start codon and sequences upstream thereof.
• Figure 3B shows the nucleotide sequence (SEQ ID NO:
• Figure 4 is a diagrammatic representation of the initially-determined organization of ubi4 and ubi9 polyubiquitin genes. Numbered white boxes indicate polyubiquitin coding repeats, unnumbered white boxes are 5' and 3' untranslated regions, black boxes are introns,
• E EcoRI
• N Nrul
• S Sail
• H Hindlll
• M putative miniature inverted-repeat transposable element.
• Figure 5 shows the nucleotide sequence (S ⁇ Q ID ⁇ O:5) (nucleotides 1 to 5512 of the 5551 nucleotide sequence deposited as GenBank accession number AF093504) (A) and translated amino acid sequence (S ⁇ Q ID NO:6) (B) of sugarcane polyubiquitin ubi4 gene.
• Figure 6 is a diagrammatic representation of the organization of ubi4 (GenBank accession number AF093504) and ubi9 (GenBank accession number AF093505) polyubiquitin genes. Numbered white boxes indicate polyubiquitin coding repeats, unnumbered white boxes are 5" and 3 " untranslated regions, black boxes are introns and lines are flanking DNA. E: EcoRI; N: Nrul; S: Sail; H: Hindlll; M: putative miniature inverted-repeat transposable element.
• Figure 7 shows the nucleotide sequence of the sugarcane polyubiquitin ubi9 gene.
• Figure 7A shows the nucleotide sequence (S ⁇ Q ID ⁇ O:3) including the translation start codon and sequences upstream thereof.
• Figure 7B shows the nucleotide sequence (S ⁇ Q ID NO:4) including the translation stop codon and sequences downstream thereof.
• Boldface indicates the putative TATA box, ATG translation start codon, TAA translation stop codon, and putative poly-A addition signal; underlining indicates the 5' and 3' UTRs; lowercase indicates that the base is most probably as depicted (see also Tables 4 and 5 below).
• Figure 8 shows the nucleotide sequence (S ⁇ Q ID NO: 8) (GenBank accession number AF093505) (A) and translated amino acid sequence (S ⁇ Q ID NO:9) (B) of the sugarcane polyubiquitin ubi9 gene.
• Figure 9 is a graph showing GUS activity following transient expression of GUS under the control of the sugarcane ubi4 promoter (ubi4), sugarcane ubi9 promoter (ubi9), and maize ubil promoter (mzubil) in sugarcane suspension cells (A, B) and tobacco leaves (C, D). Controls received no DNA. Letters within parentheses indicate least significant difference levels, i.e., mean GUS activity values with different letters being significantly different at P ⁇ 0.05 confidence level.
• Figure 10 shows the nucleotide sequence (S ⁇ Q ID NO:7) of the portion of the ubi4 gene which was ligated to the gene encoding ⁇ -glucuronidase (GUS) in plasmids pubi4-GUS and 4PI-GUS.
• S ⁇ Q ID NO:7 corresponds to nucleotides 1-1802 of S ⁇ Q ID NO:5.
• Figure 1 1 shows the nucleotide sequence (S ⁇ Q ID NO: 10) of the portion of the ubi9 gene which was ligated to the gene encoding ⁇ -glucuronidase (GUS) in plasmids pubi9-GUS and 9PI-GUS.
• S ⁇ Q ID NO:10 corresponds to nucleotides 1-3688 of S ⁇ Q ID NO:8.
• FIG. 12 is a graph showing GUS activity following stable expression in sugarcane callus lines of GUS under the control of sugarcane ubi9 promoter (sc ubi9) (A, D), sugarcane ubi4 promoter (sc ubi4) (B, D), and maize ubil (C, D).
• sugarcane ubi9 promoter sc ubi9 promoter
• sc ubi4 promoter sc ubi4 promoter
• C maize ubil
• Figure 13 is a graph showing GUS reporter gene activity in stable transgenic rice callus lines expressed under the control of the sugarcane ubi9 promoter in the presence and absence of the putative nuclear matrix attachment region (MAR).
• MAR putative nuclear matrix attachment region
• Figure 14 shows the nucleotide sequence (SEQ ID NO:l l) encoding polyphenol oxidase (GenBank accession number s40548).
• Figure 15 shows the nucleotide sequence (SEQ ID NO:2) encoding maize sucrose phosphate synthase enzyme (GenBank accession number m97550).
• transgenic when used in reference to a cell refers to a cell which contains a transgene, or whose genome has been altered by the introduction of a transgene.
• transgenic when used in reference to a tissue or to a plant refers to a tissue or plant, respectively, which comprises one or more cells that contain a transgene, or whose genome has been altered by the introduction of a transgene.
• Transgenic cells, tissues and plants may be produced by several methods including the introduction of a "transgene” comprising nucleic acid (usually DNA) into a target cell or integration of the transgene into a chromosome of a target cell by way of human intervention, such as by the methods described herein.
• transgene refers to any nucleic acid sequence which is introduced into the genome of a cell by experimental manipulations.
• a transgene may be an "endogenous DNA sequence," or a “heterologous DNA sequence” ⁇ i.e. , “foreign DNA”).
• endogenous DNA sequence refers to a nucleotide sequence which is naturally found in the cell into which it is introduced so long as it does not contain some modification (e.g., a point mutation, the presence of a selectable marker gene, etc.) relative to the naturally- occurring sequence.
• heterologous DNA sequence refers to a nucleotide sequence which is ligated to, or is manipulated to become ligated to, a nucleic acid sequence to which it is not ligated in nature, or to which it is ligated at a different location in nature.
• Heterologous DNA is not endogenous to the cell into which it is introduced, but has been obtained from another cell.
• Heterologous DNA also includes an endogenous DNA sequence
• heterologous DNA encodes RNA and proteins that are not normally produced by the cell into which it is expressed.
• heterologous DNA include reporter genes, transcriptional and translational regulatory sequences, selectable marker proteins (e.g., proteins which confer drug resistance), etc.
• foreign gene refers to any nucleic acid (e.g., gene sequence) which is introduced into the genome of a cell by experimental manipulations and may include gene sequences found in that cell so long as the introduced gene contains some modification (e.g. , a point mutation, the presence of a selectable marker gene, etc.) relative to the naturally- occurring gene.
• transformation refers to the introduction of a transgene into a cell. Transformation of a cell may be stable or transient.
• transient transformation or “transiently transformed” refers to the introduction of one or more transgenes into a cell in the absence of integration of the transgene into the host celfs genome. Transient transformation may be detected by, for example, enzyme-linked immunosorbent assay (ELISA) which detects the presence of a polypeptide encoded by one or more of the transgenes.
• ELISA enzyme-linked immunosorbent assay
• transient transformation may be detected by detecting the activity of the protein (e.g., ⁇ -glucuronidase) encoded by the transgene (e.g., the uid A gene) as demonstrated herein [e.g., histochemical assay of GUS enzyme activity by staining with X-gluc which gives a blue precipitate in the presence of the GUS enzyme; and a chemiluminescent assay of GUS enzyme activity using the GUS-Light kit (Tropix)].
• the term "transient transformant” refers to a cell which has transiently incorporated one or more transgenes.
• stable transformation refers to the introduction and integration of one or more transgenes into the genome of a cell.
• Stable transformation of a cell may be detected by Southern blot hybridization of genomic DNA of the cell with nucleic acid sequences which are capable of binding to one or more of the transgenes.
• stable transformation of a cell may also be detected by the polymerase chain reaction of genomic DNA of the cell to amplify transgene sequences.
• stable transformant refers to a cell which has stably integrated one or more transgenes into the genomic DNA.
• a stable transformant is distinguished from a transient transformant in that, whereas genomic DNA from the stable transformant contains one or more transgenes, genomic DNA from the transient transformant does not contain a transgene.
• nucleotide sequence of interest refers to any nucleotide sequence, the manipulation of which may be deemed desirable for any reason (e.g.. confer improved qualities), by one of ordinary skill in the art.
• nucleotide sequences include, but are not limited to. coding sequences of structural genes (e.g., reporter genes, selection marker genes, oncogenes. drug resistance genes, growth factors, etc.), and non-coding regulatory sequences which do not encode an mRNA or protein product, (e.g., promoter sequence, polyadenylation sequence, termination sequence, enhancer sequence, etc.).
• isolated when used in relation to a nucleic acid, as in “an isolated nucleic acid sequence” refers to a nucleic acid sequence that is identified and separated from at least one contaminant nucleic acid with which it is ordinarily associated in its natural source.
• Isolated nucleic acid is nucleic acid present in a form or setting that is different from that in which it is found in nature.
• non-isolated nucleic acids are nucleic acids such as DNA and RNA which are found in the state they exist in nature.
• a given DNA sequence e.g., a gene
• RNA sequences such as a specific mRNA sequence encoding a specific protein, are found in the cell as a mixture with numerous other mRNAs which encode a multitude of proteins.
• an isolated nucleic acid sequence comprising SEQ ID NO:l includes, by way of example, such nucleic acid sequences in cells which ordinarily contain SEQ ID NO:l where the nucleic acid sequence is in a chromosomal or extrachromosomal location different from that of natural cells, or is otherwise flanked by a different nucleic acid sequence than that found in nature.
• the isolated nucleic acid sequence may be present in single-stranded or double-stranded form.
• the nucleic acid sequence will contain at a minimum at least a portion of the sense or coding strand ⁇ i.e., the nucleic acid sequence may be single-stranded). Alternatively, it may contain both the sense and anti-sense strands ⁇ i.e., the nucleic acid sequence may be double- stranded).
• purified refers to molecules, either nucleic or amino acid sequences, that are removed from their natural environment, isolated or separated.
• An “isolated nucleic acid sequence” is therefore a purified nucleic acid sequence.
• substantially purified molecules are at least 60%) free, preferably at least 75% free, and more preferably at least 90% free from other components with which they are naturally associated.
• Complementarity can be “partial” or “total.”
• Partial complementarity is where one or more nucleic acid bases is not matched according to the base pairing rules.
• Total or “complete” complementarity between nucleic acids is where each and every nucleic acid base is matched with another base under the base pairing rules. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands.
• a "complement" of a nucleic acid sequence as used herein refers to a nucleotide sequence whose nucleic acids show total complementarity to the nucleic acids of the nucleic acid sequence.
• the term "homology" when used in relation to nucleic acids refers to a degree of complementarity. There may be partial homology ⁇ i.e., partial identity) or complete homology ⁇ i.e., complete identity).
• a partially complementary sequence is one that at least partially inhibits a completely complementary sequence from hybridizing to a target nucleic acid and is referred to using the functional term "substantially homologous.”
• the inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or Northern blot, solution hybridization and the like) under conditions of low stringency.
• a substantially homologous sequence or probe ⁇ i.e., an oligonucleotide which is capable of hybridizing to another oligonucleotide of interest) will compete for and inhibit the binding ⁇ i.e., the hybridization) of a completely homologous sequence to a target under conditions of low stringency.
• low stringency conditions are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (/. e. , selective) interaction.
• the absence of non-specific binding may be tested by the use of a second target which lacks even a partial degree of complementarity (e.g., less than about 30% identity); in the absence of non-specific binding the probe will not hybridize to the second non- complementary target.
• substantially homologous refers to any probe which can hybridize to either or both strands of the double-stranded nucleic acid sequence under conditions of low stringency as described infra.
• substantially homologous refers to any probe which can hybridize to the single-stranded nucleic acid sequence under conditions of low stringency as described infra.
• hybridization includes "any process by which a strand of nucleic acid joins with a complementary strand through base pairing.” [Coombs J ( 1994) Dictionary of Biotechnology, Stockton Press, New York NY]. Hybridization and the strength of hybridization ⁇ i.e., the strength of the association between the nucleic acids) is impacted by such factors as the degree of complementarity between the nucleic acids, stringency of the conditions involved, the T m of the formed hybrid, and the G:C ratio within the nucleic acids.
• T m is used in reference to the "melting temperature.”
• the melting temperature is the temperature at which a population of double-stranded nucleic acid molecules becomes half dissociated into single strands.
• Low stringency conditions when used in reference to nucleic acid hybridization comprise conditions equivalent to binding or hybridization at 68°C in a solution consisting of 5X SSPE (43.8 g/1 NaCl, 6.9 g/1 NaH 2 PO 4 » H 2 O and 1.85 g/1 EDTA, pH adjusted to 7.4 with NaOH), 1% SDS, 5X Denhardt's reagent [50X Denhardt's contains the following per 500 ml: 5 g Ficoll (Type 400, Pharmacia), 5 g BSA (Fraction V; Sigma)] and 100 ⁇ g/ml denatured salmon sperm DNA followed by washing in a solution comprising 0.2X SSPE, and 0.1 % SDS at room temperature when a DNA probe of about 100 to about 1000 nucleotides in length is employed.
• 5X SSPE 43.8 g/1 NaCl, 6.9 g/1 NaH 2 PO 4 » H 2 O and 1.85 g/1 EDTA, pH adjusted to 7.4 with NaOH
• High stringency conditions when used in reference to nucleic acid hybridization comprise conditions equivalent to binding or hybridization at 68°C in a solution consisting of
• 5X SSPE 5X SSPE. 1% SDS, 5X Denhardt's reagent and 100 ⁇ g/ml denatured salmon sperm DNA followed by washing in a solution comprising 0.1X SSPE, and 0.1 % SDS at 68°C when a probe of about 100 to about 1000 nucleotides in length is employed.
• hybridization condition when made in reference to a hybridization condition as it relates to a hybridization condition of interest means that the hybridization condition and the hybridization condition of interest result in hybridization of nucleic acid sequences which have the same range of percent (%) homology. For example, if a hybridization condition of interest results in hybridization of a first nucleic acid sequence with other nucleic acid
• Another hybridization condition is said to be equivalent to the hybridization condition of interest if this other hybridization condition also results in hybridization of the first nucleic acid sequence with the other nucleic acid sequences that have from 50% to 70% homology to the first nucleic acid sequence.
• promoter refers to a DNA sequence which when ligated to a nucleotide sequence of interest is capable of controlling the transcription of the nucleotide sequence of interest into mRNA.
• a promoter is typically, though not necessarily, located 5' ⁇ i.e., upstream) of a nucleotide sequence of interest whose transcription into mRNA it controls, and provides a site for specific binding by RNA polymerase and other transcription factors for initiation of transcription.
• Promoters may be tissue specific or cell specific.
• tissue specific refers to a promoter that is capable of directing selective expression of a nucleotide sequence of interest to a specific type of tissue (e.g., petals) in the relative absence of expression of the same nucleotide sequence of interest in a different type of tissue (e.g., roots).
• Tissue specificity of a promoter may be evaluated by, for example, operably linking a reporter gene to the promoter sequence to generate a reporter construct, introducing the reporter construct into the genome of a plant such that the reporter construct is integrated into every tissue of the resulting transgenic plant, and detecting the expression of the reporter gene
• tissue type specific refers to a promoter which is capable of directing selective expression of a nucleotide sequence of interest in a specific type of cell in the relative absence of expression of the same nucleotide sequence of interest in a different type of cell within the same tissue.
• cell type specific when applied to a promoter also means a promoter capable of promoting selective expression of a nucleotide sequence of interest in a region within a single tissue.
• Cell type specificity of a promoter may be assessed using methods well known in the art, e.g., immunohistochemical staining. Briefly, tissue sections are embedded in paraffin, and paraffin sections are reacted with a primary antibody which is specific for the polypeptide product encoded by the nucleotide sequence of interest whose expression is controlled by the promoter.
• a labeled (e.g., peroxidase conjugated) secondary antibody which is specific for the primary antibody is allowed to bind to the sectioned tissue and specific binding detected ⁇ e.g. , with avidin/biotin) by microscopy.
• Promoters may be constitutive or regulatable.
• the term "constitutive" when made in reference to a promoter means that the promoter is capable of directing transcription of an operably linked nucleic acid sequence in the absence of a stimulus (e.g. , heat shock, chemicals, light, etc.).
• constitutive promoters are capable of directing expression of a transgene in substantially any cell and any tissue.
• a "regulatable" promoter is one which is capable of directing a level of transcription of an operably linked nuclei acid sequence in the presence of a stimulus ⁇ e.g., heat shock, chemicals, light, etc.) which is different from the level of transcription of the operably linked nucleic acid sequence in the absence of the stimulus.
• infectious and “infection” with a bacterium refer to co-incubation of a target biological sample, (e.g., cell, tissue, etc.) with the bacterium under conditions such that nucleic acid sequences contained within the bacterium are introduced into one or more cells of the target biological sample.
• a target biological sample e.g., cell, tissue, etc.
• Agrobacterium refers to a soil-borne, Gram-negative, rod-shaped phytopathogenic bacterium which causes crown gall.
• Agrobacterium includes, but is not limited to, the strains Agrobacterium tumefaciens, (which typically causes crown gall in
• Agrobacterium rhizogens which causes hairy root disease in infected host plants.
• Infection of a plant cell with Agrobacterium generally results in the production of opines (e.g.. nopaline, agropine, octopine etc.) by the infected cell.
• opines e.g.. nopaline, agropine, octopine etc.
• nopaline-type Agrobacteria referred to as "nopaline-type" Agrobacteria
• Agrobacterium strains which cause production of octopine are referred to as "nopaline-type" Agrobacteria; Agrobacterium strains which cause production of octopine
• strain LBA4404, Ach5, B6 are referred to as "octopine-type” Agrobacteria; and Agrobacterium strains which cause production of agropine (e.g., strain EHA105, EHA101, A281 ) are referred to as "agropine-type” Agrobacteria.
• biolistic bombardment refers to the process of accelerating particles towards a target biological sample (e.g., cell, tissue, etc.) to effect wounding of the cell membrane of a cell in the target biological sample and/or entry of the particles into the target biological sample.
• a target biological sample e.g., cell, tissue, etc.
• Methods for biolistic bombardment are known in the art (e.g., U.S. Patent No. 5.584,807, the contents of which are herein incorporated by reference), and are commercially available (e.g., the helium gas-driven microprojectile accelerator (PDS-1000/He) (BioRad).
• microwounding when made in reference to plant tissue refers to the introduction of microscopic wounds in that tissue. Microwounding may be achieved by, for example, particle bombardment as described herein.
• plant refers to a plurality of plant cells which are largely differentiated into a structure that is present at any stage of a plant's development. Such structures include, but are not limited to, a fruit, shoot, stem, leaf, flower petal, etc.
• plant tissue includes differentiated and undifferentiated tissues of plants including, but not limited to, roots, shoots, leaves, pollen, seeds, tumor tissue and various types of cells in culture (e.g., single cells, protoplasts, embryos, callus, protocorm-like bodies, etc.). Plant tissue may be in planta, in organ culture, tissue culture, or cell culture.
• the present invention provides nucleic acid sequences having promoter activity.
• the nucleic acid sequences provided herein direct constitutive expression of operably linked nucleotide sequences in cells, tissues and organs of monocotyledonous and dicotyledonous plants.
• the promoter sequences provided herein were discovered by screening highly expressed sugarcane polyubiquitin genes.
• the sequences of the invention are capable of driving expression of operably linked nucleotide sequences in plant cells at a level which is
• nucleic acid sequence of interest in plants.
• the nucleic acid sequences and methods of the invention allow generation of transgenic plants which exhibit agronomically desirable characteristics.
• the invention is further described under (A) Sugarcane Polyubiquitin Promoter Sequences, (B) Using Probes To Identify And Isolate Homologs of The Sugarcane Promoter Sequences, (C) Using Primers to Amplify Nucleotide Sequences, and (D) Generating Transgenic Plants.
• Ubiquitin protein is abundant throughout the plant body, and several polyubiquitin genes have been shown to be expressed in most or all cell types under most or all environmental conditions [Kawalleck et al., Plant Mol Biol 21, 673-84 (1993)]. Numerous other polyubiquitin genes, however, are expressed in a tissue-specific manner [Callis et al., Proc Natl Acad Sci U S A 91, 6074-7 (1994); Plesse et al, Mol Gen Genet 254, 258-66 (1997)], or in response to environmental signals such as heat stress [Christensen et al., Plant
• sugarcane hybrids may have at least twelve alleles for each of the multiple genes that make up the polyubiquitin gene family.
• the nucleic acid sequences of the invention were discovered during a search by the inventors for promoters which are suitable for high-level constitutive transgene expression in monocotyledonous and dicotyledonous plants.
• the inventors isolated five polyubiquitin cDNA clones (scubi221, 241, 511, 561, and 5121) from sugarcane stem tissue [Albert et al, Plant Physiology 109, 337 (1995)].
• the inventors Based on comparison of their 3' untranslated sequences, the inventors then grouped these five genes into four "sub-families.” The inventors' investigation of the expression of two members of these four sub-families and isolated genomic clones, led to isolation of clones which contained promoters for two members of the most highly expressed sub-family.
• the invention provides the nucleic acid sequence of two members of the sugarcane polyubiquitin family, the ubi4 gene and the ubi9 gene.
• the initially determined nucleic acid sequence (SEQ ID NO:l) of the ubi4 gene including the translation start codon (ATG) and the sequence upstream of the translation start codon is shown in Figure 3A
• the nucleic acid sequence (SEQ ID NO:2) of the ubi4 gene including the translation stop codon and sequences downstram of the translation stop codon is shown in Figrue 3B.
• the subsequently determined nucleic acid sequence (SEQ ID NO:5) of the entire ubi4 gene is shown in Figure 5A with the subsequently determined nucleic acid sequence (SEQ ID NO:7) located upstream of the translation start codon of the ubi4 gene being shown in Figure 10.
• the nucleotide sequence of Figure 5 A represents nucleotides 1 to 5512 of the 5551 nucleotide sequence deposited as GenBank accession number AF093504.
• Fragments of the ubi4 gene sequence which were identical in the initially determined and the subsequently determined nucleic acid sequences were as follows (the nucleotide numbers refer to the nucleotide number in SEQ ID NO:5): Fragment A: 1-242; fragment B:
• nucleotide sequence upstream of the transcription start codon of the ubi4 gene ⁇ i.e.. nucleotides 1-1810 of SEQ ID NO:l, and nucleotides 1-1802 of SEQ ID NOs:5 and 7) contained three regions: (a) an upstream of the 5' UTR sequence ⁇ i.e., nucleotides 1-378 of SEQ ID NO:l, and nucleotides
• the initially determined nucleic acid sequence (SEQ ID NO:3) of the ubi9 gene including the translation start codon and sequences upstream thereof is shown in Figure 7A and the initially determined nucleic acid sequence (SEQ ID NO:4) of the ubi9 gene including the translation stop codon and sequences downstream thereof is shown in Figure 7B.
• the subsequently determined nucleic acid sequence (SEQ ID NO:8) of the entire ubi9 gene is shown in Figure 8A, with the nucleic acid sequence (SEQ ID NO: 10) of the ubi9 gene upstream of the translation start codon being shown in Figure 11.
• any reference herein to SEQ ID NO:8 is intended to mean each and every one of the three nucleotide sequences described in the preceding sentence.
• any reference herein to SEQ ID NO: 10 is intended to mean each and every one of the three nucleotide sequences described in the preceding sentence.
• Fragments of the ubi9 gene sequence which were identical in the initially determined and the subsequently determined nucleic acid sequences were as follows (the nucleotide number refers to the nucleotide number in SEQ ID NO:8): Fragment A: 1-3600; fragment B: 3602-3612: and fragment C: 3614-3691.
• the nucleotide sequence upstream of the translation start codon of the ubi9 gene ⁇ i.e., nucleotides 1-3691 of SEQ ID NO:3, and nucleotides 1-
• 3691 of SEQ ID NO:8) contained three regions: (a) an upstream of the 5' UTR sequence ⁇ i.e., nucleotides 1-2248 of SEQ ID NO:3, and nucleotides 1-2248 of SEQ ID NOs:8 and 10), (b) a 5 ' UTR sequence ⁇ i.e., nucleotides 2249-2313 of SEQ ID NO:3, and nucleotides 2249- 2313 of SEQ ID NOs:8 and 10), and (c) an intron sequence ⁇ i.e., nucleotides 2314-3688 of SEQ ID NO:3. and nucleotides 2314-3688 of SEQ ID NOs:8 and 10).
• a BLAST search of the GenBank database showed 100% homology to only a 20-22 bp region of nucleotides 1- 3688 of SEQ ID NOs:8 and 10 ⁇ i.e. the region of the ubi9 gene which contained the sequence upstream of the 5' UTR, the 5' UTR sequence, and the intron sequence), 100% homology to only a 20 bp region of nucleotides 1-2248 of SEQ ID NOs:8 and 10 ⁇ i.e., the sequence upstream of the 5' UTR), and 87% homology between a 135 bp fragment of the sequence upstream of the 5' UTR of SEQ ID NOs:8 and 10 and a 118 bp fragment of Saccharum sp. glucose transporter mRNA, 3' end (GenBank accession number L21752).
• Example 10 (which is equivalent to the initially determined SEQ ID NO:3) of the ubi9 gene successfully drive transient expression of GUS in monocotyledonous sugarcane suspension cultured cells (Example 3), monocotyledonous sorghum callus (Example 5), monocotyledonous pineapple leaves, protocorm-like bodies, roots and fruit (Example 6), and in dicotyledonous tobacco leaves (Example 4), as well as stable expression in monocotyledonous sugar cane callus (Example 7). monocotyledonous rice callus (Example 8), and dicotyledonous tobacco leaves (Example 9).
• portion when made in reference to a nucleic acid sequence refers to a fragment of that sequence.
• the fragment may range in size from ten (10) contiguous nucleotide residues to the entire nucleic acid sequence minus one nucleic acid residue.
• a nucleic acid sequence comprising "at least a portion of a nucleotide sequence comprises from ten (10) contiguous nucleotide residues of the nucleotide sequence to the entire nucleotide sequence.
• portions contemplated to be within the scope of the invention include, but are not limited to, portions larger than 20 nucleotide bases, more preferably larger than 100 nucleotide bases, the sequence upstream of the 5 * UTR sequence
• nucleotide sequence from position 1 to 377 of SEQ ID NO:7) the 5 " UTR sequence ⁇ i.e.. nucleotides sequence from position 378 to 442 of SEQ ID NO:7). and the intron sequence ⁇ i.e., nucleotide sequence from position 443 to 1802 of SEQ ID NO:7).
• portions within the scope of the invention include portions larger than 20 nucleotide bases, more preferably larger than 100 nucleotide bases, those sequences which are upstream of the translation start codon and which are identical in the initially determined and subsequently determined sequence of the ubi4 gene, and are exemplified by the nucleotide sequence from position 1 to 242, from position 245 to 787, from position 788 to 1020, from position 1021 to 1084, from position 1085 to 1168, from position 1169 to 1173, from position 1174 to 1648, and from position 1649 to 1802 of SEQ
• the portion contains the 377 bp sequence which is upstream of the 5 'UTR and which is highly homologous (>90% identity) in both the ubi4 and ubi9 gene sequences, i.e., the nucleotide sequence from position 1 to 377 of SEQ ID NO:7. It is contemplated that the present invention is not limited to SEQ ID NO:3 but specifically includes portions thereof.
• portions contemplated to be within the scope of the invention include, but are not limited to, portions larger than 20 nucleotide bases, more preferably larger than 100 nucleotide bases, the sequence upstream of the 5' UTR sequence ⁇ i.e., nucleotide sequence from position 1 to 2248 of SEQ ID NO: 10), the 5' UTR sequence (i.e., nucleotides sequence from position 2249 to 2313 of SEQ ID NO: 10), the 5' UTR sequence (i.e., nucleotides sequence from position 2249 to 2313 of SEQ ID
• portions within the scope of the invention include portions larger than 20 nucleotide bases, more preferably larger than 100
• the portion contains the sequence which is upstream of the transcription start codon and which is highly homologous (>90% identity) in both the ubi4 and ubi9 gene sequences, i.e., the nucleotide sequence from position 1671 to 2248 of SEQ ID NO: 10.
• This sequence includes the MITE (from position 1706 to 1906) which is not homologous to sequences in the polyubiquitin ubi4 promoter.
• the sequences of the present invention are not limited to SEQ ID NOs:l and 10 and portions thereof, but also include homologs of SEQ ID NOs:l and 10, as well as portions of these homologs.
• a nucleotide sequence which is a "homolog" of SEQ ID NOs: l and 10 is defined herein as a nucleotide sequence which exhibits greater than 61% identity (but not 100%) identity) to the sequence of SEQ ID NOs: l and 10. respectively.
• the present invention also contemplates functioning or functional homologs of SEQ
• a "functional homolog" of SEQ ID NOs:l and 10 is defined as a nucleotide sequence having less than 100%) homology with SEQ ID NOs:l and 10, respectively, and which has promoter activity having some or all the characteristics (e.g., constitutive promoter activity) of the promoter activity of SEQ ID NOs:l and 10, respectively.
• Homologs of SEQ ID NOs:l and 10, and of portions thereof include, but are not limited to, nucleotide sequences having deletions, insertions or substitutions of different nucleotides or nucleotide analogs as compared to SEQ ID NOs: l and 10, respectively. Such homologs may be produced using methods well known in the art.
• the invention also contemplates at least a portion of SEQ ID NOs:l and 10, and homologs thereof having promoter activity.
• promoter activity when made in reference to a nucleic acid sequence refers to the ability of the nucleic acid sequence to initiate transcription of an operably linked nucleotide sequence into mRNA.
• operably linked when made in reference to a nucleic acid sequence refers to the ability of the nucleic acid sequence to initiate transcription of an operably linked nucleotide sequence into mRNA.
• operably linked in operable combination
• in operable order refer to the linkage of nucleic acid sequences in a manner such that a nucleic acid molecule is capable of directing the transcription of nucleic acid sequence of interest and/or the synthesis of a polypeptide sequence of interest.
• Promoter activity may be determined using methods known in the art. For example, a candidate nucleotide sequence whose promoter activity is to be determined is ligated in-frame
• a nucleic acid sequence of interest e.g., a reporter gene sequence, a selectable marker gene sequence
• a reporter vector introducing the reporter vector into plant tissue using methods described herein, and detecting the expression of the reporter gene (e.g., detecting the presence of encoded mRNA or encoded protein, or the activity of a protein encoded by the reporter gene).
• the reporter gene may express a visible markers.
• Reporter gene systems which express visible markers include ⁇ -glucuronidase and its substrate (X-Gluc), luciferase and its substrate (luciferin), and ⁇ -galactosidase and its substrate (X-Gal) which are widely used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system [Rhodes CA et al. (1995) Methods Mol Biol 55: 121-131].
• the reporter gene is a GUS gene.
• the selectable marker gene may confer antibiotic or herbicide resistance.
• reporter genes include, but are not limited to, dhfr which confers resistance to methotrexate [Wigler M et al., (1980) Proc Natl Acad Sci 77:3567-70]; npt, which confers resistance to the aminoglycosides neomycin and G-418 [Colbere-Garapin F et ai, (1981) J. Mol. Biol. 150:1-14] and als or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyl transferase, respectively. Detecting the presence of encoded mRNA or encoded protein, or the activity of a protein encoded by the reporter gene or the selectable marker gene indicates that the candidate nucleotide sequence has promoter activity.
• Sequences within a promoter which affect promoter activity may be determined by using deletion constructs such as those described by Sherri et al. for the determination of
• HSP70 intron alterations which impact transcription of genes operably linked thereto [U.S. patent number 5,593,874, hereby incorporated by reference].
• several expression plasmids are constructed to contain a reporter gene under the regulatory control of different candidate nucleotide sequences which are obtained either by restriction enzyme deletion of internal sequences in SEQ ID NOs:l and 10, restriction enzyme truncation of sequences at the
• DNA sequences may also be included, e.g., a 3' untranslated region containing a polyadenylation site and transcription termination sites.
• the present invention is not limited to sense molecules of SEQ ID NOs: l and 10 but contemplates within its scope antisense molecules comprising a nucleic acid sequence complementary to at least a portion (e.g., a portion greater than 100 nucletide bases in length and more preferably greater than 200 nucleotide bases in length) of the nucleotide sequence of SEQ ID NOs:l and 10.
• antisense molecules find use in, for example, reducing or preventing expression of a gene whose expression is controlled by SEQ ID NOs: l and 10.
• nucleotide sequence of SEQ ID NOs:l and 10 may be synthesized by synthetic chemistry techniques which are commercially available and well known in the art [see Caruthers MH et ⁇ l, (1980) Nuc. Acids Res. Symp. Ser. 215-223; Horn T. et ⁇ l., (1980) Nuc. Acids Res. Symp. Ser. 225-232].
• fragments of SEQ ID NOs:l and 10 can be made by treatment of SEQ ID NOs: l and 10 with restriction enzymes followed by purification of the fragments by gel electrophoresis.
• sequences may also produced using the polymerase chain reaction (PCR) as described by Mullis [U.S. Patent Nos. 4,683,195, 4,683.202 and 4,965,188, all of which are hereby incorporated by reference].
• PCR polymerase chain reaction
• the nucleotide sequence of synthesized sequences may be confirmed using commercially available kits as well as using methods well known in the art which utilize enzymes such as the Klenow fragment of DNA polymerase I, Sequenase ® , T ⁇ q DNA polymerase, or thermostable T7 polymerase. Capillary electrophoresis may also be used to analyze the size and confirm the nucleotide sequence of the products of nucleic acid synthesis, restriction enzyme digestion or PCR amplification.
• sequences of the present invention may be used in a variety of ways. For example, these sequences are useful in directing the expression of polypeptide sequences in vitro and in vivo. In plants, this is useful in determining the role of the polypeptide in disease development as well an in producing transgenic plants with desirable agronomic characteristics as described below.
• portions of the sequences of the invention can be used as probes for the detection and isolation of complementary DNA sequences, and for the amplification of nucleotide sequences as described below.
• the invention provided herein is not limited to SEQ ID NO: l and 10, homologs thereof, and portions thereof, having promoter activity, but includes sequences having no promoter activity (i.e., non-functional homologs and non-functional portions of homologs).
• SEQ ID NOs: 1 and 10 may be desirable, for example, where a portion of SEQ ID NOs: 1 and 10 is used as a probe to detect the presence of SEQ ID NOs:l and 10, respectively, or of portions thereof in a sample.
• probe refers to an oligonucleotide, whether occurring naturally as in a purified restriction digest or produced synthetically, recombinantly or by
• a probe may be single-stranded or double-stranded. It is contemplated that any probe used in the present invention will be labelled with any "reporter molecule,” so that it is detectable in any detection system including, but not limited to enzyme (e.g., ELISA, as well as enzyme- based histochemical assays), fluorescent, radioactive, calorimetric, gravimetric, magnetic, and luminescent systems. It is not intended that the present invention be limited to any particular detection system or label.
• probes provided herein are useful in the detection, identification and isolation of, for example, sequences such as those listed as SEQ ID NOs:l and 10 as well as of homologs thereof.
• Preferred probes are of sufficient length (e.g., from about 9 nucleotides to about 20 nucleotides or more in length) such that high stringency hybridization may be employed. In one embodiment, probes from 20 to 50 nucleotide bases in length are employed.
• the invention provided herein is not limited to SEQ ID NO:l and 10, homologs thereof, and portions thereof, having promoter activity, but includes sequences having no promoter activity. This may be desirable, for example, where a portion of the nucleic acid sequences set forth as SEQ ID NOs:l and 10 is used as a primer for the amplification of nucleic acid sequences by, for example, polymerase chain reactions (PCR) or reverse transcription-polymerase chain reactions (RT-PCR).
• PCR polymerase chain reactions
• RT-PCR reverse transcription-polymerase chain reactions
• amplification is defined as the production of additional copies of a nucleic acid sequence and is generally carried out using polymerase chain reaction technologies well known in the art [Dieffenbach CW and GS Dveksler (1995) PCR Primer, a Laboratory Manual, Cold Spring Harbor Press, Plainview
• PCR polymerase chain reaction
• the primers are extended with a polymerase so as to form a new pair of complementary strands.
• the steps of denaturation, primer annealing and polymerase extension can be repeated many times (i.e., denaturation, annealing and extension constitute one "cycle”: there can be numerous "cycles") to obtain a high concentration of an amplified segment of the desired target sequence.
• the length of the amplified segment of the desired target sequence is determined by the relative positions of the primers with respect to each other, and therefore, this length is a controllable parameter.
• the method is referred to as the "polymerase chain reaction” (hereinafter "PCR”). Because the desired amplified segments of the target sequence become the predominant sequences (in terms of concentration) in the mixture, they are the to be "PCR amplified.”
• PCR it is possible to amplify a single copy of a specific target sequence in genomic DNA to a level detectable by several different methodologies (e.g., hybridization with a labeled probe; incorporation of biotinylated primers followed by avidin-enzyme conjugate detection; and or incorporation of 32 P-labeled deoxyribonucleotide triphosphates, such as dCTP or dATP, into the amplified segment).
• any nucleotide sequence can be amplified with the appropriate set of primer molecules.
• the amplified segments created by the PCR process itself are, themselves, efficient templates for subsequent PCR amplifications.
• Amplified target sequences may be used to obtain segments of DNA (e.g., genes) for the construction of targeting vectors, transgenes, etc.
• primer refers to an oligonucleotide, whether occurring naturally as in a purified restriction digest or produced synthetically, which is capable of
• the primer is preferably single stranded for maximum efficiency in amplification, but may alternatively be double stranded. If double stranded, the primer is first treated to separate its strands before being used to prepare extension products.
• the primer is an oligodeoxyribonucleotide. The primer must be sufficiently long (e.g..
• the present invention employs probes from 20 to 50 nucleotide bases in length.
• the primers contemplated by the invention are useful in, for example, identifying sequences which are homologous to the sugarcane ubi4 and ubi9 gene sequences in plants and in other organisms.
• the present invention provides methods for constitutively expressing a nucleotide sequence of interest in a cell, tissue, organ, and/or organism.
• the methods provided herein direct constitutive expression of a nucleotide sequence of interest in monocotyledonous and dicotyledonous plant cells. In one embodiment, this is accomplished by introducing into a plant cell a vector that contains a nucleotide sequence of interest operably linked to sequences provided herein which have promoter activity.
• the transformed plant cell is allowed to develop into a transgenic plant in which the nucleotide sequence of interest is preferably, though not necessarily, expressed in substantially every tissue.
• the methods of the invention involve transformation of monocotyledonous tissue (sugarcane suspension cultured cells, sugarcane callus, rice callus, maize embryos, pineapple leaves, protocorm-like bodies, roots and fruit, and sorghum callus) and dicotyledonous tissue (tobacco leaves, tomato plants, and soybean excised embryonic meristems) with expression vectors in which the ⁇ -glucuronidase (GUS) gene is under the
• vector refers to a recombinant DNA molecule containing a desired coding sequence and appropriate nucleic acid sequences necessary for the expression of the operably linked coding sequence in a particular host organism.
• expression vectors comprise the nucleic acid sequence of interest as well as companion sequences which allow the transcription of this sequence, and which allow cloning of the vector into a bacterial or phage host.
• the vector preferably, though not necessarily, contains an origin of replication which is functional in a broad range of prokaryotic hosts.
• a selectable marker is generally, but not necessarily, included to allow selection of cells bearing the desired vector.
• the promoter sequence is SEQ ID NO:l which is derived from the sugarcane ubi4 gene. In an alternative preferred embodiment, the promoter sequence is SEQ ID NO:3 which is derived from the sugarcane ubi9 gene.
• the invention is not limited to the promoter sequences used herein. Any sequence which is a portion, homolog, or a homolog of a portion of SEQ ID NOs:l and 10 and which has promoter activity is contemplated to be within the scope of the invention.
• the expression vector preferably contains a transcription termination sequence downstream of the nucleic acid sequence of interest to provide for efficient termination.
• exemplary termination sequences include the nopaline synthase (NOS) termination sequence, and different fragments of the sugarcane ribulose-1,5- biphosphate carboxylase/oxygenase (rubisco) small subunit (scrbcs) gene.
• NOS nopaline synthase
• scrbcs sugarcane ribulose-1,5- biphosphate carboxylase/oxygenase
• the termination sequences of the expression vectors are not critical to the invention. The termination sequence may be obtained from the same gene as the promoter sequence or may be obtained from different genes.
• polyadenylation sequences are also commonly added to the expression vector.
• polyadenylation sequences include, but are not limited to, the Agrobacterium
• nucleic acid sequence of interest is not translated into a polypeptide (e.g.. where the nucleic acid sequence of interest encodes an antisense RNA), polyadenylation signals are not necessary.
• Vectors for the transformation of plant cells are not limited to the type or nature of the expressed genes disclosed herein. Any nucleic acid sequence of interest may be used to create transgenic plant cells, tissues, organs, and plants. Nucleic acid sequences of interest include sequences which encode a protein of interest.
• protein of interest and polypeptide of interest refer to any protein or polypeptide, respectively, the manipulation of which may be deemed desirable for any reason, by one of ordinary skill in the art.
• a nucleic acid sequence which encodes a polypeptide sequence having, for example, enzyme activity is desirable to express a nucleic acid sequence which encodes a polypeptide sequence having, for example, enzyme activity.
• an enzyme is the 1-aminocyclopropane-l-carboxylic acid (ACC) deaminase enzyme which metabolizes ACC in plant tissue thereby lowering the level of ethylene which is responsible for fruit ripening (U.S. Patent No. 5,512,466. the contents of which are hereby incorporated by reference).
• ACC 1-aminocyclopropane-l-carboxylic acid
• sucrose phosphate synthase enzyme which increases the level of sucrose in the fruit.
• the nucleic acid sequence of the gene encoding this enzyme is known [e.g., in maize; Worrell et al. (1991) Plant Cell 3: 1121-1 130] ( Figure 15) (SEQ ID NO:12) and has been assigned GenBank accession number m97550.
• EPSP synthase (5-enolpyruvyl-3- phosphoshikimate synthase; EC:25.1.19) which is an enzyme involved in the shikimic acid pathway of plants.
• the shikimic acid pathway provides a precursor for the synthesis of aromatic amino acids essential to the plant.
• EPSP synthase catalyzes the conversion of phosphoenol pyruvate and 3-phosphoshikimic acid to 5-enolpyruvyl-3- phosphoshikimate acid.
• a herbicide containing N-phosphonomethylglycine inhibits the EPSP synthase enzyme and thereby inhibits the shikimic acid pathway of the plant.
• glyphosate is usually used to refer to the N-phosphonomethylglycine herbicide in its acidic or anionic forms.
• Novel EPSP synthase enzymes have been discovered that exhibit an increased tolerance to glyphosate containing herbicides.
• an EPSP synthase enzyme having a single glycine to alanine substitution in the highly conserved region having the sequence: -L-G-N-A-G-T-A- located between positions 80 and 120 in the mature
• a glyphosate-tolerant EPSP synthase plant gene encodes a polypeptide which contains a chloroplast transit peptide (CTP) which enables the EPSP synthase polypeptide (or an active portion thereto) to be transported into a chloroplast inside the plant cell.
• CTP chloroplast transit peptide
• the EPSP synthase gene is transcribed into mRNA in the nucleus and the mRNA is translated into a precursor polypeptide (CTP/mature EPSP synthase) in the cytoplasm.
• the precursor polypeptide is transported into the chloroplast.
• enzymes suitable for use in this invention are acetolactate synthase.
• RNase to impart male sterility [Mariani et al. (1990) Nature 347: 737-741], and wheat germ agglutinin.
• nucleic acid sequence are those which encode the sweetness protein.
• the nucleic acid sequence for the gene encoding the sweetness protein is known in the art (see, e.g. , U.S. Patent Application No. 08/670,186, the contents of which are herein incorporated by reference). Transformation of plants with the sweetness protein is useful in, for example, providing a base level of sweetness in the fruit, thus reducing the effects of differences in fruit maturity by providing more uniform sweetness in different parts of the fruit.
• suitable proteins for use in this invention are Bacillus thuringiensis (B.t.) crystal toxin proteins which when expressed in plants protect the plants from insect infestation because the insect, upon eating the plant containing the B.t. toxin protein either dies or stops feeding.
• B.t. toxin proteins which are toxic to either Lepidopteran or Coleopteran insects may be used.
• Examples of particularly suitable DNA sequences encoding B.t. toxin protein are described in the EP patent application 385,962 entitled "Synthetic Plant Genes and Method for Preparation," published Sep. 5, 1990.
• nucleic acid sequence which encodes an antisense RNA that hybridizes with a genomic plant DNA sequence it may be of advantage to express antisense RNA which is specific for genomic plant DNA sequences that encode an enzyme whose activity is sought to be decreased.
• DNA sequences whose reduced expression may be desirable are known in the art including, but not limited to, the ethylene inducible sequences in fruit (U.S. Patent No. 5,545,815, the entire
• RNA sequences which is homologous with these ethylene inducible sequences is useful in delaying fruit ripening and in increasing fruit firmness.
• Other DNA sequences whose expression may be desirably reduced include the ACC synthase gene which encodes the ACC synthase enzyme that is the first and rate limiting step in ethylene biosynthesis. Nucleic acid sequences for this gene have been described from a number of plant sources (e.g., Picton et al. (1993) The Plant J. 3:469- 481 ; U.S. Patent Nos. 5,365,015 and 5,723,766, the contents of both of which are herein incorporated by reference).
• antisense RNA which hybridizes with ACC synthase genomic sequences in plants may be desirable to delay fruit ripening.
• Yet another sequence whose expression may be advantageously reduced is the genomic sequence encoding the enzyme polyphenol oxidase. This enzyme is involved in the browning reaction that occurs during chilling injury. Nucleic acid sequences encoding this enzyme have been previously described in the art (e.g., Shahar et al. (1992) Plant Cell 4:135- 147], as shown in Figure 14 (SEQ ID NO:l l) (GenBank accession number s40548). The use of antisense polyphenol antisense sequences has been reported to inhibit polyphenol oxidase
• the antisense DNA segment to be introduced into the plant may include the full length coding region of the targeted gene or a portion thereof. Complete homology between the nucleotide sequences of the antisense RNA and the targeted genomic DNA is not required. Rather, antisense DNA sequences which encode antisense RNA sequences that are partially homologous to a targeted genomic DNA sequence are contemplated to be within the scope of the invention so long as the antisense RNA sequences are capable of repressing expression of the target genomic DNA sequence.
• the invention is not limited to vectors which express a single nucleic acid sequence of interest.
• Vectors which contain a plurality of (i.e., two or more) nucleic acid sequences under the transcriptional control of the same promoter sequence are expressly contemplated to be within the scope of the invention. Such vectors may be desirable, for example, where the expression products of the plurality of nucleic acid sequences contained within the vector provide protection against different pathogens, and where simultaneous protection against these different pathogens is deemed advantageous.
• vectors which contain the same or different nucleic acid sequences under the transcriptional control of different promoter
• Such vectors may be desirable to, for example, to control different levels of expression of different nucleic acid sequences of interest in plant tissues.
• transgenic plants and plant cells are obtained by introducing the expression vectors into plants and plant cells using methods known in the art.
• the present invention is suitable for any member of the monocotyledonous (monocot) plant family including, but not limited to, maize, rice, barley, oats, wheat, sorghum, rye, sugarcane, pineapple, yams, onion, banana, coconut, dates and hops.
• the present invention is also suitable for any member of the dicotyledonous (dicot) plant family including, but not limited to, tobacco, tomato, soybean, and papaya.
• the expression vectors are introduced into plant cells by particle mediated gene transfer.
• Particle mediated gene transfer methods are known in the art, are commercially available, and include, but are not limited to, the gas driven gene delivery instrument descried in McCabe, U.S. Patent No. 5,584,807, the entire contents of which are herein incorporated by reference.
• This method involves coating the nucleic acid sequence of interest onto heavy metal particles, and accelerating the coated particles under the pressure of compressed gas for delivery to the target tissue.
• Other particle bombardment methods are also available for the introduction of heterologous nucleic acid sequences into plant cells. Generally, these methods involve depositing the nucleic acid sequence of interest upon the surface of small, dense particles of a material such as gold, platinum, or tungsten.
• the coated particles are themselves then coated onto either a rigid surface, such as a metal plate, or onto a carrier sheet made of a fragile material such as mylar.
• the coated sheet is then accelerated toward the target biological tissue.
• the use of the flat sheet generates a uniform spread of accelerated particles which maximizes the number of cells receiving particles under uniform conditions, resulting in the introduction of the nucleic acid sample into the target tissue.
• an expression vector may be inserted into the genome of plant cells by infecting the cells with a bacterium, including but not limited to an Agrobacterium strain previously transformed with the nucleic acid sequence of interest. Since most dicotyledonous plant are natural hosts for Agrobacterium, almost every dicotyledonous plant may be transformed by Agrobacterium in vitro. Although monocotyledonous plants, and in particular,
• Plant genera that may be transformed by Agrobacterium include Chrysanthemum, Dianthus, Gerbera, Euphorbia. Pelaronium, Ipomoea, Passiflora, Cyclamen, Malus. Prunus. Rosa. Rubus, Populus, Santalum, Allium, Lilium, Narcissus, Ananas. Arachis,
• Agrobacterium For transformation with Agrobacterium, disarmed Agrobacterium cells are transformed with recombinant Ti plasmids o ⁇ Agrobacterium tumefaciens or Ri plasmids o ⁇ Agrobacterium rhizogenes (such as those described in U.S. Patent No. 4,940,838, the entire contents of which are herein incorporated by reference) which are constructed to contain the nucleic acid sequence of interest using methods well known in the art [J. Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, NY]. The nucleic acid sequence of interest is then stably integrated into the plant genome by infection with the transformed Agrobacterium strain.
• heterologous nucleic acid sequences have been introduced into plant tissues using the natural DNA transfer system of Agrobacterium tumefaciens and Agrobacterium rhizogenes bacteria (for review, see Klee et al. (1987) Ann. Rev. Plant Phys. 38:467-486).
• Ti and Ri plasmids in general follows methods typically used with the more common bacterial vectors, such as pBR322. Additional use can be made of accessory genetic elements sometimes found with the native plasmids and sometimes constructed from foreign sequences. These may include but are not limited to structural genes for antibiotic resistance as selection genes.
• the first system is called the "cointegrate" system.
• the shuttle vector containing the gene of interest is inserted by genetic recombination into a non-oncogenic Ti plasmid that contains both the cis-acting and trans-acting elements required for plant transformation as, for example, in the pMLJl shuttle vector and the non-oncogenic Ti plasmid pGV3850.
• the second system is called the "binary" system in which two plasmids are used; the gene of interest is inserted into a shuttle vector containing the cis-acting elements required for plant transformation.
• the other necessary functions are provided in trans by the non-oncogenic Ti plasmid as exemplified by the pBIN19 shuttle vector and the non-oncogenic Ti plasmid PAL4404. Some of these vectors are commercially available.
• the first method is by co-cultivation of Agrobacterium with cultured isolated protoplasts. This method requires an established culture system that allows culturing protoplasts and plant regeneration from cultured protoplasts.
• the second method is by transformation of cells or tissues with Agrobacterium. This method requires (a) that the plant cells or tissues can be transformed by Agrobacterium and (b) that the transformed cells or tissues can be induced to regenerate into whole plants.
• the third method is by transformation of seeds, apices or meristems with Agrobacterium. This method requires micropropagation.
• Agrobacterium may be enhanced by using a number of methods known in the art. For example, the inclusion of a natural wound response molecule such as acetosyringone (AS) to the Agrobacterium culture has been shown to enhance transformation efficiency with Agrobacterium tumefaciens [Shahla et al. (1987) Plant Molec. Biol. 8:291-298].
• transformation efficiency may be enhanced by wounding the target tissue to be transformed. Wounding of plant tissue may be achieved, for example, by punching, maceration, bombardment with microprojectiles, etc. [see, e.g., Bidney et al. (1992) Plant Molec. Biol. 18:301-313].
• nucleic acid sequence of interest may be target to a particular locus on the plant genome.
• Site-directed integration of the nucleic acid sequence of interest into the plant cell genome may be achieved by, for example, homologous recombination using
• _4grob ⁇ cter/z.m-derived sequences Plant cells are incubated with a strain of Agrobacterium which contains a targeting vector in which sequences that are homologous to a DNA sequence inside the target locus are flanked by Agrobacterium transfer-DNA (T-DNA) sequences, as previously described (Offringa et al, (1996), U.S. Patent No. 5,501,967, the entire contents of which are herein incorporated by reference).
• T-DNA Agrobacterium transfer-DNA
• homologous recombination may be achieved using targeting vectors which contain sequences that are homologous to any part of the targeted plant gene, whether belonging to the regulatory elements of the gene, or the coding regions of the gene. Homologous recombination may be achieved at any region of a plant gene so long as the nucleic acid sequence of regions flanking the site to be targeted is known.
• the targeting vector used may be of the replacement- or insertion-type (Offringa et al (1996), supra).
• Replacement-type vectors generally contain two regions which are homologous with the targeted genomic sequence and which flank a
• - 35 - heterologous nucleic acid sequence e.g., a selectable marker gene sequence.
• Replacement- type vectors result in the insertion of the selectable marker gene which thereby disrupts the targeted gene.
• Insertion-type vectors contain a single region of homology with the targeted gene and result in the insertion of the entire targeting vector into the targeted gene.
• Other methods are also available for the introduction of expression vectors into plant tissue, e.g., electroinjection (Nan et al. (1995) In "Biotechnology in Agriculture and Forestry.” Ed. Y.P.S. Bajaj.
• Plants, plant cells and tissues transformed with a heterologous nucleic acid sequence of interest are readily detected using methods known in the art including, but not limited to, restriction mapping of the genomic DNA, PCR-analysis, DNA-DNA hybridization, DNA- RNA hybridization, DNA sequence analysis and the like.
• selection of transformed plant cells may be accomplished using a selection marker gene. It is preferred, though not necessary, that a selection marker gene be used to select transformed plant cells.
• a selection marker gene may confer positive or negative selection.
• a positive selection marker gene may be used in constructs for random integration and site-directed integration.
• Positive selection marker genes include antibiotic resistance genes, and herbicide resistance genes and the like.
• the positive selection marker gene is the NPTII gene which confers resistance to geneticin (G418) or kanamycin.
• the positive selection marker gene is the HPT gene which confers resistance to hygromycin.
• the choice of the positive selection marker gene is not critical to the invention as long as it encodes a functional polypeptide product.
• Positive selection genes known in the art include, but are not limited to, the ALS gene (chlorsulphuron resistance), and the DHFR-gene (methothrexate resistance).
• a negative selection marker gene may also be included in the constructs.
• the use of one or more negative selection marker genes in combination with a positive selection marker gene is preferred in constructs used for homologous recombination. Negative selection
• the negative selection marker gene serves to provide a disadvantage (preferably lethality) to cells that have integrated these genes into their genome in an expressible manner. Cells in which the targeting vectors for homologous recombination are randomly integrated in the genome will be harmed or killed due to the presence of the negative selection marker gene. Where a positive selection marker gene is included in the construct, only those cells having the positive selection marker gene integrated in their genome will survive.
• the choice of the negative selection marker gene is not critical to the invention as long as it encodes a functional polypeptide in the transformed plant cell.
• the negative selection gene may for instance be chosen from the aux-2 gene from the Ti-plasmid of Agrobacterium, the t/ -gene from SV40, cytochrome P450 from Streptomyces griseolus, the J/Vgene from Maize or Arabidopsis, etc. Any gene encoding an enzyme capable of converting a substance which is otherwise harmless to plant cells into a substance which is harmful to plant cells may be used.
• the present invention provides transgenic plants.
• the transgenic plants of the invention are not limited to plants in which each and every cell expresses the nucleic acid sequence of interest under the control of the sequences provided herein. Included within the scope of this invention is any plant which contains at least one cell which expresses the nucleic acid sequence of interest (e.g., chimeric plants). It is preferred, though not necessary, that the transgenic plant express the nucleic acid sequence of interest in more than one cell, and more preferably in one or more tissue. Once transgenic plant tissue which contains an expression vector has been obtained, transgenic plants may be regenerated from this transgenic plant tissue using methods known in the art.
• regeneration means growing a whole plant from a plant cell, a group of plant cells, a plant part or a plant piece (e.g., from a protoplast, callus, protocorm-like body, or tissue part).
• Species from the following examples of genera of plants may be regenerated from transformed protoplasts: Fragaria, Lotus, Medicago, Onobrychis, Trifolium. Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Hyoscyamus, Lycopersicon, Nicotiana, Solanum, Petunia, Digitalis,
• Ciohorium Helianthus. Lactuca, Bromus. Asparagus. Antirrhinum, Hererocallis, Nemesia, Pelargonium. Panicum. Pennisetum, Ranunculus. Senecio. Salpiglossis. Cucumis, Browaalia, Glycine, Lolium, Zea. Triticum, Sorghum, and Datura.
• a suspension of transformed protoplasts or a petri plate containing transformed explants is first provided.
• Callus tissue is formed and shoots may be induced from callus and subsequently rooted. Alternatively, somatic embryo formation can be induced in the callus tissue. These somatic embryos germinate as natural embryos to form plants.
• the culture media will generally contain various amino acids and plant hormones, such as auxin and cytokinins. It is also advantageous to add glutamic acid and proline to the medium, especially for such species as corn and alfalfa. Efficient regeneration will depend on the medium, on the genotype, and on the history of the culture. These three variables may be empirically controlled to result in reproducible regeneration.
• Plants may also be regenerated from cultured cells or tissues. Dicotyledonous plants which have been shown capable of regeneration from transformed individual cells to obtain transgenic whole plants include, for example, apple (Malus pumila), blackberry (Rubus). Blackberry /raspberry hybrid (Rubus), red raspberry (Rubus), carrot (Daucus carota), cauliflower (Brassica oleracea), celery (Apium graveolens), cucumber (Cucumis sativus), eggplant (Solanum melongena). lettuce (Lactuca sativa), potato (Solanum tuberosum), rape (Brassica napus), wild soybean (Glycine canescens), strawberry (Fragaria x ananassa), tomato
• Monocotyledonous plants which have been shown capable of regeneration from transformed individual cells to obtain transgenic whole plants include, for example, rice (Oryza sativa), rye (Secale cereale), and maize.
• the regenerated plants are transferred to standard soil conditions and cultivated in a conventional manner. After the expression vector is stably incorporated into regenerated
• the mature transgenic plants can be transferred to other plants by vegetative propagation or by sexual crossing.
• vegetatively propagated crops the mature transgenic plants are propagated by the taking of cuttings or by tissue culture techniques to produce multiple identical plants.
• the mature transgenic plants are self crossed to produce a homozygous inbred plant which is capable of passing the transgene to its progeny by Mendelian inheritance.
• the inbred plant produces seed containing the nucleic acid sequence of interest. These seeds can be grown to produce plants that would produce the selected phenotype.
• the inbred plants can also be used to develop new hybrids by crossing the inbred plant with another inbred plant to produce a hybrid.
• Confirmation of the transgenic nature of the cells, tissues, and plants may be performed by PCR analysis, antibiotic or herbicide resistance, enzymatic analysis and/or Southern blots to verify transformation. Progeny of the regenerated plants may be obtained and analyzed to verify whether the transgenes are heritable. Heritability of the transgene is further confirmation of the stable transformation of the transgene in the plant.
• the plant materials used for the cDNA library and for expression studies were sugarcane hybrid H65-7052 plants grown in the greenhouse of the Hawaii Agriculture Research Center. Aiea, Hawaii.
• the genomic library used to isolate the genomic clones was made from the related sugarcane hybrid H32-8560 [Albert et al, Plant Mol Biol 20, 663-71 (1992)]. Internodes were numbered consecutively down the culm, with number one defined as that internode subtending the youngest fully expanded leaf, as previously described [Moore P. H.: Anatomy and Morphology. In: Heinz DJ (ed) Sugarcane Improvement Through Breeding, pp. 85-142. Elsevier, Amsterdam (1987)].
• scubi241 contained four copies of the polyubiquitin coding repeat, whereas scubi511 contained five of these repeats (data not shown).
• Polyubiquitin cDNA plasmid clones were digested with appropriate restriction enzymes and size fractionated by gel electrophoresis. DNA was transferred to Hybond-N+ (Amersham) membranes by capillary transfer. Identical DNA gel blots of the five clones were hybridized to 3 'UTR probes at high stringency. High stringency hybridization and stringency washes at 65°C were by the method of [Church et al, Proc. Natl. Acad. Sci. USA
• Probe templates were prepared by PCR amplification of the 3' UTR of each cDNA clone. Probes were 32 P labeled by the method of [Feinberg et al, Anal. Biochem. 132. 6-13 (1983)]. Blots were exposed to Kodak X-Omat RP XRP-5 film for five to 10 min at room temperature.
• RNA gel blots each containing 15 ⁇ g total RNA from mature leaves, immature leaves, stem apices, internode 1. internode 2, internode 3, roots, and callus cultures at control (26°C) and heat shock (37°C) temperatures, were hybridized to each of the four
• RNA from each indicated tissue was hybridized to equal activities of each gene-specific probe.
• Ethidium bromide stained gel indicates equal loading of RNA from each tissue.
• M.L. mature leaves; I.L., immature leaves; S.A., shoot apex; II , internode 1 ; 12, internode 2; 13, internode 3; R, roots; C, callus 26°C; C-HS, callus 37°C.
• Autoradiogram for scubi221 probe was exposed for 72 h. all others for 16 h. With this exposure time of 16 h, transcripts homologous to scubi221 were not detected except in callus tissue under 37°C heat-shock, where a single band was barely detectable.
• the scubi241/51 1 probe detected transcripts of two size classes (on the 16 h autoradiogram exposure shown in Figure 1 the two bands overlap, however on shorter exposures two bands can be resolved), with both transcripts present in approximately equal amounts in all tested tissues. Transcripts for this sub-family were present at the highest levels of all tested polyubiquitin genes; heat shock at 37°C did not induce a significant change in transcript accumulation.
• the scubi561 probe also detected two mRNA size classes; however, the levels of these transcripts were considerably lower than those detected with the 241/51 1 probe. Transcript pools hybridizing to the 561 probe were elevated significantly by 37°C heat shock.
• the scubi5121 probe hybridized to a single size class that was moderately abundant, but significantly lower than the scubi241/511 pool.
• the 5121 levels were very similar in all tissues except callus.
• Callus at control temperature 26°C contained less scubi5121 mRNA than did other tissues; 37°C heat shock elevated transcript levels in callus to levels approximately equal to those in other tissues at 26°C. This pattern of reduced transcript levels in control temperature callus tissue could be seen to some extent for all probes except scubi561.
• sugarcane polyubiquitin genes While expression of these sugarcane polyubiquitin genes was little affected by cell- type, several of them responded dramatically to an environmental stimulus: heat stress. mRNA pools homologous to scubi221, 561 and 5121 in sugarcane callus tissue subjected to 37°C heat shock all rose substantially, whereas the pool homologous to scubi241/511 did not show a substantial increase. Overall, scubi241 and scubi51 1 most nearly fit the stereotype of "constitutive" genes, with uniformly high levels of mRNA accumulation in all tested tissues and little induction of expression by heat stress.
• Subclone pubi4 sequence and organization were initially determined to be as shown in Figures 3 A, 3B and 4.
• Tables 1-2 provide the meaning of sequence symbols other than the bases G, A, T, and C which indicates ambiguities where two or more bases are equally possible in the sequences shown in Figures 3A and 3B.
• KS+ (Stratagene) to generate plasmids pubi4a and pubi4b. Plasmids pubi4a and pubi4b were introduced into the host Escherichia coli DH5alpha and the transformed Escherichia coli cells were deposited at the Agricultural Research Service Culture Collection (NRRL) under the terms of the Budapest Treaty on March 8, 1999 as NRRLB-30112 (containing pubi4a) and NRRLB-301 14 (containing pubi4b). NRRLB-30112 contains the 2227 bp EcoRI/Sall fragment of SEQ ID NO:5, i.e., including the 1802 bp 1802 bp SEQ ID NO:7, plus the first coding repeat and part of the second repeat.
• NRRLB-301 14 contains the 3329 bp S ⁇ /I/EcoRI fragment which includes the remainder of the coding region, the 3' UTR, and further downstream sequences.
• An Xbal restriction site was added at the 3 ' end of the ubi4 promoter shown in S ⁇ Q
• Table 3 shows the ambiguity codes and the bases they represent in the ubi4 sequences shown in Figures 5 and 10.
• Subclone pubi4 ( Figures 3, 4, 5 and 6) contained four copies of the polyubiquitin coding repeat, 238 bp of 3' UTR, which is approximately 95%) identical to the corresponding region of the scubi241/511 cDNAs, a possible poly- A addition signal 215 bp 3 * of the TAA stop codon, and approximately 2.6 kb of further downstream sequence.
• the pubi4 subclone contained an additional 377 bp upstream of the transcription start codon, with a TATA consensus at -30 bp relative to the beginning of the cDNAs. Approximately 320 bp upstream of the transcription start codon were two 10 bp sequences that showed homology to the heat stress promoter element (HSE) consensus sequence (aGAAnnTTCt) [Scharf et al.: Heat stress promoters and transcription factors. In: Nover L (ed) Plant Promoters and Transcription Factors, pp. 125-162. Springer- Verlag, Berlin (1994)]. The second of these 10 bp sequences, however, lacked the G residue at position two that has been found to be invariant in HSEs [Scharf et al. (1994) supra].
• HSE heat stress promoter element
• Subclone pubi9 sequence and organization were initially determined to be as shown in Figures 7A, 7B and 4.
• Tables 4-5 provide the meaning of sequence symbols other than the bases G, A, T, and C which indicates ambiguities where two or more bases are equally possible in the sequences shown in Figures 7 A and 7B.
• An Xbal restriction site was added at the 3 ' end of the ubi9 promoter shown in SEQ ID NO: 10 by way of PCR amplification with an Xbal adapter primer.
• the ubi9 promoter so modified was ligated upstream of a GUS coding sequence and a NOS 3' terminator in the vector plasmid pUC19 to form pubi9-GUS.
• This plant expression plasmid was transformed into E. coli DH5a host cells and deposited with the NRRL under the terms of the Budapest Treaty on March 15, 1999 as accession number NRRLB-30116.
• Subclone pubi9 ( Figures 4, 6, 7 and 8) contained five copies of the polyubiquitin coding repeat. 244 bp of 3' UTR, which were 98%> identical to the corresponding region of scubi241/51 1 and 95%> identical to the corresponding region of pubi4.
• a possible poly-A addition signal was present 221 bp down stream of the TAA stop codon, and there was approximately 2 kb additional downstream sequence.
• an intron was located immediately 5' of the initiation codon; this intron was 1374 bp.
• the subclone contained an additional 2247 bp of upstream sequence, including a TATA consensus sequence at -30 bp relative to the beginning of the cDNA clones.
• upstream of the 5'UTR a 577 bp region of ubi9 from position 1671 to 2248 of SEQ ID NO:10 was highly homologous (>90% identity) to the corresponding region of ubi4 (positions 1 to 377 of SEQ ID NO:5). Partial sequence from an additional subclone of ⁇ ubi4 indicated that this high degree of homology continues at least as far as 2kb upstream of the transcribed region of the genes (unpublished data). Within this highly homologous region, approximately 344 bp upstream of transcription start codon, is an apparent insertion of approximately 200 bp not
• this insertion is not believed to have a functional role in the promoter activity of the polyubiquitin ubi9 promoter since this insertion is inserted in the 3 'UTR (not the promoter) of the glucose transporter gene, and since it is not present in the polyubiquitin ubi4 gene.
• the ubi9 gene also contained two HSE-like sequences about 320 bp upstream of the transcription start codon; however, both of these HSE-like sequences lacked the invariant G residue.
• a comparison of the sequences upstream of the translation start codon of the sugarcane ubi9 gene sequence with the maize polyubiquitin promoter showed only 61%) homology when comparing a fragment containing the sequence upstream of the 5' UTR, the 5' UTR sequence and the intron sequence, only 63%> homology when comparing a fragment containing the sequence upstream of the transcription start codon, only 66%> homology when comparing a fragment containing the 5 'UTR sequence, and only 59% homology when comparing a fragment containing the intron sequence.
• HSEs Some heat-shock-inducible polyubiquitin promoters have been found to contain HSEs (Binet, et al., 1991 , supra; Christensen et al. (1992) supra]. Both the ubi4 and ubi9 genes contained two short sequence elements that have some homology to HSEs; however, three out of four of these elements lacked the G residue that has been found to be invariant at position 2 of the HSE (aGAAnnTTCt) (Scharf et al. (1994) supra]. Given the very marginal
• Both the ubi4 and ubi9 genes contained a large intron immediately upstream of the protein coding region preceded by an approximately 65 bp fragment which was highly homologous to the 5 * UTR of scubi241/511.
• An intron at this position i.e., immediately upstream of the initiation codon has been found in many other plant polyubiquitin genes
• the cDNA clones scubi241 and scubi511 contain three and five copies of the polyubiquitin coding sequence, respectively.
• Genomic clones pubi4 and pubi9 contain four and five copies of the polyubiquitin coding sequence, respectively. Without limiting the invention to any particular mechanism, this may mean that the scubi241/51 1 sub-family contains at least three different genes, containing three (i.e., scubi 241/511), four (i.e., pubi4) and five (i.e., pubi9) ubiquitin repeats.
• the difference in the number of copies of the polyubiquitin coding sequence reflects a difference between the cultivars, with the scubi241/511 sub-family in H65-7052 containing genes with three and five ubiquitin repeats, while the same sub-family in H32-8560 contains genes with four and five ubiquitin repeats.
• Reporter plasmids were made placing the uid A gene encoding ⁇ -glucuronidase (GUS) [Jefferson et al, Proc. Natl. Acad. Sci. USA 83, 8447-8451 (1986)] and the nopaline synthase (NOS) terminator under the control of the sugarcane polyubiquitin promoter disclosed herein.
• GUS ⁇ -glucuronidase
• NOS nopaline synthase
• the promoter sequence in plasmid pubi4-GUS contained nucleotides 1-1810 of SEQ ID NO:l (i.e.. nucleotides 1-1802 of SEQ ID NO:5) and and Xbal site (TCTAGA) added immediately after bp 1802. by way of an adapter on a PCR primer.
• the promoter sequence in plasmid pubi9-GUS contained nucleotides 1-3688 of SEQ ID NO:3 (i.e.. nucleotides 1-3688 of SEQ ID NO:8) and and Xbal site (TCTAGA) added immediately after bp 3688, by way of an adapter on a PCR primer.
• the ExpandTM PCR system (Boehringer Mannheim) was used to amplify part of the 5' UTR and the intron including the 3 ' splice site; this PCR product was used to join the sequence upstream of the 5' UTR, the 5' UTR, and intron to the GUS gene using a unique Nrul site in the 5' UTR and an Xbal site added as an adapter to the 3 " PCR primer.
• pHA9 contained the maize ubil promoter driving a neomycin phosphotransferase II (NPTll) gene and NOS terminator.
• 35S-GUS contained the uid A gene encoding GUS under the control of the cauliflower mosaic virus (CaMV) 35S R ⁇ A promoter sequence (Clontech).
• Binary plasmids 9PI-GUS, 4PI-GUS and MPI-GUS for Agrobacterium transformation were made by ligating the promoter-intron-GUS- ⁇ OS cassettes from pubi9-GUS, pubi4-GUS, and pAHC27 [Christensen et al. (1996) supra] respectively, as Hindlll - EcoRI fragments, into the Hindlll - EcoRI sites of pCAMBIA1300 [Roberts et al. Rockefeller Foundation
• Binary plasmid pHW537 contained a putative 5' nuclear matrix attachment region (MAR) from ⁇ ubi4, ubi9 promoter and intron, GUS, and 3' terminator and putative 3' MAR from ⁇ ubi4 as Hindlll - EcoRI fragment in the Hindlll - EcoRI sites of pCAMBIA1300.
• MAR nuclear matrix attachment region
• Sugarcane suspension cell cultures (variety H50-7209) were maintained as described by [ ⁇ ickell et al, Physiol. Plant. 22, 117-125 (1969)].
• D ⁇ A reporter plasmids (pubi4-GUS, pubi9-GUS.or pAHC27) were introduced into sugarcane suspension culture cells by particle bombardment as previously described [Klein et al, Nature 327, 70-73 (1987)] using a PDS1000 Biolistic particle accelerator (BioRad) at 1100 psi. Controls were not bombarded
• Transient assays were carried out in a randomized complete block design with four treatments (promoters) and six replications. Each replication consisted of bombardment of five samples. Two days after bombardment, plant material was assayed for GUS expression. Each sample was divided into two equal parts, one for histochemical analysis and one for chemiluminescent measure of GUS enzyme activity using the GUS-Light kit (Tropix) and an MLX plate reader luminometer (DYNEX). GUS enzyme activity assays were performed according to the manufacturer's protocol, with 60 minutes incubation in GUS reaction buffer before chemiluminescence was measured. GUS activity was expressed as relative light units (RLU) per nanogram total protein [Bradford, Anal. Biochem.
• RLU relative light units
• Figure 9A shows that the average number of blue foci detected after bombardment with GUS expression plasmids containing the ubi9 promoter was higher than observed for either the ubi4 or maize polyubiquitin ubil [Christensen et al. (1996), supra] promoters. Because of high levels of variability, it could not be determined from histochemical staining of these transient expression experiments whether the results seen in sugarcane callus are in fact significantly different. However, using a chemiluminescent assay to measure GUS activity again indicated the average level of expression was higher for the ubi9 promoter than for the sugarcane ubi4 or maize ubil promoters ( Figure 9B). Statistical analysis indicated that the difference, as measured by this assay, was significant at P ⁇ 0.05.
• Tobacco cultivar Wisconsin 38 was grown in Magenta boxes on MSNT medium [IX Murashige and Skoog salts (GIBCO BRL #11117-074), IX minimal organics (GIBCO BRL
• DNA reporter plasmids (pubi4-GUS, pubi9-GUS, or pAHC27) were introduced into tobacco leaves by particle bombardment as previously described [Klein et al, (1987) supra] using a PDS1000 Biolistic particle accelerator (BioRad) at 650 psi. Controls were not bombarded with DNA. Transient assays were carried out in a randomized complete block design with four treatments
• Sorghum immature embryo derived callus was cultured and bombarded as previously described with the reporter plasmid ubi4-GUS or ubi9-GUS (prepared as described in Example 2) and with several reporter plasmids in which the uid A gene encoding GUS was
• Culture media N6 maintenance medium [Macro elements (mg/1 final concentration), 2830 KNO 3 ,
• the Petri dish containing the target callus tissue was placed in the biolistic device and 10 ml of the DNA-gold suspension pipetted onto the center of a macroprojectile. The distance between the stopping plate and the target callus tissue was adjusted to 13 cm. The tissue was bombarded under vacuum with the rupture disk strength at 1 100 p.s.i.
• Pineapple cultivar F153 leaves, protocorm-like bodies (plbs), roots and fruit were bombarded with a reporter plasmid [pAHC27, pubi9-GUS or 35S-GUS] described supra (Example 2).
• Target tissue (leaves, plbs, roots and fruit) was plated in the center (2.5 cm
• Histochemical GUS staining was performed 48 hours following bombardment to determine transient transformion. Five (5) or three (3) replicates were performed for each promoter in each type of bombarded tissue. The number of blue foci/plate of each bombarded tissue is shown in Table 4.
• Agrobacterium strain EHA105 [Hood et al. J. Bacteriol. 168:1291-1301 (1986)] was used to transform rice callus.
• Reporter plasmids (9PI-GUS. 4PI-GUS, MPI-GUS, or
• Rice callus was induced from scutellum tissue of rice (cv. Taipei 309) and transformed by Agrobacterium co-cultivation as previously described [Hiei et al, (1994) supra]. After 2- 3 months on selection medium containing 100 mg/1 hygromycin B (CalBiochem), small calli from selected lines were assayed for GUS activity by the chemiluminescence method described supra (Example 3).
• PCR using one primer within the T-DNA and one outside of the T-DNA right border was used to confirm the absence of Agrobacterium contamination in tested callus lines using methods known in the art. Because rice transformation was by Agrobacterium. there is the possibility that the Agrobacterium were not killed after transformation, and thus that the GUS expression seen is from the Agrobacterium, not from transgenic rice cells. To test for this possibility, two PCRs were performed: one to test for the presence of the GUS gene, the second to test for the presence of vector plasmid sequences outside of the T-DNA. The Agrobacterium harbor a binary plasmid, one section of which contains the GUS encoding gene under the control of sugarcane promoter sequences.
• This section of the vector plasmid is called the T-DNA, and only this part is ordinarily transferred to the plant genome.
• a positive PCR for GUS indicates that the isolate plant DNA may be successfully amplified by PCR and the GUS gene is pressent (i.e., confirming the observation of GUS activity).
• a negative PCR for the vector plasmid outside of the T-DNA confirms that the entire plasmid, which is what is present in the Agrobacterium, is no longer present, i.e., that the T-DNA (which contains the GUS sequences under the control of the sugarcane promoter sequences) is successfully integrated into the plant genome.
• transgenic rice callus lines were selected following co-cultivation of rice callus with Agrobacterium which had been transformed with the 4PI-GUS, 9PI-GUS, pHW537, and MPI-GUS reporter plasmids, respectively.
• GUS expression in six transgenic lines transformed with the ubi9 promoter sequence is shown in Figure 13.
• GUS expression in six transgenic lines transformed with the ubi9 promoter sequence averaged 681.0 RLU/ng protein 30 min.
• Four stably transformed transgenic rice callus lines were selected following co- cultivation of rice callus with Agrobacterium which had been transformed with the pHW537 reporter plasmid.
• GUS expression in these transgenic lines averaged 567.7 RLU/ng protein/30 min. Since the pHW537 reporter plasmid differed from the 9PI-GUS plasmid in
• Agrobacterium tumefaciens was used to transform tobacco leaves.
• Reporter plasmids (9PI-GUS, 4PI-GUS, MPI-GUS, or 35S-GUS, which were prepared as described in Example
• MSNTS liquid media per liter of medium: one package MS salt mix [GIBCO BRL #111 17-066], 30 g sucrose, 1.0 ml 1000X B5 vitamins, 50 ⁇ l 2 mg/ml ⁇ -naphthaleneacetic acetic acid [GIBCO BRL #21570-015], and 50 ⁇ l 20 mg/1 benzyladenine [GIBCO BRL #16105-017]).
• Aseptically grown tobacco leaves were harvested and placed in petri plates containing 20 ml MSNTS with 0.6 ml of the resuspended Agrobacterium and cut into approx. 1 cm squares with a sterile scalpel. After one to five minutes the leaf pieces were removed from the liquid, gently blotted on dry sterile paper, and placed on 0.8%> agar MSNT plates (per liter of medium: one package MS salt mix [GIBCO BRL #11 117-066], 30 g sucrose, 1.0 ml 1000X B5 vitamins, 8 g Bacto- Agar) with 500 ⁇ g/ml Cefotaxime (PhytoTechnology Laboratories).
• GUS expression under the control of the maize ubil promoter was greater than that under the control of either the sugarcane ubi4 or ubi9 promoters (data not shown).
• Embryogenic corn cultures are initiated from immature maize embryos, bombarded simultaneously with a reporter plasmid (pubi4-GUS, pubi9-GUS, or mzubil-GUS) and a selection plasmid (pHA9), and stably transformed corn plants regenerated as previously described by Brown et al, U.S. Patent Number 5,593,874, incorporated by reference.
• a reporter plasmid pubi4-GUS, pubi9-GUS, or mzubil-GUS
• pHA9 selection plasmid
• embryogenic corn cultures are initiated from immature maize embryos of the "Hi-Ir" genotype which had been cultured 18-33 days on N6 2-100-25-Ag medium modified to contain 2 mg/L 2,4-dichlorophenoxyacetic acid, 180 mg/L casein hydrolysate, 25 mm
• L-proline 10 ⁇ M silver nitrate, pH5.8, solidified with 0.2% PhytagelTM (Sigma). These embryogenic cultures are used as target tissue for transformation by particle gun bombardment.
• a 1 1 mixture of the reporter vector (pubi-4-GUS, pubi-GUS or mzubil-GUS) and selection plasmid (pHA9) is precipitated onto tungsten M10 particles by adding 12.5 ⁇ l of particles (25 mg/ml in 50% glycerol), 2.5 ⁇ l plasmid DNA (1 ⁇ g/ ⁇ l), 12.5 ⁇ l 1M calcium chloride, and 5 ⁇ l 0.1M spermidine, and vortexing briefly. The particles are allowed to settle for 20 minutes, after which 12.5 ⁇ l of supernatant is removed and discarded. Each sample of
• the bombarded tissue is transferred to fresh, nonselective medium the day after bombardment.
• the material is transferred to selective media containing 50 mg/L G418 (Agri-bio).
• the cultures are transferred to fresh media which contains 200 mg/L G418.
• the cultures are maintained on the 200 mg/L G418 media, transferred at 2-3 week intervals, until G418-resistant calli could be distinguished.
• G418-resistant calli are recovered from the embryogenic material.
• G418-resistant lines are bulked up and assayed for GUS expression using a histochemical or chemiluminescent assay as described supra (Example 3).
• Plants are regenerated from the G418-resistant calli which express GUS activity in a three step regeneration protocol. All regeneration is performed on 200 mg/L G418. The first two steps are carded out in the dark at 28°C, and the final step under a 16:8 hour photoperiod. at about 25°C. Small green shoots that formed on Regeneration Medium 3 in 100X 25 mm Petri plates are transferred to Regeneration Medium 3 in 200X 25 mm
• the plants are transplanted from the 2.5" pots to 6" pots and finally to 10" pots during growth.
• Corn plants regenerated from G418-resistant embryogenic calli which express GUS activity are tested for GUS expression using histochemical of chemiluminescent assays as described supra (Example 3).
• GUS expression e.g., as determined by blue staining in the histochemical assay or by luminescence in the chemiluminescent assay
• tissue of corn plants which are generated from calli that had been bombarded with pubi4- GUS or pubi9-GUS demonstrates that the ubi4 and ubi9 nucleotide sequences in pubi4-GUS and pubi9-GUS, respectively, are sufficient to direct stable expression in regenerated monocotyledonous maize plants.
• a reporter plasmid (4PI-GUS or 9PI-GUS, prepared as described in Example 2) or a control plasmid (i.e.. a plasmid which contains the uid A gene encoding GUS and which lacks a promoter sequence) are transformed into Agrobacterium. and the transformed Agrobacterium is used to infect tomato plants as previously described in Theologis et al. U.S. Patent Number 5.723,766, incorporated by reference.
• a reporter plasmid or control plasmid is introduced into Agrobacterium strain LBA4404 as follows: Agrobacterium tumefaciens LBA-4404 (2 ml) is grown overnight at
• tomato seeds are sterilized using a protocol which consists of treatment with 70%) ethanol for 2 min with mixing; followed by treatment with 10%) sodium hypochlorite and 0.1 % SDS for 10 min with mixing, followed by treatment with
• Feeder plates are prepared from a tobacco cell suspension in liquid medium at 25°C. prepared with shaking at 130-150 rpm. The suspension is transferred to fresh medium at 1 :10
• Cotyledons from two of the feeder plates are scraped into each tube and rocked gently for 10-30 min.
• the cotyledons are then removed from the bacterial culture onto sterile filter paper (abaxial side up) on a tobacco feeder plate and incubated for 48 h in low light in a growth room.
• the cotyledons are then transferred axial side up to callus inducing medium.
• callus inducing Medium approximately four plates are used per magenta box, and the explants are crowded. The box is placed in a growth room for three weeks, and small masses of callus are expected to form at the surface of the cotyledons.
• the explants are transferred to fresh plates containing the callus inducing medium every three weeks. When the calli exceed
• GUS expression by one or more tissues of tomato plants which are generated from tissue that had been transformed with 4PI-GUS or 9PI-GUS demonstrates that the ubi4 and ubi9 nucleotide sequences in 4PI-GUS and 9PI-GUS. respectively, are sufficient to direct stable expression in regenerated dicotyledonous tomato plants.
• Soybean explants are derived from excised meristems, bombarded simultaneously with a reporter plasmid (pubi4-GUS, pubi9-GUS, or mzubil-GUS) and a selection plasmid (pHA9), and stably transformed soybean plants are regenerated as previously described by Christou et al, U.S. Patent Number 5,015,580, incorporated by reference.
• a reporter plasmid pubi4-GUS, pubi9-GUS, or mzubil-GUS
• pHA9 selection plasmid
• soybean explants of cultivar Williams 82 are derived from meristems excised from the embryonic axes of immature seeds. Primary leaves are removed and the explant plated on a target plate containing 1%> water agar. The explants are transformed with a reporter plasmid or a selection plasmid loaded at 1.0-0.001 ⁇ g/ml of beads. The particle accelerator is charged at 13-16 kV. The carrier is loaded with 0.05-0.40 mg of loaded beads per square centimeter, with a preferred level of loading of 0.2 mg/cm 2 .
• the bombarded explants are then plated in the dark on modified MS basal medium which has a high level (i.e., 13.3 ⁇ M) of the cytokinin benzylaminopurine. Following incubation of 1 to 2 weeks in the dark, the tissues are transferred onto the same basal medium at a lower (1.7 ⁇ M) level of cytokinin to promote shoot elongation. Shoots are harvested at 0.5 to 1 cm in height. The success of the transformation protocol is verified by fixing transformed explants at each stage to assay for GUS activity as described supra (Example 3). Two days after DNA particle injection, dozens of GUS active cells are expected to be detected in each explant. At 6 to 8 weeks, the plants are assayed for GUS activity in the shoot. Most plants are expected to be chimeric, having streaks of blue (i.e., GUS-expression cells) when assayed using the histochemical assay.
• the transformed excised meristem tissue is used to regenerate fully mature, and sexually mature chimeric plants using methods known in the art such as those described in U.S. Patent No. 5,015,580 to Christou et al. (incorporated by reference).
• GUS expression by one or more tissues of soybean plants which are regenerated from excised embryonic meristems that had been transformed with pubi4-GUS or pubi9-GUS demonstrates that the ubi4 and ubi9 nucleotide sequences in pubi4-GUS and pubi9-GUS, respectively, are sufficient to direct stable expression in regenerated dicotyledonous soybean plants.
• the invention provides promoter sequences which are capable of driving transgene expression in both monocotyledonous and dicotyledonous plant cells, and which are useful for generating transgenic plants with desirable agronomic characteristics.

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