The present invention relates to DNA sequences, comprising nucleic acid fragments encoding dehiscence zone-selective proteins, particularly cell wall hydrolases such as polygalacturonases, the regulatory regions of the corresponding plant genes and their use for modifying dehiscence properties in plants, more particularly pod dehiscence properties in Brassica napus. 
Loss of yield due to seed shedding by mature fruits or pods, also called pod dehiscence or pod shatter, as well as concomitant increase in volunteer growth in the subsequent crop year, are a universal problem with crops that develop dry dehiscent fruits. An economically important crop to which these adverse properties specifically apply is oilseed rape: up to 50% of the potential yield may be lost under adverse weather conditions.
Dry dehiscent fruits, also commonly called pods, may develop from a single carpel (such as the legume in many Fabaceae) or from more than one carpel (such as the silique in many Brassicaceae). In case of the silique, the pod consists of two carpels joined margin to margin. The suture between the margins forms a thick rib, called replum. As pod maturity approaches, the two valves separate progressively from the replum, eventually resulting in the shattering of the seeds that were attached to the replum.
Ultrastructural investigation have demonstrated that pod shatter is associated with the precise degradation of cell wall material at the site of pod valve separation (i.e., the suture). The degradation of the cell wall and loss of cellular cohesion prior to dehiscence is predominantly attributed to solubilization of the middle lamella of the cell wall. This middle lamella is found between primary cell walls and is the cement that holds the individual cells together to form a tissue. Cell separation is preceded by an ethylene climacteric, which temporally correlates with a tissue-specific increase in the activity of the hydrolytic enzyme cellulase (beta-1,4-glucanase) and this occurs specifically in a layer of cells along the suture, which is called the dehiscence zone. In contrast, the activity of the cell wall degrading enzyme polygalacturonase exhibits no correlation either temporally or spatially with pod dehiscence [Meakin and Roberts (1990), J. Exp. Bot. 41; 1003]. Pod dehiscence at an early stage of development is characteristic of infestation by the pod midge Dasineura brassicae. A localized enhancement of both polygalacturonase and cellulase activity has been observed. However, regulation of midge-induced and maturation-associated shatter was found to be different [Meakin and Roberts (1991), Annals of Botany 67: 193].
At first sight, the process of pod dehiscence shares a number of features with abscission wherein plants shed organs, such as leaves, flowers and fruits. It has been observed that ethylene induces or accelerates abscission, whereas auxin inhibits or delays abscission. A decisive step in abscission is the highly coordinated expression, synthesis and secretion of cell wall hydrolytic enzymes in a discrete layer of cells, called the abscission zone. Cellulases (beta-1,4-glucanases) constitute one class of such cell wall hydrolases. Cellulase activity has been identified in various tissues including leaf abscission zones, fruit abscission zones, ripening fruit, senescent cotyledons and styles and anthers [Kemmerer and Tucker (1994), Plant Physiol. 104: 557 and references therein]. A second class of hydrolases involved in abscission of mainly fruits are polygalacturonases of which distinctive isoforms have been identified [Bonghi et al.(1992), Plant Mol. Biol. 20: 839; Taylor et al (1990) Planta 183: 133].
Kadkol et al [(1986), Aust. J. Biol. 34: 79] reported increased resistance towards shattering in a single, Australian accession of rape. Variation in pod maturation has further been observed in mutants of rape stemming from irradiated seeds [Luczkiewicz (1987), Proc. 7th Int. Rapeseed Congress 2: 463]. It can however be concluded that traditional methods for breeding have been unsuccessful in introducing shatter resistance into rape cultivars, without interference in other desirable traits such as early flowering, maturity and blackleg resistance [Prakash and Chopra (1990), Genetical Research 56: 1].
Despite its economic impact very little is known concerning the molecular events and changes in gene expression that occur during oilseed pod dehiscence. At present, two pod-specific mRNAs whose expression is spatially and temporally correlated with pod development have been described. However, the function of the encoded proteins is unknown. [Coupe et al (1993), Plant Mol. Biol. 23: 1223; Coupe et al. (1994), Plant Mol. Biol. 24: 223]. PCT publication WO94/23043 in general terms describes an approach for regulating plant abscission and dehiscence.
Accordingly, it is an object of the present invention to provide dehiscence zone-selective genes in plants.
These and other objects are achieved by the present invention, as evidenced by the summary of the invention, description of the preferred embodiments and claims.
The present invention provides dehiscence zone(xe2x80x9cDZxe2x80x9d)-selective genes of plants, cDNAs prepared from mRNAs encoded by such genes, and promoters of such genes. In particular this invention provides the cDNA of SEQ ID NO: 1 and the promoter of a gene encoding a mRNA wherein a cDNA of that mRNA has substantially the nucleotide sequence of SEQ ID NO: 1, particularly the promoter as contained within the 5xe2x80x2 regulatory region of SEQ ID NO: 14 starting at position 1 and ending at position 2,328.
In another aspect, the present invention also provides DZ-selective chimeric genes, that can be used for the transformation of a plant to obtain a transgenic plant that has modified dehiscence properties, particularly modified pod-dehiscence properties, when compared to plants that do not contain the DZ-selective chimeric gene, due to the expression of the DZ-selective chimeric gene in the transgenic plant.
In yet another aspect, the present invention thus provides a plant containing at least one DZ-selective chimeric gene incorporated in the nuclear genome of its cells, wherein said DZ-selective chimeric gene comprises the following operably linked DNA fragments:
a) a transcribed DNA region encoding:
1) a RNA which, when produced in the cells of a particular DZ of the plant, prevents, inhibits or reduces the expression in such cells of an endogenous gene of the plant, preferably an endogenous DZ-selective gene, encoding a cell wall hydrolase, particularly an endo-polygalacturonase (an xe2x80x9cendo-PGxe2x80x9d), or,
2) a protein or polypeptide, which when produced in cells of the DZ, kills or disables them or interferes with their normal metabolism, physiology or development,
b) a plant expressible promoter which directs expression of the transcribed DNA region at least in cells of the DZ, provided that if the transcribed DNA region encodes a protein or polypeptide, or encodes an antisense RNA or ribozyme directed to a sense RNA encoded by an endogenous plant gene that is expressed in the plant in cells other than those of the DZ, the plant expressible promoter is a DZ-selective promoter, i.e., a promoter which directs expression of the transcribed region selectively in cells of the DZ.
Preferably the transcribed DNA region encodes a protein or polypeptide which is toxic to the cells in which it is produced, such as a barnase; a protein or polypeptide that increases the level of auxins or auxin analogs in the cells in which it is produced, such as a tryptophan monooxygenase and/or a indole-3-acetamide hydrolase; a protein or polypeptide that increases the sensitivity to auxin in the cells in which it is produced, such as the roIB gene product; or a protein or polypeptide that decreases the sensitivity to ethylene in the cells in which it is produced, such as the mutant ETR1-1 protein or a another ethylene receptor protein.
In another preferred embodiment of this invention, the transcribed DNA encodes an RNA, such as an antisense RNA or a ribozyme, part of which is complementary to the mRNA encoded by a gene which is naturally expressed in the DZ, preferably a DZ-selective gene.
As used herein, the term xe2x80x9cdehiscencexe2x80x9d refers to the process wherein a plant organ or structure, such as an anther or fruit, opens at maturity along a certain line or in a definite direction, resulting in the shedding of the content of said organ or structure. In some of its aspects the process of dehiscence is reminiscent of the process of abscission, wherein a part or organ, such as a leaf, flower or fruit, is separated from the rest of the plant.
As used herein, the term xe2x80x9cpodxe2x80x9d means a dry dehiscent fruit that consists of one, two or more carpels. In oilseed rape the pod is a bivalve silique, wherein the valves are delineated by longitudinal dorsal and ventral sutures, which comprise the dehiscence zones.
As used herein, the term xe2x80x9cpod dehiscencexe2x80x9d means the process wherein a fruit, particularly a pod, splits open along a discrete layer of cells, eventually resulting in the separation of the valves and subsequent shedding of the seeds contained within the fruit, particularly the pod. Pod dehiscence occurs in a large variety of plants that develop dry fruits, such as in most genera of the Cruciferae.
The term xe2x80x9cdehiscence zonexe2x80x9d (DZ) in its most general sense includes the tissues in the zone along which a plant organ or structure splits open during the process of dehiscence. Macroscopically the DZ can usually be recognized by the presence of a clear suture in the organ. In the strict sense the DZ may comprise a region of only 1-3 parenchymatous cells wide. In a pod, this region usually comprises densely packed cells and is adjacent to the periphery of vascular tissue of the replum separating it from the valve edges. For the purpose of this invention the DZ may also include the cell layers surrounding this region. The DZ extends from the locule of the pod to the epidermal suture.
As used herein, the term xe2x80x9cpromoterxe2x80x9d denotes any DNA which is recognized and bound (directly or indirectly) by a DNA-dependent RNA-polymerase during initiation of transcription. A promoter includes the transcription initiation site, and binding sites for transcription initiation factors and RNA polymerase, and can comprise various other sites (e.g., enhancers), at which gene regulatory proteins may bind.
As used herein, the term xe2x80x9cplant-expressible promoterxe2x80x9d means a promoter which is capable of driving transcription in a plant cell. This includes any promoter of plant origin, but also any promoter of non-plant origin which is capable of directing transcription in a plant cell, i.e., certain promoters of viral or bacterial origin such as the CaMV 35S or the T-DNA promoters.
The term xe2x80x9cregulatory regionxe2x80x9d, as used herein, means any DNA, that is involved in driving transcription and controlling (i.e., regulating) the timing and level of transcription of a given DNA sequence, such as a DNA coding for a protein or polypeptide. For example, a 5xe2x80x2 regulatory region (or promoter region) is a DNA sequence located upstream (i.e., 5xe2x80x2) of a coding sequence and which comprises the promoter and the 5xe2x80x2-untranslated leader sequence. A 3xe2x80x2 regulatory region is a DNA sequence located downstream (i.e., 3xe2x80x2) of the coding sequence and which comprises suitable transcription termination (and/or regulation) signals, including one or more polyadenylation signals.
As used herein, the term xe2x80x9ccell wall hydrolasexe2x80x9d means an enzyme that is involved in the degradation of cell wall material, e.g., during the process of dehiscence. Examples of such enzymes include, but are not limited to, polygalacturonase, cellulase (beta-1,4-glucanase), beta-galactosidase, proteases hydrolyzing cell wall proteins, and the like.
The term xe2x80x9cgenexe2x80x9d means any DNA fragment comprising a DNA region (the xe2x80x9ctranscribed DNA regionxe2x80x9d) that is transcribed into a RNA molecule (e.g., a mRNA) in a cell under control of suitable regulatory regions, e.g., a plant expressible promoter. A gene may thus comprise several operably linked DNA fragments such as a promoter, a 5xe2x80x2 untranslated leader sequence, a coding region, and a 3xe2x80x2 untranslated region comprising a polyadenylation site. An endogenous plant gene is a gene which is naturally found in a plant species. A chimeric gene is any gene which is not normally found in a plant species or, alternatively, any gene in which the promoter is not associated in nature with part or all of the transcribed DNA region or with at least one other regulatory regions of the gene.
The term xe2x80x9cexpression of a genexe2x80x9d refers to the process wherein a DNA region under control of regulatory regions, particularly the promoter, is transcribed into an RNA which is biologically active i.e., which is either capable of interaction with another nucleic acid or which is capable of being translated into a biologically active polypeptide or protein. A gene is said to encode an RNA when the end product of the expression of the gene is biologically active RNA, such as an antisense RNA or a ribozyme. A gene is said to encode a protein when the end product of the expression of the gene is a biologically active protein or polypeptide.
The phenotypic effect of expression of a gene refers to the biochemical, physiological and/or developmental effects of the production of the RNA or protein, encoded by the gene, on the plant cells (or plants) in which it is produced. Phenotypic effects of gene expression may be reduced or prevented by reducing or preventing the production of the encoded RNA or protein, or by otherwise interfering with the biological activity of such RNA or protein.
As defined herein, whenever it is stated in the specification that a xe2x80x9ccDNA of such mRNA comprises the nucleotide sequence of SEQ ID NO: Xxe2x80x9d the RNA thus has the same nucleotide sequence as represented in SEQ ID NO: X except that the U-residues (in the RNA sequence) are replaced by T-residues (in the DNA sequence).
In accordance with this invention, DZ-selective cDNAs and their corresponding plant genomic DNA fragments are identified as follows:
1) a cDNA library is constructed starting from mRNA isolated from DZ tissue and the cDNA library is subjected to differential screening in order to identify an mRNA which is selectively present in tissues of a particular DZ when compared to other plant tissues including but not limited to: pod walls, seeds, replum, leaves, stems, roots, reproductive organs, and the like. Alternatively, the cDNA library is screened with oligonucleotides, that are deduced from a determined amino acid sequence of an isolated protein, such as, for example, a cell wall hydrolase, that is identified to be selectively present in the DZ. Furthermore, it is possible to use the same oligonucleotides in a nested-PCR approach and to use the amplified fragment(s) as a probe to screen the library. The DZ-selective cDNA library can be constructed from a pool of mRNAs, isolated at different stages of DZ development;
2) a cDNA, encoding the DZ-selective mRNA or protein, is isolated and characterized;
3) this cDNA is used as a probe to identify and isolate the region in the plant genome, comprising the nucleotide sequence encoding the DZ-selective mRNA or protein. Alternatively, the genomic DNA can be isolated utilizing inverse PCR using oligonucleotides deduced from the cDNA sequence; and
4) optionally, RNA probes corresponding to the cDNAs are constructed and used in conventional RNA-RNA in-situ hybridization analysis [see e.g., De Block et al. (1993), Anal. Biochem. 215: 86] of different plant tissues, including the particular DZ of interest, to confirm the selective presence of the mRNA produced by the presumed DZ-selective endogenous plant gene in that DZ.
The term xe2x80x9cdehiscence zone-selectivexe2x80x9d, with respect to the expression of a DNA in accordance with this invention, refers to, for practical purposes, the highly specific, preferably exclusive, expression of a DNA in cells of one particular DZ, particularly a pod DZ, or a limited series of DZs.
Thus a DZ-selective gene is an endogenous gene of a plant that is selectively expressed in the cells of certain dehiscence zones, particularly in the cells of the pod dehiscence zone of the plant. Any plant which possesses the DZ of interest may be used for the isolation of DZ-selective genes. Suitable plants for the isolation of DZ-selective genes are plants of the family Cruciferae including but not limited to Arabidopsis thaliana, Brassica campestris, Brassica juncea, and especially Brassica napus; plants of the family Leguminosae including but not limited to Glycine max, Phaseolus vulgaris and the like. The mRNA (or the cDNA obtained thereof) transcribed from such a gene is a DZ-selective mRNA (or cDNA). A promoter that drives and controls the transcription of such a mRNA is referred to as a DZ-selective promoter. A DZ-selective promoter can for instance be used to express a cytotoxic gene (e.g., a barnase gene) in a plant so that normal growth and development, and agronomical performance (as measured for instance by seed yield) of the plant is not negatively affected by expression of the cytotoxic gene in cells other than the DZ cells, preferably in cells other than the pod DZ cells.
Once the DZ-selective gene (i.e., the genomic DNA fragment, encoding the DZ-selective mRNA from which the DZ-selective cDNA can be prepared) is obtained, the promoter region containing the DZ-selective promoter is determined as the region upstream (i.e., located 5xe2x80x2 of from the codon coding for the first amino acid of the protein encoded by the mRNA. It is preferred that such promoter region is at least about 400 to 500 bp, preferably at least about 1000 bp, particularly at least about 1500 to 2000 bp, upstream of the start codon. For convenience, it is preferred that such promoter region does not extend more than about 3000 to 5000 bp upstream of the start codon. The actual DZ-selective promoter is the region of the genomic DNA upstream (i.e., 5xe2x80x2) of the region encoding the DZ-selective mRNA. A chimeric gene comprising a DZ-selective promoter operably linked to the coding region of the gus gene [Jefferson et al. (1986), Proc. Natl. Acad. Sci. USA 83: 8447] will selectively produce, in transgenic plants, detectable beta-glucuronidase activity (encoded by the qus gene)in the cells of the particular DZ of interest, as assayed by conventional in-situ histochemical techniques [De Block and Debrouwer (1992), The Plant Journal 2: 261; De Block and Debrouwer (1993), Planta 189: 218].
Preferred DZ-selective genes from which DZ-selective promoters can be obtained, are genes, preferably Brassica napus genes, that encode a DZ-selective mRNA from which a cDNA can be prepared that contains the sequence corresponding to the sequence of oligonucleotide PG1 (SEQ ID NO: 3) between nucleotide positions 11 and 27 and/or the sequence of oligonucleotide PG3 (SEQ ID NO: 5) between nucleotide positions 11 and 27 (i.e. starting at position 11 and ending at position 27); and/or contains the sequence complimentary to the oligonucleotide PG2 (SEQ ID NO: 4) between nucleotide positions 11 and 25 and/or the sequence of the oligonucleotide PG5 (SEQ ID NO: 6) between nucleotide positions 11 and 27. Preferably, such DZ-selective cDNA contains aforementioned sequences of oligonucleotides PG1 and PG3 and PG2 and PG5, or encodes a protein encoded by the region of SEQ ID NO: 1 between nucleotide positions 95 and 1,393.
A particularly preferred DZ-selective gene is the Brassica napus gene that encodes a DZ-selective mRNA from which a cDNA can be prepared that contains the sequence of SEQ ID NO: 1 at least between nucleotides 10 and 1600. Another preferred DZ-selective gene is the Brassica napus gene, that encode a DZ-selective mRNA from which a cDNA can be prepared that contains the sequence of SEQ ID NO: 11.
A preferred promoter of the present invention is the promoter contained in the 5xe2x80x2 regulatory region of a genomic clone corresponding to the cDNA of SEQ ID NO: 1, e.g. the 5xe2x80x2 regulatory region with the sequence of SEQ ID NO: 14 starting at position 1 and ending at position 2,328. A convenient promoter region is the DNA fragment comprising the sequence of SEQ ID NO: 14 starting anywhere between the unique SphI site (positions 246-251) and the HindII site (positions 1,836-1,841), particularly between the SphI site and the BamHI site (positions 1,051-1,056), and ending at nucleotide position 2,328 (just before the ATG translation start codon). Such a promoter region comprises the DZ-selective promoter of the subject invention and the 5xe2x80x2 untranslated leader region and is used for the construction of DZ-selective chimeric genes. In this regard a particular useful promoter region is the DNA fragment (hereinafter referred to as xe2x80x9cPDZxe2x80x9d) with the sequence of SEQ ID NO: 14 between positions 251 (the SphI site) and 2,328.
However, smaller DNA fragments can be used as promoter regions in this invention and it is believed that any fragment of the DNA of SEQ ID NO: 14 which contains at least the about 490 basepairs, more preferably at least about 661 basepairs and most preferably about 1326 basepairs, upstream from the translation inititation codon can be used. Particularly preferred smaller fragments to be used as promoter region in this invention have a DNA sequence comprising the sequence of SEQ ID NO: 14 between nucleotides 1002 and 2328.
It is assumed that DZ-specificity of the promoter of the 5xe2x80x2 regulatory region of SEQ ID NO: 14 can be considerably improved by inclusion of the nucleotide sequence of SEQ ID NO: 14 between nucleotides 1002 and 1674. Therefore promoters comprising this nucleotide sequence are particularly preferred.
Alternatively, artificial promoters can be constructed which contain those internal portions of the promoter of the 5xe2x80x2 regulatory region of SEQ ID NO: 14 that determine the DZ-selectivity of this promoter. These artifical promoters can contain a xe2x80x9ccore promoterxe2x80x9d or xe2x80x9cTATA box regionxe2x80x9d of another promoter capable of expression in plants, such as a CaMV 35S xe2x80x9cTATA box regionxe2x80x9d as described in WO 93/19188. Suitable promoter fragments or artificial promoters can be identified, for example, by their approriate fusion to a reporter gene (such as the gus gene) and the detection of the expression of the reporter gene in the appropriate tissue(s) and at the appropriate developmental stage. It is known that such smaller promoters and/or artificial promoters comprising those internal portions of the 5xe2x80x2 regulatory region of SEQ ID NO:. 14 that determine the DZ selectivity can provide better selectivity of transcription in DZ-specific cells and/or enhanced levels of transcription if the transcribed regions of the DZ-selective chimeric genes of the invention.
Besides the actual promoter, the 5xe2x80x2 regulatory region of the DZ-selective gene of this invention also comprises a DNA fragment encoding a 5xe2x80x2 untranslated leader (5xe2x80x2UTL) sequence of an RNA located between the transcription start site and the translation start site. It is believed that the 5xe2x80x2 transcription start site is located between position 2,219 and 2,227 (in SEQ ID NO: 14), resulting in a 5xe2x80x2UTL of about 102 to 110 nucleotides in length. It is also believed that this region can be replaced by another 5xe2x80x2UTL, such as the 5xe2x80x2UTL of another plant-expressible gene, without substantially affecting the specificity of the promoter.
Other useful DZ-selective genes or cDNAs for use in this invention are those isolated from other sources, e.g., from other cultivars of B. napus or even from other plant species, for instance by using the cDNA of SEQ ID NO: 1 (or SEQ ID NO: 11) as a probe to screen genomic libraries under high stringency hybridization conditions using conventional methods as described in Nucleic Acid Hybridization: A Practical Approach (1985), IRL Press Ltd UK (Eds. B. D. Hames and S. J. Higgins). A useful gene for the purpose of this invention is thus any gene characterized by encoding a mRNA from which a cDNA variant can be prepared that contains a coding region with a nucleotide sequence that is essentially similar to that of the coding region of the cDNA clone of SEQ ID NO: 1, and coding for a protein with polygalacturonase activity. Also promoter regions and promoters can be identified, for example, using such cDNA variants, which are essentially similar to a promoter region or promoter with a sequence as contained in SEQ ID NO: 14.
With regard to nucleotide sequences (DNA or RNA), such as sequences of cDNAs or of regulatory regions of a gene, xe2x80x9cessentially similarxe2x80x9d means that when two sequences are aligned, the percent sequence identityxe2x80x94i.e., the number of positions with identical nucleotides divided by the number of nucleotides in the shorter of the two sequencesxe2x80x94is higher than 80%, preferably higher than 90%, especially with regard to regulatory regions. The alignment of the two nucleotide sequences is performed by the Wilbur and Lipmann algorithm [Wilbur and Lipmann (1983), Proc. Nat. Acad. Sci. U.S.A. 80: 726] using a window-size of 20 nucleotides, a word length of 4 nucleotides, and a gap penalty of 4.
Two essentially similar cDNA variants will typically encode proteins that are essentially similar to each other. For example, a variant of the cDNA of SEQ ID NO: 1 will typically encode a protein with an amino acid sequence which is essentially similar to the amino acid sequence of the protein encoded by the cDNA of SEQ ID NO: 1. With regard to xe2x80x9camino acid sequencesxe2x80x9d, essentially similar means that when the two relevant sequences are aligned, the percent sequence identityxe2x80x94i.e., the number of positions with identical amino acid residues divided by the number of residues in the shorter of the two sequencesxe2x80x94is higher than 80%, preferably higher than 90%. The alignment of the two amino acid sequences is performed by the Wilbur and Lipmann algorithm [Wilbur and Lipmann (1983), Proc. Nat. Acad. Sci. U.S.A. 80: 726] using a window-size of 20 amino acids, a word length of 2 amino acids, and a gap penalty of 4. Computer-assisted analysis and interpretation of sequence data, including sequence alignment as described above, can be conveniently performed using the programs of the Intelligenetics(trademark) Suite (Intelligenetics Inc., CA).
In accordance with this invention, the DZ-selective cDNAs and genomic DNAs, as well as the regulatory regions obtained from the genomic DNAs are used to modify the dehiscence properties in plants, particularly pod dehiscence properties in Brassica napus. 
Thus, in accordance with this invention, a recombinant DNA is provided which comprises at least one DZ-selective chimeric gene comprising a plant expressible promoter and a transcribed DNA region, one or both of which is derived from a DZ-selective gene of this invention.
Expression of a DZ-selective chimeric gene in a transgenic plant will have phenotypic effects only in the cells of the DZ. Thus, expression of a DZ-selective gene may selectively prevent, suppress, inhibit or reduce the phenotypic effects of expression of endogenous plant genes in a certain dehiscence zone (such as a pod DZ), may selectively kill or disable cells of the dehiscence zone, or may interfere with the normal metabolism of DZ cells, resulting in the delay or prevention of dehiscence, particularly pod dehiscence. For the purpose of this invention, a plant cell (such as a DZ cell) is killed or disabled if either all biochemical and/or physiological processes of the cell are stopped or, alternatively, if the biochemical and/or physiological processes of the cell are changed to effectively reduce the extracellular production of at least one enzyme involved in the degradation of plant cell walls, particularly a pectin degrading enzyme such as a polygalacturonase, preferably by at least 30%, particularly by at least 75%, more particularly by at least 90%.
For the purpose of the present invention, the phenotypic effects of expression of an endogenous gene in a plant cell is prevented, suppressed, inhibited or reduced if the amount of mRNA and/or protein produced by the cell by expression of the endogenous gene is reduced, preferably by at least 30%, particularly by at least 75%, more particularly by at least 90%.
Plants, in which dehiscence is delayed to different extents, or even prevented, are produced by transforming a plant with a recombinant DNA comprising at least one DZ-selective chimeric gene of this invention whose expression in the plant results in the production of RNA or a protein or polypeptide which interferes to different degrees with the normal functioning of the cells of the dehiscence zone, for example, by reducing the phenotypic effects of expression of one or more endogenous genes that encode cell wall hydrolytic enzymes, or by killing the DZ cells. A delay in the onset of dehiscence, particularly fruit dehiscence, whereby pre-harvest shattering of seeds can be reduced or prevented, will find its application in those plants that suffer from pre-mature (i.e., prior to harvest) seed loss.
In a preferred embodiment of the present invention the DZ-selective chimeric gene comprises a transcribed DNA region which is transcribed into an RNA the production of which in the cells of the DZ reduces, inhibits or prevents the expression of an endogenous gene, preferably a gene encoding a cell wall hydrolase, particularly an endo-polygalacturonase, in the cells of the DZ. The reduction of the expression of the endogenous gene can be demonstrated by the reduction of the cytoplasmic levels of the mRNA normally produced by the endogenous gene. The endogenous gene as isolated from the plant will hereinafter be designated as the sense gene which encodes a sense mRNA (or sense pre-mRNA, i.e., an unprocessed mRNA which may include intron regions).
It is preferred that the endogenous sense gene encodes an enzyme involved in cell wall hydrolysis, preferably a pectin-degrading enzyme, such as a pectin esterase, a pectin methyl esterase, a pectin lyase, a pectate lyase, a polygalacturonase and the like, and particularly an endo-PG. It is believed that pectin degrading enzymes, particularly endo-polygalacturonases, play an important role in the degradation of the middle lamella material of plant cell walls and in the process of dehiscence, and that selective inhibition of the production of such enzymes in the dehiscence zone or in the region surrounding the dehiscence zone (e.g., by expression of an antisense RNA to the endo-PG encoding mRNA) on the average delays pod shatter for at least 1 day, preferably 2-5 days.
Although the sense gene may encode any cell wall hydrolase, that is secreted by the cells of the DZ during the process of dehiscence, and that is involved in the degradation of cell wall material in a certain dehiscence zone, such as for example a cellulase, a glucanase, or a beta-galactosidase, it is preferred that the sense gene is an endogenous DZ-selective gene.
Thus, in one aspect of this invention the DZ-selective chimeric gene of this invention encodes an antisense RNA which is complementary to at least part of a sense mRNA or sense pre-mRNA. Such antisense RNA is said to be directed to the sense RNA (or sense pre-mRNA). In this regard, the encoded antisense RNA comprises a region which is complementary to a part of the sense mRNA or sense pre-mRNA, preferably to a continuous stretch thereof of at least 50 bases in length, preferably of at least between 100 and 1000 bases in length. The upper limit for the length of the region of the antisense RNA which is complementary to the sense RNA is of course the length of the full-length sense pre-mRNA, or to the full length sense mRNA (which may or may be not processed from a sense pre-mRNA), produced by the plant cells can be used. However, the antisense RNA can be complementary to any part of the sequence of the sense pre-mRNA and/or of the processed sense mRNA: it may be complementary to the sequence proximal to the 5xe2x80x2 end or capping site, to part or all of the 5xe2x80x2 untranslated region, to an intron or exon region (or to a region bridging an exon and intron) of the sense pre-mRNA, to the region bridging the noncoding and coding region, to all or part of the coding region including the 3xe2x80x2 end of the coding region, and/or to all or part of the 3xe2x80x2 untranslated region. In case the sense gene is a member of a gene family, it is preferred that the antisense RNA encoded by the DZ-selective chimeric gene of this invention contains a sequence which is complementary to a region of the sense RNA, e.g., a DZ-selective sense RNA, of at least 50 nucleotides and which has a percent sequence identity (see above) of less than 50%, preferably less than 30%, with any region of 50 nucleotides of any sense RNA encoded by any other member of the gene family.
The transcribed DNA region in the DZ-selective chimeric gene of this invention can also encode a specific RNA enzyme, or so-called ribozyme (see, e.g., WO89/05852), capable of highly specific cleavage of the sense mRNA or sense pre-mRNA. Such ribozyme is said to be directed to the sense RNA (or sense pre-mRNA).
Expression of the endogenous gene producing a sense mRNA in a plant can also be inhibited or repressed by a DZ-selective chimeric gene which encodes part or all, preferably all, of such sense RNA [Jorgensen et al. (1992), AgBiotech News Info 4: 265N].
The sense RNA to which the antisense RNA or ribozyme encoded by the DZ-selective chimeric gene of this invention is directed is preferably a mRNA, wherein a (doublestranded) cDNA of such mRNA comprises the nucleotide sequence of SEQ ID NO: 1 (or SEQ ID NO: 11) or variants thereof. A preferred region of the sense RNA to which the antisense RNA or ribozyme encoded by the DZ-selective chimeric gene of this invention is directed comprise a nucleotide sequence of SEQ ID NO:. 1 starting anywhere between nucleotide 890 and 950 and ending anywhere between nucleotide 1560 and 1620. Another preferred region of the sense RNA to which the antisense RNA or ribozyme encoded by the DZ-selective chimeric gene of this invention is directed comprise a nucleotide sequence of SEQ ID NO:. 1 starting anywhere between nucleotide 1280 and 1340 and ending anywhere between nucleotide 1560 and 1620, such as, but not limited to, the nucleotide sequence between nucleotides 1296 and 1607.
A DZ-selective chimeric gene encoding a antisense RNA or ribozyme, as described above, is preferably under the control of a DZ-selective promoter. Particularly useful DZ-selective promoters are the promoters from the DZ-selective genes described above, particularly the promoter as conained within the 5xe2x80x2 regulatory region of SEQ ID NO: 14 between position 1 and 2,328. However, if the DZ-selective gene encodes an antisense RNA and/or ribozyme which is directed to a sense RNA produced by an endogenous DZ-selective gene, preferably a gene encoding a endo-polygalacturonase, it is not required that the promoter of the DZ-selective chimeric gene be a DZ-selective promoter. Nevertheless, in such case the promoter of the DZ-selective gene should direct expression at least in cells of the DZ. Indeed, because the sense RNA is produced selectively in the cells of the DZ, the production of the antisense RNA or ribozyme encoded by the DZ-selective gene in cells other than the cells of the DZ, will not have a noticeable phenotypic effect on such cells. Examples of promoters that direct expression at least in cells of the DZ are constitutive plant expressible promoters such as the promoter (P35S) of the 35S transcript of Cauliflower mosaic virus (CaMV)[Guilley et al. (1982), Cell 30: 763], or the promoter (Pnos) of the nopaline synthase gene of Agrobacterium tumefaciens [Depicker et al. (1982), J. Mol. Appl Genet. 1: 561].
In another preferred embodiment of this invention, the DZ-selective chimeric gene encodes an mRNA which, when produced in plant cells, is translated into a protein or polypeptide which interferes with the metabolism and/or physiology of the plant cells. In most cases production of such protein or polypeptide will be undesired in cells other than the DZ cells and in this regard it is preferred that such chimeric genes comprise a DZ-selective promoter. Particular useful DZ-selective promoters are again the promoters from the DZ-selective genes described above.
In one aspect of this invention the DZ-selective chimeric gene of this invention comprises a transcribed DNA region encoding a protein the activity of which will result in an increase in biologically active auxins or auxin analogs within the cells. Such protein may for instance be involved in auxin biosynthesis, such as tryptophan monooxygenase and/or the indole-3-acetamide hydrolase, encoded by the Agrobacterium tumefaciens T-DNA gene 1 (iaaM) and/or gene 2 (iaaH), respectively [Gielen et al. (1984), The EMBO J. 3: 835], or may be the amidohydrolase, encoded by the Arabidopsis thaliana ILR1 gene, which releases active indole-3-acetic acid (IAA) from IAA-conjugates [Bartel and Fink (1995), Science 268: 1745]. In view of the observed decline in IAA levels prior to pod dehiscence (see Example 1), it is believed that production of such auxin increasing proteins selectively in the DZ cells of a plant, will not result in the killing of the cells due to overproduction of IAA, but will rather result in the maintenance and/or restoration of the IAA levels substantially as found before the observed decline. This delays the onset of pod dehiscence, through a prolonged inhibition by IAA of production and/or activity of cell wall hydrolytic enzyme normally produced by the cells in the dehiscence zone.
Alternatively the transcribed DNA region of the DZ-selective chimeric gene of this invention can comprise the open reading frame of the Agrobacterium rhizogenes roIB gene [Furner et al. (1986), Nature 319: 422]. Expression of such DZ-selective chimeric gene in a plant will result in an increase of the sensitivity of the plant cells towards auxin through the production of the roIB gene product in cells of the pod DZ thereby countering the normal decline in IAA concentration in the DZ prior to pod shattering.
In another aspect of the present invention, the DZ-selective chimeric gene of this invention comprises a transcribed DNA region encoding a protein, the activity of which results in a decrease of the sensitivity towards ethylene of the plant cells in which it is produced. Indeed, several genes involved in the ethylene signal transduction pathway in plants have been identified by mutational analysis (e.g. ETR1, ETR2, EIN4, ERS, CTR1, EIN2, EIN3, EIN5, EIN6, HLS1, EIR1, AUX1, EIN7) and for a number of them, the corresponding genes have been cloned [Chang (1996), TIBS 21:129; Bleecker and Schaller (1996), Plant Physiol 111:653]. It is thought that ETR1, ETR2, EIN4, ERS all encode ethylene receptors, while the rest of the genes would be involved in the ethylene signal transduction pathway downstream of the receptors [Ecker (1995), Science 268: 667]. The ethylene receptors which have been sequenced, bear homology to the receiver domain of the response regulator component and/or to the histidine protein kinase domain of the sensor component of the so-called bacterial two-component regulators and are divided in two classes according to the presence or absence of the receiver domain homology. Class I ethylene receptors comprise both the sensor and receiver homologous domains and are exemplified by ETR1 (Arabidopsis), and eTAE1 (tomato). Class II ethylene receptors comprise only the domain homologous to the histidine protein kinase domain of the sensor component and are exemplified by ERS (Arabidopsis) and NR (tomato). Receptors encoded by mutant alleles of the identified genes confer a dominant insensitivity to ethylene [Chang (1996), supra; Bleecker and Schaller (1996), supra]. Therefore an example of a DZ-selective chimeric gene, comprising a transcribed DNA region encoding a protein whose activity results in a decrease of the sensitivity towards ethylene of the plant cells in which it is produced, is one which comprises the open reading frame of a dominant, ethylene-insensitive, mutant allele of the Arabidopsis thaliana ETR1 gene, such as ETR1-1 [Chang et al. (1993), Science 262: 539]. A plant in which such DZ-selective chimeric gene is expressed produces a mutant ethylene receptor (the ETR1-1 protein) selectively in the cells of the DZ and these cells therefore become insensitive towards the phytohormone ethylene and do not respond (metabolically) to changes in the concentration of the hormone, such as the ethylene climacteric observed prior to the onset of pod dehiscence. It is thought that alternatively, a transcribed DNA region comprising an open reading frame of a dominant, ethylene-insensitive, mutant allele of any one of the mentioned class I ethylene receptors can be used to the same effect. In another example of such a DZ-selective chimeric gene, conferring ethylene-insensitivity to the plants cells expressing the DZ-selective chimeric gene, a transcribed DNA region comprising an open reading frame of a dominant, ethylene-insensitive, mutant allele of any one of the mentioned class II ethylene receptors, such as the Arabidopsis thaliana ERS gene [Hua et al. (1995), Science 269: 1712] or the tomato NR gene [Wilkinson et al. (1995), Science 270:1807] can be used for the same purpose.
It is further assumed that the rest of the products encoded by the genes, involved in the ethylene signal transduction pathway, mentioned above, act downstream of the receptors. For CTR1, EIN2 and EIN3 the genes have been cloned [Ecker (1995), Science 268: 667]. Modulation of the expression of the after genes in the dehiscence zone, e.g. by antisense RNA or ribozyme RNA, transcribed under control of a DZ-specific promoter, which is targetted towards the mentioned genes, will also influence sensitivity towards ethylene.
In another aspect of this invention the DZ-selective chimeric gene of this invention comprises a transcribed DNA region encoding a protein or polypeptide which, when produced in a plant cell, such as a cell of a pod DZ, kills such cell or at least interferes substantially with its metabolism, functioning or development. Examples of such transcribed DNA regions are those comprising DNA sequences encoding ribonucleases such as RNase T1 and especially barnase [Hartley (1988), J. Mol. Biol. 202:913]; cytotoxins such as the A-domain of diphtheria toxin [Greenland et al. (1983), Proc. Natl. Acad. Sci. USA 80: 6853] or the Pseudomonas exotoxin A. Several other DNA sequences encoding proteins with cytotoxic properties can be used in accordance with their known biological properties. Examples include, but are not limited to, DNA sequences encoding proteases such as papain; glucanases; lipases such as phospholipase A2; lipid peroxidases; methylases such as the E. coli Dam methylase; DNases such as the EcoRI endonuclease; plant cell wall inhibitors, and the like.
In still another aspect of this invention the DZ-selective chimeric gene of this invention comprises a transcribed DNA region encoding a protein or polypeptide which is capable of being secreted from plant cells and of inhibiting at least the activity of at least one endo-polygalacturonase that is produced in a dehiscence zone (such as a pod DZ), particularly the endo-PG encoded by the cDNA of SEQ ID NO: 1.
In the DZ-selective chimeric gene of this invention it is preferred that the 5xe2x80x2 untranslated region of encoded RNA is normally associated with the promoter, such as a DZ-selective promoter, of the chimeric gene. However, the 5xe2x80x2 untranslated region may also be from another plant expressible gene. Thus, it is preferred that a DZ-selective chimeric gene of this invention comprises the complete 5xe2x80x2 regulatory region (including the 5xe2x80x2 untranslated region) of a DZ-selective gene. A particularly useful 5xe2x80x2 regulatory region is a region of SEQ ID NO: 14, immediately upstream of position 1,329, preferably a region of at least 490 bp, more preferably a region extending to the first SphI site upstream of position 2,329.
The DZ-selective chimeric genes of this invention preferably also comprise 3xe2x80x2 untranslated regions, which direct correct polyadenylation of mRNA and transcription termination in plant cells. These signals can be obtained from plant genes such as polygalacturonase genes, or they can be obtained from genes that are foreign to the plants. Examples of foreign 3xe2x80x2 transcription termination and polyadenylation signals are those of the octopine synthase gene [De Greve et al. (1982), J. Mol. Appl. Genet 1: 499], of the nopaline synthase gene [Depicker et al. (1982), J. Mol. Appl. Genet. 1: 561] or of the T-DNA gene 7 [Velten and Schell (1985), Nucl. Acids Res. 13: 6998] and the like.
Preferably, the recombinant DNA comprising the DZ-selective chimeric gene also comprises a conventional chimeric marker gene. The chimeric marker gene can comprise a marker DNA that is; under the control of, and operatively linked at its 5xe2x80x2 end to, a plant-expressible promoter, preferably a constitutive promoter, such as the CaMV 35S promoter, or a light inducible promoter such as the promoter of the gene encoding the small subunit of Rubisco; and operatively linked at its 3xe2x80x2 end to suitable plant transcription termination and polyadenylation signals. The marker DNA preferably encodes an RNA, protein or polypeptide which, when expressed in the cells of a plant, allows such cells to be readily separated from those cells in which the marker DNA is not expressed. The choice of the marker DNA is not critical, and any suitable marker DNA can be selected in a well known manner. For example, a marker DNA can encode a protein that provides a distinguishable color to the transformed plant cell, such as the A1 gene (Meyer et al. (1987), Nature 330: 677), can provide herbicide resistance to the transformed plant cell, such as the bar gene, encoding resistance to phosphinothricin (EP 0,242,246), or can provided antibiotic resistance to the transformed cells, such as the aac(6xe2x80x2) gene, encoding resistance to gentamycin (WO94/01560).
The DZ-selective promoters of this invention are believed to be highly specific in activity or effect with regard to directing gene expression in cells of the DZ. However the characteristics (e.g., tissue-specificity) of a promoter contained in a chimeric gene may be slightly modified in some plants that are transformed with such chimeric gene. This can, for example, be attributed to xe2x80x9cposition effectsxe2x80x9d as a result of random integration in the plant genome.
Therefore in some plants transformed with the DZ-selective chimeric gene of this invention low-level expression of the chimeric gene may be observed in certain non-DZ cells. Thus, optionally, the plant genome can also be transformed with a second chimeric gene comprising a second transcribed DNA region, that is under control of a second plant-expressible promoter and that encodes a RNA, protein or polypeptide which is capable of counteracting, preventing or inhibiting the activity of the gene product of the DZ-selective chimeric gene. If the DZ-selective chimeric gene encodes barnase it is preferred that the second chimeric gene encodes a barstar, i.e., an inhibitor of barnase [Hartley (1988), J. Mol. Biol. 202: 913]. Other useful proteins encoded by the second chimeric genes are antibodies or antibody fragments, preferably single chain antibodies, that are capable of specific binding to the protein encoded by the DZ-selective chimeric gene whereby such protein is biologically inactivated.
Preferably the second promoter is capable of driving expression of the second transcribed DNA region at least in non-DZ cells of the plant to counteract, prevent or inhibit the undesired effects of low expression of the DZ-selective chimeric gene in such cells in some transformed plants. Examples of useful second promoters are the CaMV minimal 35S promoter [Benfey and Chua (1990), Science 250: 959] or the promoter of the nopaline synthase gene of Agrobacterium tumefaciens T-DNA [Depicker et al. (1982), J. Mol. Appl. Genet. 1: 561]. Other useful promoters are promoters from genes that are known not to be active in the DZ, such as Brassica napus genes encoding a mRNA from which a cDNA can be prepared that comprises the sequence of SEQ ID. No 8, SEQ ID NO: 10, or SEQ ID NO: 12.
In plants the second chimeric gene is preferably in the same genetic locus as the DZ-selective chimeric gene so as to ensure their joint segregation. This can be obtained by combining both chimeric genes on a single transforming DNA, such as a vector or as part of the same T-DNA. However, in some cases a joint segregation is not always desirable. Therefore both constructs can be present on separate transforming DNAs, so that transformation might result in the integration of the two constructs at different location in the plant genome.
In still a further embodiment of the present invention, a plant with modified dehiscence properties can be obtained from a single plant cell by transforming the cell in a known manner, resulting in the stable incorporation of a DZ-selective chimeric gene of the invention into the nuclear genome.
A recombinant DNA comprising a DZ-selective chimeric gene can be stably incorporated in the nuclear genome of a cell of a plant, particularly a plant that is susceptible to Agrobacterium-mediated transformation. Gene transfer can be carried out with a vector that is a disarmed Ti-plasmid, comprising a DZ-selective chimeric gene of the invention, and carried by Agrobacterium. This transformation can be carried out using the procedures described, for example, in EP 0,116,718. Ti-plasmid vector systems comprise a DZ-selective chimeric gene between the T-DNA border sequences, or at least to the left of the right T-DNA border. Alternatively, any other type of vector can be used to transform the plant cell, applying methods such as direct gene transfer (as described, for example, in EP 0,233,247), pollen-mediated transformation (as described, for example, in EP 0,270,356, WO85/01856 and U.S. Pat. No. 4,684,611), plant RNA virus-mediated transformation (as described, for example, in EP 0,067,553 and U.S. Pat. No. 4,407,956), liposome-mediated transformation (as described, for example, in U.S. Pat. No. 4,536,475), and the like.
Other methods, such as microprojectile bombardment as described, for example, by Fromm et al. [(1990), Bio/Technology 8: 833] and Gordon-Kamm et al. [(1990), The Plant Cell 2: 603], are suitable as well. Cells of monocotyledonous plants, such as the major cereals, can also be transformed using wounded or enzyme-degraded intact tissue capable of forming compact embryogenic callus, or the embryogenic callus obtained thereof, as described in WO92/09696. The resulting transformed plant cell can then be used to regenerate a transformed plant in a conventional manner.
The obtained transformed plant can be used in a conventional breeding scheme to produce more transformed plants with the same characteristics or to introduce the DZ-selective chimeric gene of the invention in other varieties of the same or related plant species. Seeds obtained from the transformed plants contain the DZ-selective chimeric gene of the invention as a stable genomic insert.
The following Examples describe the isolation and characterization of a DZ-selective gene from Brassica napus, the identification of DZ-selective promoter, and the use of such a promoter for the modification of dehiscence properties in plants. Unless stated otherwise in the Examples, all recombinant DNA techniques are carried out according to standard protocols as described in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, NY and in Volumes 1 and 2 of Ausubel et al. (1994) Current Protocols in Molecular Biology, Current Protocols, USA. Standard materials and methods for plant molecular work are described in Plant Molecular Biology Labfax (1993) by R. D. D. Croy, jointly published by BIOS Scientific Publications Ltd (UK) and Blackwell Scientific Publications, UK.
In the examples and in the description of the invention, reference is made to following sequences of the Sequence Listing:
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