Wooden leg gene, promoter and uses thereof

Abstract

The structure and function of a regulatory gene, WOODEN LEG (WOL), is described. The WOL gene is expressed specifically in the vasculature during early stages of embryogenesis with expression continuing throughout development. WOL encodes a novel two component signal transducer and is required for asymmetric cell divisions during vascular tissue morphogenesis. Also described are WOL nucleic acids, WOL gene products, (including, but not limited to, transcriptional products such as mRNAs, antisense, and ribozyme molecules, and translational products such WOL proteins, polypeptides, peptides and fusion proteins related thereto), antibodies to WOL gene products, WOL promoters and regulatory regions and the use of the foregoing to improve agronomically valuable plants.

Description

1. TECHNICAL FIELD

[0002] The present invention generally relates to the WOODEN LEG (WOL) gene family and its promoter. The invention more particularly relates to ectopic expression of members of the WOODEN LEG gene family in transgenic plants to artificially modify plant structures. The invention also relates to utilization of the WOODEN LEG promoter for expression of heterologous gene products in certain tissues and organs during stages of development. In trees, members of the WOODEN LEG gene family are active in the cambial zone of the trunk. Thus, in one embodiment, transgenic expression of WOL coding sequences in trees is used to improve wood production. In another embodiment, the WOL promoter is used to drive expression of a heterologous coding sequence in trees to improve wood production.

2. BACKGROUND OF THE INVENTION

[0003] The plant vascular system is responsible for transporting water, nutrients and photosynthates between plant organs. It also undergoes developmental adaptations such as wood formation, which involve specific proliferation of the vascular tissue. Therefore, the pattern of cell divisions is an important determinant of the cellular organization of this tissue (Esau, 1977, Anatomy of seed Plants. John Wiley & Sons, New York, N.Y., ed. 2.). Vascular tissue is first established during embryogenesis as an undifferentiated procambial tissue in the innermost domain of the plant embryo, enclosed by the epidermal and ground tissue layers (Esau 1977 supra; Steeves & Sussex, 1989, Patterns in Plant Development. Cambridge University Press, Cambridge, UK). After differentiation of the phloem and xylem strands within this domain, cell proliferation originates primarily from the initial cells of the procambial tissue immediately proximal to the mitotically quiescent regions of the terminal meristems (Esau 1977, supra; Steeves and Sussex 1989, supra; Scheres et al. 1994, Development 120:2475-87). Later in development, a lateral meristem (the cambium) is formed, as the undifferentiated cells begin to divide in the procambial tissue between the phloem and xylem strands. There is a high degree of diversity of the cell division patterns within the vascular tissue in plants, especially with regards to the formation and activity of the cambium. Since these patterns are species-specific, it is conceivable that the control of cell proliferation within the vascular tissue is largely under genetic regulation.

[0004] Several factors have been implicated in the regulation of cell proliferation of the vascular tissue. Based on mutation analyses, signal transduction pathways related to auxin (Carland & McHale, 1996, Development 122:1811-9; Oyama et al., 1997, Genes Dev. 11:2983-95; Hardtke & Berleth, 1998, EMBO J. 17:1405-11; Hobbie et al., Development 127:23-32; Steinmann et al., 1999, Science 286:316-8; Koizumi et al., 2000, Development 127:3197-204) and brassinosteroid (Schrick et al., 2000, Genes Dev. 14:1471-84; Jang et al., 2000, Genes Dev. 14:1485-97) phytohormones are involved. Physiological and genetic experiments have also indicated a role for other phytohormones (such as gibberellins, cytokinins and ethylene; see Aloni, 1987, Annu. Rev. Plant Physiol. 38:179-204; Eriksson et al., 2000, Nat Biotechnol. 7:784-8), sucrose (Warren Wilson, 1978, Proc. Roy. Soc. London Series B 203:153-76) and physical pressure (Zimmerman, 1964, The Formation of Wood in Forest Trees. Academic Press, New York, N.Y. pp. 389-404). Furthermore, a few genetic loci have been identified that are essential for normal cell proliferation but function in a yet uncharacterized molecular context (Carland et al., 1999, Plant Cell 11:2123-37; Scheres et al., 1995, Development 121:53-62).

[0005] Root organization is established during embryogenesis. This organization is propagated during postembryonic development by the root meristem. Following germination, the development of the postembryonic root is a continuous process, a series of initials or stem cells continuously divide to perpetuate the pattern established in the embryonic root (Steeves & Sussex, 1972, Patterns in Plant Development, Englewood Cliffs, N.J.: Prentice-Hall, Inc.).

[0006] Due to the organization of the Arabidopsis root, it is possible to follow the fate of cells from the meristem to maturity and identify the progenitors of each cell type (Dolan et al., 1993, Development 119:71-84). The Arabidopsis root is a relatively simple and well characterized organ. The radial organization of the mature tissues in the Arabidopsis root has been likened to tree rings with the epidermis, cortex, endodermis and pericycle forming radially symmetric cell layers that surround the vascular cylinder (Dolan et al., 1993, Development 119:71-84). These mature tissues are derived from four sets of stem cells or initials: i) the columella root cap initial; ii) the pericycle/vascular initial; iii) the epidermal/lateral root cap initial; and iv) the cortex/endodermal initial (Dolan et al., 1993, supra). It has been shown that these initials undergo asymmetric divisions (Scheres et al., 1995, Development 121:53-62). The cortex/endodermal initial, for example, first divides anticlinally (in a transverse orientation). This asymmetric division produces another initial and a daughter cell. The daughter cell, in turn, expands and then divides periclinally (in the longitudinal orientation). This second asymmetric division produces the progenitors of the endodermis and the cortex cell lineages.

[0007] Citation or identification of any reference herein shall not be construed as an admission that such reference is available as prior art to the present invention.

3. SUMMARY OF THE INVENTION

[0008] There is a need in the art for improved methods of regulating the development of tissues and organs in plants, and to express heterologous gene products in certain tissues and organs during selected stages of plant development. This invention provides compositions and methods that address this need. The structure and function of a regulatory gene, WOODEN LEG (WOL), is described. The WOL gene is expressed specifically in the vasculature during early stages of embryogenesis with expression continuing throughout development. WOL expression is essential for a set of asymmetric cell divisions that establish vascular tissue during root and hypocotyl development. The invention provides isolated nucleic acids (which encompass Arabidopsis WOL nucleic acids and orthologs), WOL gene products (including, but not limited to, transcriptional products such as mRNAs, antisense and ribozyme molecules, and translational products such as WOL proteins, polypeptides, peptides and fusion proteins related thereto), antibodies to WOL gene products, WOL regulatory regions and the use of the foregoing to improve agronomically valuable plants, including but not limited to trees.

[0009] The invention is based, in part, on the discovery, identification and cloning of the gene responsible for the wooden leg phenotype. WOL is believed by the inventors to be the first identified gene specifically dedicated for the regulation of vascular patterning in plants. WOL regulates vascular patterning in plants. Furthermore, WOL's structure as a two component hybrid molecule is novel with at least one receiver, and preferably, two receiver domains.

[0010] One aspect of the invention encompasses the heterologous expression of WOL nucleic acids and related nucleotide sequences, and specifically the Arabidopsis WOL nucleic acids or orthologs thereof, in stably transformed higher plant species. Modulation of WOL expression levels can be used to advantageously modify vasculature in transgenic plants and enhance the agronomic properties of such plants.

[0011] Another aspect of the invention encompasses the use of promoters of WOL genes, and specifically the use of the Arabidopsis WOL promoter to control the expression of protein and RNA products in plants. Plant WOL promoters have a variety of uses, including, but not limited to, expressing heterologous nucleic acids in the vascular tissue, including the pericycle, in roots of transformed plants.

[0012] The invention provides nucleic acid molecules that are at least 45% (or 55%, 65%, 75%, 85%, 95%, 98%, or 99%) identical to the nucleotide sequence of SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof.

[0013] The invention provides nucleic acid molecules that are at least 45% (or 55%, 65%, 75%, 85%, 95%, 98%, or 99%) identical to the nucleotide sequence of SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof, wherein such nucleic acid molecules encode polypeptides or proteins that exhibit at least one structural and/or functional feature of a polypeptide of the invention.

[0014] The invention provides nucleic acid molecules that include a fragment of at least 300 (325, 350, 375, 400, 425, 450, 500, 550, 600, 650, 700, 800, 900, 1000, 1200, 1400, 1600, 1800, 2000, 2400, 2600, 2800, 3000, 3200, 3400, 3600, 3800, or 4000) nucleotides of the nucleotide sequence of SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof.

[0015] The invention also provides nucleic acid molecules that include a nucleotide sequence encoding a protein having an amino acid sequence that is at least 45% (or 55%, 65%, 75%, 85%, 95%, 98%, or 99%) identical to the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30.

[0016] The invention also provides nucleic acid molecules that include a nucleotide sequence encoding a protein having an amino acid sequence that is at least 45% (or 55%, 65%, 75%, 85%, 95%, 98%, or 99%) identical to the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30,wherein the protein encoded by the nucleotide sequence also exhibits at least one structural and/or functional feature of a polypeptide of the invention.

[0017] In preferred embodiments, the nucleic acid molecules have the nucleotide sequence of SEQ ID NOs: 1, 2, 3, 4, 25, or 26, or a complement thereof.

[0018] Also provided by the invention are nucleic acid molecules that encode a fragment of a polypeptide having the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30, or a fragment including at least 15 (25, 30, 50, 100, 150, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, or 1400) contiguous amino acids of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29,or 30.

[0019] The invention provides nucleic acid molecules that encode a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule consisting of a nucleic acid sequence encoding SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof under stringent conditions.

[0020] The invention provides nucleic acid molecules that encode a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule consisting of a nucleic acid sequence encoding SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof under stringent conditions, wherein such nucleic acid molecules encode polypeptides or proteins that exhibit at least one structural and/or functional feature of a polypeptide of the invention.

[0021] Also within the invention are isolated polypeptides or proteins having an amino acid sequence that is at least about 60%, preferably 65%, 75%, 85%, 95%, 98%, or 99% identical to the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30.

[0022] Also within the invention are isolated polypeptides or proteins that are encoded by a nucleic acid molecule having a nucleotide sequence that is at least about 60%, preferably 65%, 75%, 85%, 95%, 98%, or 99% identical the nucleic acid sequence encoding SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, and isolated polypeptides or proteins that are encoded by a nucleic acid molecule having a nucleotide sequence that hybridizes under stringent hybridization conditions to a nucleic acid molecule having the nucleotide sequence of SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or complement thereof.

[0023] Also within the invention are isolated polypeptides or proteins that are encoded by a nucleic acid molecule having a nucleotide sequence that is at least about 60%, preferably 65%, 75%, 85%, 95%, 98%, or 99% identical the nucleic acid sequence encoding SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, and isolated polypeptides or proteins that are encoded by a nucleic acid molecule having a nucleotide sequence that hybridizes under stringent hybridization conditions to a nucleic acid molecule having the nucleotide sequence of SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or complement thereof,,wherein such nucleic acid molecules encode polypeptides or proteins that exhibit at least one structural and/or functional feature of a polypeptide of the invention.

[0024] Also within the invention are polypeptides that are naturally occurring allelic variants of a polypeptide that includes the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30, wherein the polypeptide is encoded by a nucleic acid molecule which hybridizes to a nucleic acid molecule having the sequence of SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof, under stringent conditions. Such allelic variant differ at 1%, 2%, 3%, 4%, or 5% of the amino acid residues.

[0025] The invention also provides nucleic acid molecules that hybridize under stringent conditions to a nucleic acid molecule having the nucleotide sequence of SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof. In other embodiments, the nucleic acid molecules are at least 300 (325, 350, 375, 400, 425, 450, 500, 550, 600, 650, 700, 800, 900, 1000, 1200, 1400, 1600, 1800, 2000, 2200, 2400, 2600, 2800, 3000, 3200, 3400, 3600, 3800, 4000, or 4200) nucleotides in length and hybridize under stringent conditions to a nucleic acid molecule consisting of the nucleotide sequence of SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof.

[0026] In other embodiments, the isolated nucleic acid molecules encode an extracellular, transmembrane, cytoplasmic domain, a short N-terminal domain, histidine kinase domain, receiver domain DA, or a receiver domain DB of a polypeptide of the invention.

[0027] The invention is illustrated by working examples, described infra, which demonstrate the isolation and use of Arabidopsis WOL nucleic acids.

[0028] Structural analysis of the deduced amino acid sequence of Arabidopsis WOL protein indicates that WOL encodes a two component signal transducer and is required for asymmetric cell divisions during vascular tissue morphogenesis. Northern analysis and in situ hybridization analysis show expression of Arabidopsis WOL in vascular tissues, including the vascular cylinder and pericycle of mature roots as well as localized expression in the vascular cylinder and pericycle in embryos.

[0029] The invention encompasses methods for altering development of vascular tissues and pericycle in roots and other organs by modifying expression of a WOL protein or polypeptide. In one embodiment, root length is increased by overexpression of a WOL protein or polypeptide. In another embodiment, root length is decreased by disrupting or inactivating the endogenous WOL gene. In other embodiments, properties of wood in trees are altered. In one such embodiment, overexpression of a WOODEN LEG protein or polypeptide in a transgenic plant is used to increase layers of wood (vascular) tissues in trees. In another embodiment, ectopic expression of a WOODEN LEG protein or polypeptide in a transgenic plant is driven by a promoter other than the WOL promoter in order to increase vascular development in certain tissue layers, thus resulting in the formation of more wood. In still other embodiments, the WOL promoters of the invention are linked to a heterologous gene known to be involved in aspects of wood formation and genetically engineered into a plant. Such heterologous genes include, but are not limited to, genes known to have an effect on lignin production and/or composition such as the Caffeic Acid O-Methyltransferase (cOMT) gene of Moyle, et al., 1999. Plant Physiol. 119: 1147 and the SAM gene of Meng and Campbell,1995. Plant Physiol. 108:1749. Genes related to cellulose production and degradation are also of great interest such as the cellulose synthase gene of Arioli et al., 1998. Science 279:717-720. In still other embodiments, a gene controlling pigmentation and aspects of vascular patterning effecting wood grain appearance is expressed under the control of a WOL promoter incorporated into the invention. Thus, the invention provides methods that utilize WOL promoters to improve the quality of wood and/or adjust the characteristics of wood to meet specific, e.g. commercial, specifications.

[0030] The invention also encompasses methods of expressing transgene products in the pericycle and the vascular tissue of the hypocotyl, as well as in other organs, by associating a nucleic acid encoding a gene product of interest with a WOODEN LEG promoter. The various embodiments of the claimed invention presented herein are by the way of illustration and are not meant to limit the invention.

3.1. Definitions/Abbreviations

[0031] As used herein, the terms listed below will have the meanings indicated.

[0032] 35S=Cauliflower mosaic virus promoter for the 35S transcript.

[0033] cDNA=Complementary DNA.

[0034] CAPS=Cleaved amplified polymorphic sequences.

[0035] Cis-regulatory element=A sequence in the proximity of a promoter that confers a specific regulatory response to that promoter. A promoter may be influenced by one or more cis-regulatory elements, each responsible for a particular regulatory response. The cis-regulatory sequence can be located 5′ upstream of the promoter TATA box, in the introns, and 3′ downstream of the coding sequence.

[0036] Coding sequence=A sequence that encodes a complete or partial gene product (e.g., a complete protein or a fragment thereof).

[0037] DNA=Deoxyribonucleic acid

[0038] DNase=Deoxyribonuclease

[0039] EST=Expressed sequence tag

[0040] Functional portion of a promoter=With respect to a promoter, a functional portion is any portion of the promoter that is capable of causing transcription of a linked nucleotide sequence, e.g., a truncated promoter.

[0041] Functionally equivalent=In one embodiment of the invention, “functionally equivalent,” as utilized herein with respect to a WOL nucleic acid (or a WOL protein), refers to a nucleic acid encoding a protein (or a protein) that has the ability to regulate the set of asymmetric cell divisions that establish vascular tissue during root and hypocotyl development, and that indirectly regulates xylem differentiation by controlling the number of cells in the vascular cylinder. In another embodiment of the invention, “functionally equivalent,” as utilized herein with respect to a WOL nucleic acid (or a WOL protein), refers to a nucleic acid encoding a protein (or a protein) that is expressed in a tissue-specific and developmental stage specific manner, and includes one or more of the following: At the globular stage of embryogenesis, expression is apparent in the four innermost cells, which are the precursors of the vascular tissue (procambium). During the heart, torpedo, and nearly mature stages of embryogenesis expression is apparent in the procambium of the developing vasculature at the base of the embryonic leaves, cotyledon shoulders, prospective hypocotyl and embryonic root, including pericycle, through at least five days after germination. In the mature plant, expression is predominantly localized in the root. Within the mature root tissues, expression is limited to the developing vascular cylinder, including the pericycle/vascular initial cells, pericycle, and procambium. In shoots, lower levels of expression are detected in comparison to the root, however tissue specificity could not be determined. In siliques, expression is observed in developing vascular tissues just below the site of fruit attachment. In trees, e.g., Betula, expression is apparent in the vascular cambium and developing vascular tissue.

[0042] Gene product=transcripts or protein encoded by a gene. With respect to the WOL gene, polypeptides or peptide fragments of the WOL protein are referred to as WOL polypeptides or WOL peptides. Fusions of WOL protein, polypeptides, or peptide fragments to an unrelated protein, polypeptide or peptide are referred to herein as WOL fusion proteins.

[0043] GUS=1,3-β-Glucuronidase.

[0044] Initial cell=A cell in its earliest stage of differentiation.

[0045] Isolated nucleic acid molecule=A nucleic acid molecule that is separated from other nucleic acid molecules that are present in the natural source of the nucleic acid molecule. Preferably, an “isolated” nucleic acid molecule is free of nucleic acid sequences preferably protein encoding sequences) that naturally flank the nucleic acid (i.e., sequences located at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. In other embodiments, the “isolated” nucleic acid is free of intron sequences. For example, in various embodiments, the isolated nucleic acid molecule can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived. Moreover, an “isolated” nucleic acid molecule, such as a cDNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.

[0046] mRNA=Messenger RNA.

[0047] Operably linked=A linkage between a promoter and gene sequence such that the transcription of said gene sequence is controlled by said promoter.

[0048] Ortholog=Genes related by common phylogenetic descent that have the same function in various organisms. In a preferred embodiment, potential orthologous genes may be identified using alignment software including the NBLAST and XBLAST programs of Altschul, et al., 1990, J. Mol. Biol. 215:403-410 or the CLUSTAL W multiple sequence alignment program of Thompson, et al., 1994. Nucleic Acids Research, 22:4673-4680, with default parameters set for the respective programs. In a more preferred embodiment, CLUSTAL alignments are further analyzed by generating a phylogenetic tree with the PAUP (Phylogenetic Analysis Using Parsimony) software of David Swofford, 2000. Sinauer Associates, Inc. Sunderland Mass. Orthologous genes, having similar sequences and a common ancestry group together on adjoining branches, further confirming there status as orthologs.

[0049] Paralog=A related gene in the same plant (e.g., Arabidopsis MXH1.16 and F17L21.11 are paralogs of Arabidopsis WOL gene).

[0050] RACE=Rapid amplification of cDNA ends. A method of PCR designed to isolate the ends (either 5′ or 3′) of a particular cDNA clone.

[0051] RNA=Ribonucleic acid.

[0052] RNase=Ribonuclease.

[0053] Vascular cylinder=Vascular tissue of the root, including the pericycle.

[0054] WOL=WOODEN LEG, and is used with respect to nucleic acids, encompasses WOL and its orthologs.

[0055] WOL=WOODEN LEG, and is used with respect to proteins, polypeptides or peptides.

[0056] wol=wooden leg mutant.

[0057] WOL protein means a protein containing sequences or a domain substantially similar to one or more domains of Arabidopsis WOL protein as shown in FIG. 3 (SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30). WOL proteins include WOL ortholog and paralog proteins having the structure and activities described herein.

[0058] The term “substantially similar” or “substantial similarity,” when used herein with respect to two amino acid sequences, means that the two sequences have at least 75% identical residues, preferably at least 85% identical residues, more preferably at least 95% identical residues, and most preferably at least 99% identical residues. The same term, when used herein with respect to two nucleotide sequences, means that the two sequences have at least 70% identical residues, preferably at least 85% identical residues, more preferably at least 95% identical residues, and most preferably at least 99% identical residues. Determining whether two sequences are substantially similar may be carried out using any methodologies known to one skilled in the art, preferably using computer assisted analysis.

[0059] WOL polypeptides and peptides include deleted or truncated forms of the WOL protein, and fragments corresponding to the WOL domains described herein.

[0060] WOL fusion proteins encompass proteins in which the WOL protein or an WOL polypeptide or peptide is fused to a heterologous protein, polypeptide or peptide.

[0061] WOL gene, nucleotides or coding sequences means nucleotides, e.g., genomic DNA or cDNA encoding WOL protein, WOL polypeptides or peptides, or WOL fusion proteins.

[0062] WOL gene products include transcriptional products such as mRNAs, antisense and ribozyme molecules, as well as translational products of the WOL nucleotides described herein including, but not limited to, the WOL protein, polypeptides, peptides and/or WOL fusion proteins.

[0063] WOL promoter is intended to mean the regulatory region native to the WOL gene in a variety of species, which promotes the specific pattern of WOL expression described herein.

[0064] WOL expression pattern is intended to mean a tissue-specific and developmental stage specific expression pattern. By combining their observations obtained from several experimental techniques, including in situ hybridization with WOL mRNA, northern blot analysis, and anatomical analysis of the wol mutant phenotype, the present inventors have discovered that a consistent pattern of expression of WOL emerges. Furthermore, the expression patterns generated by the WOL promoter sequences, when operatively linked to a heterologous reporter gene, match the tissue-specificity of the observed WOL gene expression pattern. This expression pattern of WOL and WOL promoters is tissue-specific and developmental stage specific, and includes one or more of the following: At the globular stage of embryogenesis, expression is apparent in the four innermost cells, which are the precursors of the vascular tissue (procambium). During the heart, torpedo, and nearly mature stages of embryogenesis expression is apparent in the procambium of the developing vasculature at the base of the embryonic leaves, cotyledon shoulders, prospective hypocotyl and embryonic root, including pericycle, through at least five days after germination. In the mature plant, expression is predominantly localized in the root. Within the mature root tissues, expression is limited to the developing vascular cylinder, including the pericycle/vascular initial cells, pericycle, and procambium. In shoots, lower levels of expression are detected in comparison to the root, however tissue specificity could not be determined. In siliques, expression is observed in developing vascular tissues just below the site of fruit attachment. In trees, e.g., Betula, expression is apparent in the vascular cambium and developing vascular tissue.

[0065] The expression pattern of WOL occurs throughout a plant in numerous organs at varying stages of development, but is consistently tissue-specific. The pattern may be utilized to target desired tissues encompassed by the expression pattern, but that targeting is not consistently exclusive to a single organ.

4. BRIEF DESCRIPTION OF THE FIGURES

[0066] FIGS. 1(A-K). Cell lineages in the vascular bundle of primary root in Arabidopsis. Panels A-I are a cross section series of the wild type primary root (3 mm thick sections). (A) is at the level of the quiescent center (QC). (B) 3 mm, (C) 6 mm, (D) 9 mm, (E) 12 mm, (F) 15 mm, (G) 27 mm, (H) 69 mm, and (I) approximately 120 mm above the QC. Panels J and K are longitudinal sections of the primary root. (J) is the primary root from a wild-type Arabidopsis. (K) is the primary root from an Arabidopsis mutant for wol. Cells of the QC are labeled with asterisks. Newly formed cell walls after the cell divisions in the procambium in panels C-G are indicated with small black arrows. The specific set of newly formed cell walls associated with phloem development (panel G) is indicated by two separate sets of three arrows. Prospective protoxylem cells are indicated with thick arrows while the pericycle is indicated by “p” and sieve elements of the protophloem are indicated by “pp”. Scale bar: 30 mm. Schematic: Cell lineages of the vascular bundle. The categories refer to the cell lineages only, the differentiation status of the cells is not known. The first and second maturing sieve elements are indicated as protophloem and metaphloem, respectively.

[0067] FIGS. 2(A-C). WOL is not necessary for metaxylem development. The confocal images were taken from whole-mounts of seedlings stained with fuchsin. (A) is wild type Arabidopsis and shows that the metaxylem is gradually differentiating in an axis flanked by two files of protoxylem cells. (B) is Arabidopsis mutant for wol and shows that the entire vascular bundle is differentiated as protoxylem. (C) is a wol x fass double mutant Arabidopsis and shows that protoxylem and metaxylem organization analogous to that in wild type. Scale bar: 30 mm.

[0068] FIGS. 3(A-D). Molecular cloning of the WOL locus. (A) Fine mapping. RNS1 SEQ ID NO:27) and rga (SEQ ID NO:28) are CAPS (cleaved amplified polymorphic sequences, see Konieczny & Ausubel, 1993, Plant J. 4:403-10) markers at the top of chromosome 2. T23K3/3 (SEQ ID NO:21) and Kin2/4 (SEQ ID NO:22) are the closest markers (designed in this study) for mutations in the BAC T23K3 (SEQ ID NO: 13). The number of recombination events between markers and the wol locus are indicated below the markers. Hatched bar represents the 13.8 kb MscI fragment of the T23K3 BAC clone fragment (cloned in pCOM32), which complemented the wol mutation. (B) Structure of the WOL gene. Exons are indicated as solid bars. Three combinations of dotted lines show the alternative splicing variations of the WOL gene (deposited in GenBank as Accession Numbers AJ278528 (SEQ ID NO:1); AJ278529 (SEQ ID NO:2); and AJ278530 (SEQ ID NO:3). All result in the identical longest open reading frame and code for an identical polypeptide of 1057 amino acids (SEQ ID NO:5). The wol mutation is located in the exon with the asterisk where it converts a cytosine to a thymidine at nucleotide position 972, 855, or 964 (for splice variant 1, 2, or 3 respectively) so that a threonine is converted to an isoleucine at amino acid residue 278 of the WOL protein. The small hatched bar represents the 256 bp probe used in hybridization analyses. (C) Complementation of the wol mutation. Left to right: Cross sections of wol, wol transformed with the pCOM32 construct and wild-type primary roots. Arrows—protoxylem in wild type and rescued root; p—pericycle; pp—sieve elements of protophloem. Scale bar: 30 mm. (D) Wild type root architecture is conferred by complementation of the wol mutation. wol mutant plants were transformed with the pCOM32 construct and displayed lateral branches and indeterminate root growth. (E) Predicted domain structure of WOL. There is a short N-terminal region at residues 1-105 of SEQ ID NO:5 (SEQ ID NO:6). The extracellular receptor domain (hatched bar, residues 127-400 of SEQ ID NO:5 (SEQ ID NO:8) is located between the two transmembrane regions (vertical solid bars) located at residues 106-126 of SEQ ID NO:5 (SEQ ID NO:7) and residues 401-421 of SEQ ID NO:5 (SEQ ID NO:9). The C-terminal domain consists of a histidine kinase domain (H, residues 449-737 of SEQ ID NO:5 (SEQ ID NO:10) and two receiver domains (DA and DB). Receiver domain DA is located at residues 762-893 of SEQ ID NO:5 (SEQ ID NO:1 1) and is followed by receiver domain DB at residues 922-1044 of SEQ ID NO:5 (SEQ ID NO:12). (F) Amino acid sequence alignment. A region in the WOL putative receptor domain which surrounds the wol mutation site was aligned with corresponding regions in two paralogs [F17L21.11 (SEQ ID NO:18) and MXH1.16 (SEQ ID NO:19)] and one ortholog [Dictyostelium discoideum DhkA (SEQ ID NO:17)]. Identical amino acids are indicated by black boxes. The altered amino acid residue in wol (isoleucine at position 278) is shown above the alignment. (G) Northern blot of total RNA from wild-type roots and shoots. Ethidium bromide stained ribosomal RNA is shown as a loading control.

[0069] FIGS. 4(A-H). Localization of WOL mRNA during embryonic and primary root development by in situ hybridization. (A-G) Antisense probe. (A) Longitudinal and (B) cross sections of the wild-type primary root. (C) Cross section of wol primary root; (D) globular stage; (E) late heart stage; (F) torpedo stage; (G) bent-cotyledon stage of the wild-type embryo. (H) Torpedo stage embryo hybridized with a sense WOL probe. The endodermal (e) and the innermost ground tissue (g) layer next to the WOL expression domain are indicated. Scale bar: 50 mm.

[0070] FIGS. 5(A-D). Arabidopsis WOODEN LEG cDNA and protein sequence of the three splice variants. (A) The sequence of WOL splice variant 1. The cDNA sequence (SEQ ID NO:1, GenBank Accession No. AJ278528) of Arabidopsis WOODEN LEG is depicted. The open reading frame of SEQ ID NO:1 extends from nucleotide 140 to 3310 of SEQ ID NO:1 (SEQ ID NO:4). (B) The sequence of WOL splice variant 2. The cDNA sequence (SEQ ID NO:2, GenBank Accession No. AJ278529 of Arabidopsis WOODEN LEG is depicted. The open reading frame of SEQ ID NO:2 extends from nucleotide 23 to 3193 of SEQ ID NO:2 (SEQ ID NO:4). (C) The sequence of WOL splice variant 3. The cDNA sequence (SEQ ID NO:3, GenBank Accession No. AJ278530) of Arabidopsis WOODEN LEG is depicted. The open reading frame of SEQ ID NO:2 extends from nucleotide 132 to 3302 of SEQ ID NO:3 (SEQ ID NO:4). (D) The predicted amino acid sequence of Arabidopsis WOODEN LEG (SEQ ID NO:5) is depicted. The 1057 residue protein is identical for all three splice variants.

[0071] FIGS. 6(A-C). The cDNA sequence and the predicted amino acid sequence of two Betula pendula WOODEN LEG orthologs are depicted. (A) Degenerate primers (SEQ ID NOs:31 and 32) used to isolate WOL genes from Betula pendula. “I” indicates inosine; brackets indicate that any of the enclosed nucleotides can be found at that position. (B) WOL gene 1 cDNA (SEQ ID NO: 25) and protein sequence (SEQ ID NO: 29) are depicted. (C) WOL gene 2 cDNA (SEQ ID NO: 26) and protein sequence (SEQ ID NO: 30) are depicted.

[0072] FIGS. 7(A-D). WOL promoter sequence. The WOL promoter sequence is located in the region 5′ to the transcription start site. The DNA sequence that includes this promoter is depicted (SEQ ID NO:33). The ATG denoted in bold represents the transcription start site of WOL.

[0073] FIG. 8. DNA sequence (SEQ ID NO: 36) of the 2.7 kb WOL promoter incorporated into the heterologous expression constructs WOLpro::GUS and WOLpro:GFP. See Section 6.8 for details.

[0074] FIGS. 9(A-H). Expression patterns in Arabidopsis driven by the WOL promoter of SEQ ID NO: 36 linked to a reporter transgene. (A) GUS staining of the stipe and silique base of a wol mutant plant transformed with the WOLpromoter::GUS construct; (B) GUS staining of a Columbia ecotype seedling transformed with the WOLpromoter::GUS construct six days after germination; (C, D) GUS staining of the apical meristem of a Columbia ecotype seedling transformed with the WOLpromoter::GUS construct six days after germination; (E, F) GUS staining of the apical meristem of a wol mutant seedling transformed with the WOLpromoter::GUS construct six days after germination; (G) GUS staining of the root tip of a Columbia ecotype seedling transformed with the WOLpromoter::GUS construct five days after germination; (H) GFP expression in the root tip of a Columbia ecotype seedling transformed with the WOLpromoter::GFP construct five days after germination. See Section 6.8 for details.

5. DETAILED DESCRIPTION OF THE INVENTION

[0075] The invention provides WOODEN LEG (WOL) nucleic acids (including, but not limited to, WOL promoters and nucleic acid sequences, WOL gene products, including, but not limited to, transcriptional products such as mRNAs, antisense and ribozyme molecules, and translational products such as the WOL protein, polypeptides, peptides and fusion proteins related thereto; antibodies to WOL gene products; WOL regulatory regions; and the use of the foregoing to improve agronomically valuable plants.

[0076] The WOL nucleic acids and promoters of the present invention have a number of important agricultural uses. The WOL promoters of the invention may be used, for example, in expression constructs to express desired heterologous gene products in the embryo, root, vascular cylinder, and pericycle of transgenic plants transformed with such constructs. In a specific embodiment, a WOL promoter may be used to express the gene product of a disease resistance gene, such as a lysozyme, cecropin, maganin, or thionin, for anti-bacterial protection. In another embodiment, a WOL promoter may be used to express a pathogenesis-related (PR) protein such as a glucanase or a chitinase for anti-fungal protection. WOL promoters also may be used to express a variety of pest resistance genes in the aforementioned plant structures and tissues. Examples of useful gene products for controlling nematodes or insects include Bacillus thuringiensis endotoxins, protease inhibitors, collagenases, chitinase, glucanases, lectins, and glycosidases.

[0077] Gene constructs that express or ectopically express WOL, and the WOL-suppression constructs of the invention in vascular tissues may be used to alter the structure of organs in transgenic plants. Since one function of WOL is to regulate cell divisions in the root, overexpression of WOL can be used to increase division of certain cells in roots and thereby form thicker and stronger roots. Thicker and stronger roots are beneficial in preventing plant lodging. Conversely, suppression of WOL expression can be used to decrease cell division in roots and thereby form thinner roots. Thinner roots are more efficient in uptake of soil nutrients. The invention also encompasses methods of directing expression in, but not exclusive to, root structures by associating a gene of interest with a WOL promoter.

[0078] In one embodiment, transgenic expression of WOL coding sequences in trees is used to improve wood production. In another embodiment, the WOL promoter is used to drive expression of a heterologous coding sequence in trees to improve wood production.

[0079] Further, a WOL nucleic acid may be used as a molecular marker for a qualitative trait, e.g., longer roots or enhanced wood production, in molecular breeding of crop plants.

[0080] For purposes of clarity, and not by way of limitation, the invention is described in the subsections below in terms of (a) WOL nucleic acids; (b) WOL gene products; (c) antibodies to WOL gene products; (d) WOL promoters and promoter elements; (e) transgenic plants that ectopically express WOL; (f) transgenic plants in which endogenous WOL expression is suppressed; and (g) transgenic plants in which expression of a transgene of interest is controlled by a WOL promoter.

5.1. WOL Nucleic Acids

[0081] The WOODEN LEG (WOL) nucleic acids of the invention include: (a) a nucleic acid comprising the nucleotide sequence shown in SEQ ID NOs:1, 2, or 3, or a segment of such nucleotide sequence; (b) a nucleic acid that encodes a protein comprising the amino acid sequence depicted in SEQ ID NO:5, or a segment of such amino acid sequence, or any segment of such genes and/or nucleotide sequences; (c) any nucleic acid comprising a nucleotide sequence that hybridizes to the complement of any one of the nucleic acids and/or nucleotide sequences described in (a) or (b) above, or any segment of such nucleic acids and/or nucleotide sequences, under highly stringent conditions, e.g., hybridization to filter-bound DNA in 0.5 M NaHPO4, 7% SDS, 1 mM EDTA at 65° C., and washing in 0.1×SSC/0.1% SDS at 68° C. (Ausubel. et al., eds., 1989, Current Protocols in Molecular Biology, Vol. 1, Green Publishing Associates, Inc., and John Wiley & Sons, Inc., New York, at p. 2.10.3) and that encodes a gene product functionally equivalent to a WOL gene product; (d) any nucleic acid comprising a nucleotide sequence that hybridizes to the complement of any one of the nucleic acids and/or nucleotide sequences described in (a) or (b) above, or any segment of such nucleic acids and/or nucleotide sequences, under less stringent conditions, such as moderately stringent conditions, e.g., washing in 0.2×SSC/0.1% SDS at 42° C. (Ausubel et al., 1989, supra), and that encodes a functionally equivalent WOL gene product; (e) any nucleic acid comprising a nucleotide sequence that hybridizes to the complement of any one of the nucleic acids and/or nucleotide sequences described in (a) or (b) above, or any segment of such nucleic acids and/or nucleotide sequences, under the following low stringency conditions: pre-hybridization in hybridization solution containing 43% formamide, 5×SSC, 1% SDS, 10% dextran sulfate, 0.1% sarkosyl, 2% block (Genius kit, Boehringer-Mannheim), followed by hybridization overnight at 30° to 33° C., followed by washing in 2×SSC/0.1% SDS two times for 15 minutes at room temperature and then two times at 50° C., and that encodes a functionally equivalent WOL gene product; and/or (f) any nucleic acid comprising a nucleotide sequence that encodes a polypeptide or protein containing a WOL domain as shown in SEQ ID NOs:6, 7, 8, 9, 10, 11, or 12 or a segment of such polypeptide or protein.

[0082] FIG. 3 indicates exon and intron boundaries of the WOL gene. Nucleic acid molecules comprising WOL exon and intron sequences are encompassed by the present invention. In one embodiment, ten exons are included (SEQ ID NO:1; GenBank Accession No. AJ278528). WOL exon 1 encompasses nucleotides 1 to 132 of the sequence shown in SEQ ID NO:1; exon 2 encompasses nucleotides 133 to 682 of the sequence shown in SEQ ID NO:1; exon 3 encompasses nucleotides 683 to 919 of the sequence shown in SEQ ID NO:1; exon 4 encompasses nucleotides 920 to 1089 of the sequence shown in SEQ ID NO:1; exon 5 encompasses nucleotides 1090 to 1308 of the sequence shown in SEQ ID NO:1; exon 6 encompasses nucleotides 1309 to 1547 of the sequence shown in SEQ ID NO:1; exon 7 encompasses nucleotides 1548 to 1777 of the sequence shown in SEQ ID NO:1; exon 8 encompasses nucleotides 1778 to 1876 of the sequence shown in SEQ ID NO:1; exon 9 encompasses nucleotides 1877 to 3081 of the sequence shown in SEQ ID NO: 1; and exon 10 encompasses nucleotides 3082 to 3620 of the sequence shown in SEQ ID NO:1.

[0083] In another embodiment ten exons are included (SEQ ID NO:2, GenBank Accession No. AJ278529). This is the splice variant that is most predominantly found in vivo. WOL exon 1 encompasses nucleotides 1 to 15 of the sequence shown in SEQ ID NO:2; exon 2 encompasses nucleotides 16 to 565 of the sequence shown in SEQ ID NO:2; exon 3 encompasses nucleotides 566 to 802 of the sequence shown in SEQ ID NO:2; exon 4 encompasses nucleotides 803 to 972 of the sequence shown in SEQ ID NO:2; exon 5 encompasses nucleotides 973 to 1191 of the sequence shown in SEQ ID NO:2; exon 6 encompasses nucleotides 1192 to 1430 of the sequence shown in SEQ ID NO:2; exon 7 encompasses nucleotides 1431 to 1660 of the sequence shown in SEQ ID NO:2; exon 8 encompasses nucleotides 1661 to 1759 of the sequence shown in SEQ ID NO:2; exon 9 encompasses nucleotides 1760 to 2964 of the sequence shown in SEQ ID NO:2; and exon 10 encompasses nucleotides 2965 to 3503 of the sequence shown in SEQ ID NO:2.

[0084] In yet another embodiment, eleven exons are included (SEQ ID NO:3, GenBank Accession No. AJ278530). WOL exon 1 encompasses nucleotides 1 to 47 of the sequence shown in SEQ ID NO:3; exon 2 encompasses nucleotides 48 to 124 of the sequence shown in SEQ ID NO:3; exon 3 encompasses nucleotides 125 to 674 of the sequence shown in SEQ ID NO:3; exon 4 encompasses nucleotides 675 to 911 of the sequence shown in SEQ ID NO:3; exon 5 encompasses nucleotides 912 to 1081 of the sequence shown in SEQ ID NO:3; exon 6 encompasses nucleotides 1082 to 1300 of the sequence shown in SEQ ID NO:3; exon 7 encompasses nucleotides 1301 to 1539 of the sequence shown in SEQ ID NO:3; exon 8 encompasses nucleotides 1540 to 1769 of the sequence shown in SEQ ID NO:3; exon 9 encompasses nucleotides 1770 to 1868 of the sequence shown in SEQ ID NO:3; exon 10 encompasses nucleotides 1869 to 3073 of the sequence shown in SEQ ID NO:3; and exon 11 encompasses nucleotides 3074 to 3612 of the sequence shown in SEQ ID NO:3.

[0085] The invention also includes nucleic acid molecules, preferably DNA molecules, that hybridize to, and are therefore the complements of the nucleotide sequences (a) through (f), in the first paragraph of this section. Such hybridization conditions may be highly stringent, less highly stringent, or low stringency as described above. In instances wherein the nucleic acid molecules are oligonucleotides (“oligos”), highly stringent conditions may refer, e.g., to washing in 6×SSC/0.05% sodium pyrophosphate at 37° C. (for 14-base oligos), 48° C. (for 17-base oligos), 55° C. (for 20-base oligos), and 60° C. (for 23-base oligos). These nucleic acid molecules may act as WOL antisense molecules, useful, for example, in WOL gene regulation and/or as antisense primers in amplification reactions of WOL gene and/or nucleic acid sequences. Further, such sequences may be used as part of ribozyme and/or triple helix sequences, also useful for WOL gene regulation. Still further, such molecules may be used as components in probing methods whereby the presence of a WOODEN LEG allele may be detected.

[0086] The invention also includes nucleic acid molecules, preferably DNA molecules, that are amplified using the polymerase chain reaction and that encode a gene product functionally equivalent to a WOL gene product.

[0087] The invention also encompasses (a) DNA vectors that contain any of the foregoing nucleic acids and/or coding sequences and/or their complements (i.e., antisense or ribozyme molecules); (b) DNA expression vectors that contain any of the foregoing nucleic acids and/or coding sequences operatively associated with a regulatory element that directs the expression of the nucleic acids and/or coding sequences; and (c) genetically engineered host cells that contain any of the foregoing nucleic acids and/or coding sequences operatively associated with a regulatory element that directs the expression of the gene and/or coding sequences in the host cell. As used herein, regulatory elements include, but are not limited to, inducible and non-inducible promoters, enhancers, operators and other elements known to those skilled in the art that drive and regulate expression of a nucleic acid.

[0088] The invention also encompasses nucleotide sequences that encode mutant WOL gene products, peptide fragments of the WOL gene product, truncated WOL gene products, and WOL fusion proteins. These gene products include, but are not limited to, nucleotide sequences encoding mutant WOL gene products; polypeptides or peptides corresponding to one or more of the domains as shown in FIG. 3, or portions of these domains; truncated WOL gene products in which one or more of the domains is deleted, e.g., a truncated, nonfunctional WOL lacking some of the domains of the WOL. The deleted WOL domains can be lacking completely or in part.

[0089] Nucleotides encoding fusion proteins may include, but are not limited to, nucleotides encoding full length WOL, truncated WOL, or peptide fragments of WOL fused to an unrelated protein or peptide, such as for example, an enzyme, fluorescent protein, or luminescent protein that can be used as a marker.

[0090] A fusion construct or gene fusion construct is a genetic construct comprising a promoter operably linked to a heterologous nucleic acid, wherein said promoter controls the transcription of the heterologous nucleic acid. With respect to fusion constructs, a heterologous nucleic acid is a nucleic acid that is linked to a promoter to which the nucleic acid is not naturally linked. The heterologous nucleic acid may or may not be from the organism contributing said promoter. The heterologous gene may encode messenger RNA (mRNA), antisense RNA or ribozymes.

[0091] In particular, the invention includes, for example, fragments of WOL genes encoding one or more of the following domains as shown in FIG. 3: amino acid residues 1-105 (SEQ ID NO:6), amino acid residues 106-126 (SEQ ID NO:7), amino acid residues 127-400 (SEQ ID NO:8), amino acid residues 401-421 (SEQ ID NO:9), amino acid residues 449-737 (SEQ ID NO:10), amino acid residues 762-893 (SEQ ID NO: 11), and amino acid residues 922-1044 (SEQ ID NO:12).

[0092] In addition to the nucleic acid and/or coding sequences described above, homologous WOL nucleic acids, and other nucleic acids related by DNA sequence, may be identified and may be readily isolated, without undue experimentation, by molecular biological techniques well known in the art. More specifically, such homologs include, for example, paralogs (i.e., members of the WOL gene family occurring in the same plant such as F17L21.11, SEQ ID NO:18; and MXH1.16, SEQ ID NO:19) as well as orthologs (i.e., members of the WOL gene family which occur in a different plant species such as Dictyostelium discoideum, SEQ ID NO:17) of the Arabidopsis WOL gene.

[0093] A specific embodiment of a WOL nucleic acid and coding sequence of the invention is Arabidopsis WOL (see FIGS. 5, 6, and 7; SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35).

[0094] Methods for isolating WOL nucleic acids and coding sequences are described in detail in Section 5.1.1, below.

[0095] The proteins encoded by WOL nucleic acids share substantial amino acid sequence similarities and nucleotide sequence similarities in their genes. As explained above in Section 3.1, the term “substantially similar” or “substantial similarity,” when used herein with respect to two amino acid sequences, means that the two sequences have at least 75% identical residues, preferably at least 85% identical residues, more preferably at least 95% identical residues, and most preferably at least 99% identical residues. The same term, when used herein with respect to two nucleotide sequences, means that the two sequences have at least 70% identical residues, preferably at least 85% identical residues, more preferably at least 95% identical residues, and most preferably at least 99% identical residues. Determining whether two sequences are substantially similar may be carried out using any methodologies known to one skilled in the art, preferably using computer assisted analysis.

[0096] The determination of percent identity between two sequences can be accomplished using a mathematical algorithm. A preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin & Altschul, 1990, Proc. Natl. Acad. Sci. USA 87:2264-2268, modified as in Karlin & Altschul, 1993, Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul, et al., 1990, J. Mol. Biol. 215:403-410. BLAST nucleotide searches can be performed with the NBLAST program, score=100, wordlength=12 to obtain nucleotide sequences homologous to a nucleic acid molecules of the invention. BLAST protein searches can be performed with the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences homologous to a protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., 1997, Nucleic Acids Res. 25:3389-3402. Alternatively, PSI-Blast can be used to perform an iterated search which detects distant relationships between molecules (Id.). When utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) can be used. See http://www.ncbi.nlm.nih.gov. Another preferred, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988, CABIOS 4:11-17. Such an algorithm is incorporated into the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used.

[0097] The percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically exact matches are counted.

[0098] Moreover, WOL genes show highly localized expression in embryos and, particularly, in vascular tissue in roots. Such expression patterns may be ascertained by Northern hybridizations and in situ hybridizations using antisense probes as described in Section 6.6 below.

[0099] Examples of WOL paralogs include, but are not limited to, genes F17L21.11 (SEQ ID NO:18); and MXH1.16 (SEQ ID NO:19), which have a similar deduced protein domain structure and which may be identified in the Arabidopsis database. This indicates that WOL belongs to a small protein family (FIG. 3F). The deduced sequence of the WOL protein was 57% identical to F17L21.11 (GenBank Accession Number AC004557 (SEQ ID NO:18)) and 54% identical to MXH1.16 (GenBank Accession Number AB011485 (SEQ ID NO:19)). To compare deduced amino acid sequences, SeqWeb Software (a web-based interface to the GCG Wisconsin Package: Gap program) was utilized with the default algorithm and parameter settings of the program: blosum62, gap weight 8, length weight 2. Furthermore, a WOL ortholog sequence has been reported in the genome of Hordeum vulgare (GenBank Accession Number AJ234550, SEQ ID NO:20). Among the characterized two component receptor molecules, these WOL homolog and paralog proteins are unique in having, at least one, and preferably two, putative D domains. The closest homologue of WOL-like genes is the DhkA receptor (GenBank Accession Number U42597, SEQ ID NO:17; see Wang et al., 1996, EMBO J. 15:3890-8 and Wang et al., 1999, Mol Cell Biol. 7:4750-6) of the slime mold Dictyostelium discoideum (FIG. 3F).

[0100] The functionality of naturally occurring or constructed variants of WOL genes may be tested using methods well known in the art, such as operably linking a reporter gene to a WOL gene variant, and which are taught in the present application at Section 5.8. Versions of the WOL genes to be tested can be fused to any number of heterologous reporter genes, including but not limited to, GUS, GFP, CAT, luciferase, β-galactosidase and C1 and R gene controlling anthocyanin production. Transgenic plants containing the WOL::reporter gene constructs can be generated using the methods described in section 5.9 for each WOL gene variant. To screen for loss-of-function variants induced by mutations, including but not limited to, deletions, point mutations, rearrangements, translocation, etc. The constructs may be transformed into the homozygous recessive wol mutant background, such as the mutant described in Section 6 below. If a wildtype WOL phenotype is restored in one of the transgenic plant lines (i.e., metaxylem and vascular bundles present, thicker roots and hypocotyl than in the mutant), then the WOL variant contained in the construct is functional.

[0101] WOL orthologs are also active in the cambial zone of a trunk of a birch tree (Betula pendula). Using degenerate oligonucleotides (forward primer is SEQ ID NO:31; reverse primer is SEQ ID NO:32) based on the sequence conservation within the WOL genes of Arabidopsis, two different WOL orthologs from a cDNA library representing the wood forming tissue of birch tree (Betula pendula) are described herein in Section 6.7 infra (SEQ ID Nos: 25 and 26, respectively). Because of their expression during wood development in trees, it is postulated that WOL and WOL orthologs and paralogs have more general roles regulation of vascular development during both the primary and secondary phases of plant development.

5.1.1. Isolation Of WOL Nucleic Acids

[0102] The following methods can be used to obtain WOL nucleic acids and coding sequences from a wide variety of plants, including, but not limited to, Arabidopsis thaliana, Zea mays, Nicotiana tabacum, Daucus carota, Oryza, Glycine max, Lemna gibba, Picea abies, as well as species of the genera Betula, Populus, Pinus, and Eucalyptus, etc.

[0103] Nucleotide sequences comprising a WOL nucleic acid or a portion thereof may be obtained by PCR amplification of plant genomic DNA or cDNA. Useful cDNA sources include “free” cDNA preparations (i.e., the products of cDNA synthesis) and cloned cDNA in cDNA libraries. Root or cambial cDNA preparations or libraries are particularly preferred.

[0104] The amplification may use, as the 5′-primer (i.e., forward primer), a degenerate oligonucleotide that corresponds to a segment of a known WOL amino acid sequence, preferably from the amino-terminal region. The 3′-primer (i.e., reverse primer) may be a degenerate oligonucleotide that corresponds to a distal segment of the same known WOL amino acid sequence (i.e., carboxyl to the sequence that corresponds to the 5′-primer). For example, the amino acid sequence of the Arabidopsis WOL protein (SEQ ID NO:5) may be used to design useful 5′ and 3′ primers. The sequence of the optimal degenerate oligonucleotide probe corresponding to a known amino acid sequence may be determined by standard algorithms known in the art. See for example, Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., Vol 2.

[0105] Further, for amplification from cDNA sources, the 3′-primer may be an oligonucleotide comprising an 3′ oligo(dT) sequence. The amplification may also use as primers nucleotide sequences of WOL genes or coding sequences.

[0106] PCR amplification can be carried out, e.g., by use of a Perkin-Elmer Cetus thermal cycler and Taq polymerase (Gene Amp™). One can choose to synthesize several different degenerate primers for use in the PCR reactions. It is also possible to vary the stringency of hybridization conditions used in priming the PCR reactions, to allow for greater or lesser degrees of nucleotide sequence similarity between the degenerate primers and the corresponding sequences in the cDNA library. One of ordinary skill in the art will know that the appropriate amplification conditions and parameters depend, in part, on the length and base composition of the primers and that such conditions may be determined using standard formulae. Protocols for executing all PCR procedures discussed herein are well known to those skilled in the art, and may be found in references such as Gelfand, 1989, PCR Technology, Principles and Applications for DNA Amplification, H. A. Erlich, ed., Stockton Press, New York; and Ausubel et al., 1988, Current Protocols In Molecular Biology, Wiley & Sons, Inc, New York, Vol. 2:Ch. 15

[0107] A PCR amplified sequence may be molecularly cloned and sequenced. The amplified sequence may be utilized as a probe to isolate genomic or cDNA clones of a WOL gene, as described below. This, in turn, will permit the determination of a WOL gene's complete nucleotide sequence, including its promoter, the analysis of its expression, and the production of its encoded protein, as described infra.

[0108] A coding sequence for a WOL gene product, e.g., a WOL protein, may also be isolated by screening a plant genomic or cDNA library using a WOL nucleotide sequence (e.g., the sequence of any of the WOL nucleic acids and sequences and EST clone sequences) as hybridization probe. For example, the whole or a segment of the Arabidopsis WOL nucleotide sequence (FIG. 5) may be used. Alternatively, a WOL nucleic acid may be isolated from such libraries using a degenerate oligonucleotide that corresponds to a segment of a WOL amino acid sequence. For example, degenerate oligonucleotide probe corresponding to a segment of the Arabidopsis WOL amino acid sequence (SEQ ID NO:5) may be used.

[0109] In preparation of cDNA libraries, total RNA is isolated from plant tissues, preferably roots. Poly(A)+ RNA is isolated from the total RNA, and cDNA prepared from the poly(A)+ RNA, all using standard procedures. See, for example, Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2d ed., Vol. 2. The cDNAs may be synthesized with a restriction enzyme site at their 3′-ends by using an appropriate primer and further have linkers or adaptors attached at their 5′-ends to facilitate the insertion of the cDNAs into suitable cDNA cloning vectors. Alternatively, adaptors or linkers may be attached to the cDNAs after the completion of cDNA synthesis.

[0110] In preparation of genomic libraries, plant DNA is isolated and fragments are generated, some of which will encode parts of the whole WOL protein. The DNA may be cleaved at specific sites using various restriction enzymes. Alternatively, one may use DNase in the presence of manganese to fragment the DNA, or the DNA can be physically sheared, as for example, by sonication. The DNA fragments can then be separated according to size by standard techniques, including, but not limited to, agarose and polyacrylamide gel electrophoresis, column chromatography and sucrose gradient centrifugation.

[0111] The genomic DNA or cDNA fragments can be inserted into suitable vectors, including, but not limited to, plasmids, cosmids, bacteriophages lambda or T4, and yeast artificial chromosome (YAC). See, for example, Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Glover, 1985, DNA Cloning: A Practical Approach, MRL Press, Ltd., Oxford, U.K., Vols. I and II.

[0112] The WOL nucleotide probe, DNA or RNA, should be at least 17 nucleotides, preferably at least 26 nucleotides, and most preferably at least 50 nucleotides in length. The nucleotide probe is hybridized under moderate stringency conditions and washed under moderate or, more preferably, high stringency conditions. Clones in libraries with insert DNA having substantial homology to the WOL probe will hybridize to the probe. Hybridization of the nucleotide probe to genomic or cDNA libraries is carried out using methods known in the art. One of ordinary skill in the art will know that the appropriate hybridization and wash conditions depend on the length and base composition of the probe and that such conditions may be determined using standard formulae. See, for example, Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., Vol. 2, pp 11.45-11.57 and 15.55-15.57.

[0113] The identity of a cloned or amplified WOL nucleic acid sequence can be verified by comparing the amino acid sequences of its three open reading frames with the amino acid sequence of a WOL gene product (e.g., Arabidopsis WOL protein, see SEQ ID NO:5). A WOL nucleic acid or coding sequence encodes a protein or polypeptide whose amino acid sequence is substantially similar to that of a WOL protein or polypeptide (e.g., the amino acid sequence of FIG. 5). The identity of the cloned or amplified WOL nucleic acid sequence may be further verified by examining its expression pattern, which reveals highly localized expression in the embryo and root vascular tissue of the plant from which the WOL nucleic acid sequence was isolated.

[0114] Comparison of the amino acid sequences encoded by a cloned or amplified sequence may reveal that it does not contain the entire WOL gene or its promoter. In such a case the cloned or amplified WOL nucleic acid sequence may be used as a probe to screen a genomic library for clones having inserts that overlap the cloned or amplified WOL nucleic acid sequence. A complete WOL gene and its promoter may be reconstructed by splicing the overlapping WOL nucleic acid sequences.

5.2. WOL Gene Products And Expression Of WOL Gene Products

[0115] WOL proteins, polypeptides and peptide fragments, mutated, truncated or deleted forms of WOL and/or WOL fusion proteins can be prepared for a variety of uses, including, but not limited to, the generation of antibodies, as reagents in assays, the identification of other cellular gene products involved in regulation of root development, etc.

[0116] WOL translational products include, but are not limited to those proteins and polypeptides encoded by the WOL nucleic acid sequences described in Section 5.1, above. The invention encompasses proteins that are functionally equivalent to the WOL gene products described in Section 5.2. Such a WOL gene product may contain one or more deletions, additions or substitutions of WOL amino acid residues within the amino acid sequence encoded by any one of the WOL nucleic acid sequences described, above, in Section 5.1, but which result in a silent change, thus producing a functionally equivalent WOL gene product. Amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues involved.

[0117] The present invention also provides variants of the polypeptides of the invention. Such variants have an altered amino acid sequence which can function as either agonists (mimetics) or as antagonists. Variants can be generated by mutagenesis, e.g., discrete point mutation or truncation. An agonist can retain substantially the same, or a subset, of the biological activities of the naturally occurring form of the protein. An antagonist of a protein can inhibit one or more of the activities of the naturally occurring form of the protein by, for example, deleting one or both of the receiver domains (DA and DB). Thus, specific biological effects can be elicited by addition of a variant of limited function.

[0118] Modification of the structure of the subject polypeptides can be for such purposes as enhancing efficacy, stability, or post-translational modifications (e.g., to alter the phosphorylation pattern of the protein). Such modified peptides, when designed to retain at least one activity of the naturally-occurring form of the protein, or to produce specific antagonists thereof, are considered functional equivalents of the polypeptides. Such modified peptides can be produced, for instance, by amino acid substitution, deletion, or addition.

[0119] For example, it is reasonable to expect that an isolated replacement of a leucine with an isoleucine or valine, an aspartate with a glutamate, a threonine with a serine, or a similar replacement of an amino acid with a structurally related amino acid (i.e. isosteric and/or isoelectric mutations) will not have a major effect on the biological activity of the resulting molecule.

[0120] Whether a change in the amino acid sequence of a peptide results in a functional homolog (e.g., functional in the sense that the resulting polypeptide mimics or antagonizes the wild-type form) can be readily determined by assessing the ability of the variant peptide to produce a response in cells in a fashion similar to the wild-type protein, or competitively inhibit such a response. Polypeptides in which more than one replacement has taken place can readily be tested in the same manner.

[0121] Variants of a protein of the invention which function as either agonists (mimetics) or as antagonists can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants, of the protein of the invention for agonist or antagonist activity. In one embodiment, a variegated library of variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library. A variegated library of variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into nucleic acid sequences such that a degenerate set of potential protein sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display). There are a variety of methods which can be used to produce libraries of potential variants of the polypeptides of the invention from a degenerate oligonucleotide sequence. Methods for synthesizing degenerate oligonucleotides are known in the art (see, e.g., Narang, 1983, Tetrahedron 39:3; Itakura et al., 1984, Annu. Rev. Biochem. 53:323; Itakura et al., 1984, Science 198:1056; Ike et al., 1983, Nucleic Acid Res.11:477).

[0122] In addition, libraries of fragments of the coding sequence of a polypeptide of the invention can be used to generate a variegated population of polypeptides for screening and subsequent selection of variants. For example, a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of the coding sequence of interest with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double stranded DNA which can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with S1 nuclease, and ligating the resulting fragment library into an expression vector. By this method, an expression library can be derived which encodes N-terminal and internal fragments of various sizes of the protein of interest.

[0123] Several techniques are known in the art for screening gene products of combinatorial libraries made by point mutations or truncation, and for screening cDNA libraries for gene products having a selected property. The most widely used techniques, which are amenable to high through-put analysis, for screening large gene libraries typically include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates isolation of the vector encoding the gene whose product was detected. Recursive ensemble mutagenesis (REM), a technique which enhances the frequency of functional mutants in the libraries, can be used in combination with the screening assays to identify variants of a protein of the invention (Arkin and Yourvan, 1992, Proc. Natl. Acad. Sci. USA 89:7811-7815; Delgrave et al., 1993, Protein Engineering 6(3):327-331).

[0124] An isolated nucleic acid molecule encoding a variant protein can be created by introducing one or more nucleotide substitutions, additions or deletions into the WOL nucleotide sequence, such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Briefly, PCR primers are designed that delete the trinucleotide codon of the amino acid to be changed and replace it with the trinucleotide codon of the amino acid to be included. This primer is used in the PCR amplification of DNA encoding the protein of interest. This fragment is then isolated and inserted into the full length cDNA encoding the protein of interest and expressed recombinantly. The resulting protein now includes the amino acid replacement.

[0125] Either conservative or non-conservative amino acid substitutions can be made at one or more amino acid residues. Both conservative and non-conservative substitutions can be made. Conservative replacements are those that take place within a family of amino acids that are related in their side chains. Genetically encoded amino acids are can be divided into four families: (1) acidic=aspartate, glutamate; (2) basic=lysine, arginine, histidine; (3) nonpolar=alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan; and (4) uncharged polar=glycine, asparagine, glutamine, cysteine, serine, threonine, tyrosine. In similar fashion, the amino acid repertoire can be grouped as (1) acidic=aspartate, glutamate; (2) basic=lysine, arginine histidine, (3) aliphatic=glycine, alanine, valine, leucine, isoleucine, serine, threonine, with serine and threonine optionally be grouped separately as aliphatic-hydroxyl; (4) aromatic=phenylalanine, tyrosine, tryptophan; (5) amide=asparagine, glutamine; and (6) sulfur -containing=cysteine and methionine. (See, for example, Biochemistry, 4th ed., Ed. by L. Stryer, W H Freeman and Co.: 1995).

[0126] In WOL, for example, the nucleotide at position 66 is thymine (T) (SEQ ID NO:4). In this embodiment, the amino acid at position 22 is aspartate (D) (SEQ ID NO:5). In an alternative embodiment, WOL can be engineered to contain a guanine (G) at nucleotide at position 66 (SEQ ID NO:23). In this embodiment, the amino acid at position 22 is glutamate (E) (SEQ ID NO:24), i.e., a conservative substitution.

[0127] Alternatively, mutations can be introduced randomly along all or part of the coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for biological activity to identify mutants that retain activity. Following mutagenesis, the encoded protein can be expressed recombinantly and the activity of the protein can be determined.

[0128] In a preferred embodiment, a mutant polypeptide that is a variant of a polypeptide of the invention can be assayed for: (1) the ability to form protein-protein interactions with proteins in a signaling pathway of the polypeptide of the invention; (2) the ability to bind a ligand of the polypeptide of the invention; or (3) the ability to bind to an intracellular target protein of the polypeptide of the invention.

[0129] The invention encompasses functionally equivalent mutant WOL proteins and polypeptides. The invention also encompasses mutant WOL proteins and polypeptides that are not functionally equivalent to the gene products described in Section 5.2. Such a mutant WOL protein or polypeptide may contain one or more deletions, additions or substitutions of WOL amino acid residues within the amino acid sequence encoded by any one the WOL nucleic acid sequences described above in Section 5.1, and which result in loss of one or more functions of the WOL protein, thus producing a WOL gene product not functionally equivalent to the wild-type WOL protein.

[0130] WOL proteins and polypeptides bearing mutations can be made to WOL DNA (using techniques discussed above as well as those well known to one of skill in the art) and the resulting mutant WOL proteins tested for activity. Mutants can be isolated that display increased function, (e.g., resulting in improved root formation), or decreased function (e.g., resulting in suboptimal root function). In particular, mutated WOL proteins in which any of the domains shown in FIG. 3 are deleted or mutated are within the scope of the invention. Additionally, peptides corresponding to one or more domains of the WOL protein (e.g., shown in FIG. 3), truncated or deleted WOL protein are also within the scope of the invention. Fusion proteins in which the full length WOL protein or a WOL polypeptide or peptide fused to an unrelated protein are also within the scope of the invention and can be designed on the basis of the WOL nucleotide and WOL amino acid sequences disclosed in Sections 5.1 and 5.2 above.

[0131] While the WOL polypeptides and peptides can be chemically synthesized (e.g. see Creighton, 1983, Proteins: Structures and Molecular Principles, W. H. Freeman & Co., NY) large polypeptides derived from WOL and the full length WOL may advantageously be produced by recombinant DNA technology using techniques well known to those skilled in the art for expressing nucleic acid sequences.

[0132] Methods which are well known to those skilled in the art can be used to construct expression vectors containing WOL protein coding sequences and appropriate transcriptional/translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques and in vivo recombination/genetic recombination. See, for example, the techniques described in Sambrook et al., 1989, supra, and Ausubel et al., 1989, supra. Alternatively, RNA capable of encoding WOL protein sequences may be chemically synthesized using, for example, synthesizers. See, for example, the techniques described in Gait, 1984, Oligonucleotide Synthesis, IRL Press, Oxford.

[0133] A variety of host-expression vector systems may be utilized to express the WOL gene products of the invention. Such host-expression systems represent vehicles by which the WOL gene products of interest may be produced and subsequently recovered and/or purified from the culture or plant (using purification methods well known to those skilled in the art), but also represent cells which may, when transformed or transfected with the appropriate nucleotide coding sequences, exhibit the WOL protein of the invention in situ. These include but are not limited to microorganisms such as bacteria (e.g., E. coli, B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing WOL protein coding sequences; yeast (e.g., Saccharomyces, Pichia) transformed with recombinant yeast expression vectors containing the WOL protein coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing the WOL protein coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV); plant cell systems transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing WOL protein coding sequences; or mammalian cell systems (e.g., COS, CHO, BHK, 293, 3T3) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter; the cytomegalovirus promoter/enhancer; etc.).

[0134] In bacterial systems, a number of expression vectors may be advantageously selected depending upon the use intended for the WOL protein being expressed. For example, when a large quantity of such a protein is to be produced, for the generation of antibodies or to screen peptide libraries, for example, vectors which direct the expression of high levels of fusion protein products that are readily purified may be desirable. Such vectors include, but are not limited, to the E. Coli expression vector pUR278 (Ruther et al., 1983, EMBO J. 2:1791), in which the WOL coding sequence may be ligated individually into the vector in frame with the lac Z coding region so that a fusion protein is produced; pIN vectors (Inouye & Inouye, 1985, Nucleic Acids Res. 13:3101-9; Van Heeke & Schuster, 1989, J. Biol. Chem. 264:5503-9); and the like. pGEX vectors may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione. The pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene protein can be released from the GST moiety.

[0135] In one such embodiment of a bacterial system, full length cDNA sequences are appended with in-frame Bam HI sites at the amino terminus and Eco RI sites at the carboxyl terminus using standard PCR methodologies (Innis et al., 1990, supra) and ligated into the pGEX-2TK vector (Pharmacia, Uppsala, Sweden). The resulting cDNA construct contains a kinase recognition site at the amino terminus for radioactive labeling and glutathione S-transferase sequences at the carboxyl terminus for affinity purification (Nilsson, et al., 1985, EMBO J. 4:1075; Zabeau and Stanley, 1982, EMBO J. 1: 1217).

[0136] The recombinant constructs of the present invention may include a selectable marker for propagation of the construct. For example, a construct to be propagated in bacteria preferably contains an antibiotic resistance gene, such as one that confers resistance to kanamycin, tetracycline, streptomycin, or chloramphenicol. Suitable vectors for propagating the construct include, but are not limited to, plasmids, cosmids, bacteriophages or viruses.

[0137] In addition, the recombinant constructs may include plant-expressible, selectable, or screenable marker genes for isolating, identifying or tracking plant cells transformed by these constructs. Selectable markers include, but are not limited to, genes that confer antibiotic resistance, (e.g., resistance to kanamycin or hygromycin) or herbicide resistance (e.g., resistance to sulfonylurea, phosphinothricin, or glyphosate). Screenable markers include, but are not be limited to, reporter genes encoding β-glucuronidase (Jefferson, 1987, Plant Mol. Biol. Rep. 5:387-405), luciferase (Ow et al., 1986, Science 234:856-9), fluorescent proteins (such as GFP as described in Kain et al., 1995, Biotech. 19:650-5; blue GFP as described by Heim and Tsien, 1996, Curr. Biol. 6:178-82; or yellow and red GFP as described by Matz et al., 1999, Nature Biotechnol. 17:969-73), B protein that regulates anthocyanin pigment production (Goff et al., 1990, EMBO J. 9:2517-22).

[0138] In embodiments of the present invention which utilize the Agrobacterium tumefacien system for transforming plants (see infra), the recombinant constructs may additionally comprise at least the right T-DNA border sequences flanking the DNA sequences to be transformed into the plant cell. Alternatively, the recombinant constructs may comprise the right and left T-DNA border sequences flanking the DNA sequence. The proper design and construction of such T-DNA based transformation vectors are well known to those skilled in the art.

5.3. Antibodies To WOL Proteins And Polypeptides

[0139] Antibodies that specifically recognize one or more epitopes of WOL, or epitopes of conserved variants of WOL, or peptide fragments of the WOL are also encompassed by the invention. Such antibodies include but are not limited to polyclonal antibodies, monoclonal antibodies (mAbs), humanized or chimeric antibodies, single chain antibodies, Fab fragments, F(ab′)2 fragments, fragments produced by a Fab expression library, anti-idiotypic (anti-Id) antibodies, and epitope-binding fragments of any of the above.

[0140] An isolated polypeptide of the invention, or a fragment thereof can be used as an immunogen to generate antibodies using standard techniques for polyclonal and monoclonal antibody preparation. Among those polypeptides suitable for use are the full length WOL protein (SEQ ID NOs:5, 29, or 30), a WOL peptide (e.g., one corresponding to a functional domain of the protein, SEQ ID NOs:6, 7, 8, 9, 10, 11, or 12), a truncated WOL polypeptide (WOL in which one or more domains has been deleted), functional equivalents of the WOL protein, or mutants of the WOL protein. Such WOL proteins, polypeptides, peptides or fusion proteins can be prepared and obtained as described in Section 5.2 supra.

[0141] The antigenic peptide of a protein of the invention comprises at least 8 (preferably 10, 15, 20, or 30) amino acid residues of the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30, and encompasses an epitope of the protein such that an antibody raised against the peptide forms a specific immune complex with the protein. Preferred epitopes encompassed by the antigenic peptide are regions that are located on the surface of the protein, e.g., hydrophilic regions. Hydropathy plots or similar analyses can be used to identify hydrophilic regions.

[0142] Host animals which may be used for injection include, but are not limited to, rabbits, mice, and rats. Various adjuvants may be used to increase the immunological response, depending on the host species, including, but not limited to, Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parvum. Polyclonal antibodies are heterogeneous populations of antibody molecules derived from the sera of the immunized animals.

[0143] Monoclonal antibodies, which are homogeneous populations of antibodies to a particular antigen, may be obtained by any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique of Kohler and Milstein, (1975, Nature 256:495-7 and U.S. Pat. No.4,376,110), the human B-cell hybridoma technique (Kosbor et al., 1983, Immunology Today 4:72; Cole et al., 1983, Proc. Natl. Acad. Sci. USA 80:2026-30), and the EBV-hybridoma technique (Cole et al., 1985, Monoclonal Antibodies And Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). Such antibodies may be of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD and any subclass thereof. The hybridoma producing the mAb of this invention may be cultivated in vitro or in vivo. Production of high titers of mAbs in vivo makes this the presently preferred method of production.

[0144] Polyclonal antibodies can be prepared as described above by immunizing a suitable subject with a polypeptide of the invention as an immunogen. Preferred polyclonal antibody compositions are ones that have been selected for antibodies directed against a polypeptide or polypeptides of the invention. Particularly preferred polyclonal antibody preparations are ones that contain only antibodies directed against a polypeptide or polypeptides of the invention. Particularly preferred immunogen compositions are those that contain no other contaminating proteins such as, for example, immunogen compositions made using a host cell for recombinant expression of a polypeptide of the invention. In such a manner, the only epitope or epitopes recognized by the resulting antibody compositions raised against this immunogen will be present as part of a polypeptide or polypeptides of the invention.

[0145] In addition, techniques developed for the production of “chimeric antibodies” (Morrison et al., 1984, Proc. Natl. Acad. Sci. USA, 81:6851-5; Neuberger et al., 1984, Nature, 312:604-8; Takeda et al., 1985, Nature, 314:452-4) by splicing the genes from a mouse antibody molecule of appropriate antigen specificity together with genes from a human antibody molecule of appropriate biological activity can be used. A chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine mAb and a human immunoglobulin constant region.

[0146] In addition, techniques have been developed for the production of humanized antibodies. (See, e.g., U.S. Pat. No. 5,585,089.) An immunoglobulin light or heavy chain variable region consists of a “framework” region interrupted by three hypervariable regions, referred to as complementarity determining regions (CDRs). The extent of the framework region and CDRs have been precisely defined (see, Kabat ET AL., 1983, Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services). Briefly, humanized antibodies are antibody molecules from non-human species having one or more CDRs from the non-human species and a framework region from a human immunoglobulin molecule.

[0147] Alternatively, techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778; Bird, 1988, Science 242:423-6; Huston et al., 1988, Proc. Natl. Acad. Sci. USA 85:5879-83; and Ward et al., 1989, Nature 334:544-6) can be adapted to produce single chain antibodies against WOL proteins or polypeptides. Single chain antibodies are formed by linking the heavy and light chain fragments of the Fv region via an amino acid bridge, resulting in a single chain polypeptide.

[0148] Antibody fragments that recognize specific epitopes may be generated by known techniques. For example, such fragments include but are not limited to: the F(ab′)2 fragments which can be produced by pepsin digestion of the antibody molecule and the Fab fragments which can be generated by reducing the disulfide bridges of the F(ab′)2 fragments. Alternatively, Fab expression libraries may be constructed (Huse et al., 1989, Science, 246:1275-81) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity.

[0149] Antibodies to a WOL protein and/or polypeptide can, in turn, be utilized to generate anti-idiotype antibodies that “mimic” WOL, using techniques well known to those skilled in the art. (See, e.g., Greenspan & Bona, 1993, FASEB J. 7:437-44; and Nissinoff, 1991, J. Immunol. 147:2429-38).

5.4. WOL Nucleic Acids Or Gene Products As Markers For Quantitative Trait Loci

[0150] Any of the nucleotide sequences (including EST clone sequences with GenBank Accession Numbers AA586219, SEQ ID NO:14; A1992824, SEQ ID NO:15; and T20648, SEQ ID NO:16) described in Section 5.1.1, and/or polypeptides and proteins described in Section 5.2, can be used as markers for qualitative trait loci in breeding programs for crop plants. To this end, the nucleic acid molecules, including, but not limited to, full length WOL coding sequences, and/or partial sequences (ESTs), can be used in hybridization and/or DNA amplification assays to identify the endogenous WOL genes, wol mutant alleles and/or WOL expression products in cultivars as compared to wild-type plants. They can also be used as markers for linkage analysis of qualitative trait loci. It is also possible that the WOL gene may encode a product responsible for a qualitative trait that is desirable in a crop breeding program. Alternatively, the WOL protein, peptides and/or antibodies can be used as diagnostic reagents in immunoassays to detect expression of the WOL gene in cultivars and wild-type plants.

5.5. Identification Of WOL-Interacting Proteins

[0151] Any of a variety of exogenous compounds, both naturally occurring and/or synthetic (e.g., libraries of small molecules or peptides), may be screened for binding capacity to a WOL protein. Such methods may comprise the step of mixing a WOL protein or peptide with library members, allowing time for any binding to occur, and assaying for any bound complexes.

[0152] In a specific embodiment, ligands capable of binding to the WOL receptor may be isolated from libraries. WOL is an orphan receptor because no known endogenous ligand is currently known. WOL protein or peptides may be used as bait to isolate those molecules competent to bind and therefore be assigned a previously unknown ligand. The activity of WOL may be either augmented or diminished through contact with isolated proteins. Such methods are known in the art.

[0153] Many libraries are known in the art that can be used, e.g., recombinant (e.g., phage display libraries or cDNA expression libraries), in vitro translation-based libraries; and chemically synthesized libraries.

[0154] Examples of phage display libraries are described in Scott & Smith, 1990, Science 249:386-390; Devlin et al., 1990, Science, 249:404-406; Christian, et al., 1992, J. Mol. Biol. 227:711-718; Lenstra, 1992, J. Immunol. Meth. 152:149-157; Kay et al., 1993, Gene 128:59-65; and PCT Publication No. WO 94/18318.

[0155] In vitro translation-based libraries include but are not limited to those described in PCT Publication No. WO 91/05058 and Mattheakis et al., 1994, Proc. Natl. Acad. Sci. USA 91:9022-9026.

[0156] Examples of chemically synthesized libraries are described in Fodor et al., 1991, Science 251:767-773; Houghten et al., 1991, Nature 354:84-86; Lam et al., 1991, Nature 354:82-84; Medynski, 1994, Bio/Technology 12:709-710; Gallop et al., 1994, J. Medicinal Chemistry 37(9):1233-1251; Ohlmeyer et al., 1993, Proc. Natl. Acad. Sci. USA 90:10922-10926; Erb et al., 1994, Proc. Natl. Acad. Sci. USA 91:11422-11426; Houghten et al., 1992, Biotechniques 13:412; Jayawickreme et al., 1994, Proc. Natl. Acad. Sci. USA 91:1614-1618; Salmon et al., 1993, Proc. Natl. Acad. Sci. USA 90:11708-11712; Brenner & Lerner, 1992, Proc. Natl. Acad. Sci. USA 89:5381-5383; and PCT Publication No. WO 93/20242.

[0157] Screening the libraries can be accomplished by any of a variety of commonly known methods. See, e.g., the following references, which disclose screening of peptide libraries: Parmley and Smith, 1989, Adv. Exp. Med. Biol. 251:215-218; Scott and Smith, 1990, Science 249:386-390; Fowlkes et al., 1992; BioTechniques 13:422-427; Oldenburg et al., 1992, Proc. Natl. Acad. Sci. USA 89:5393-5397; Yu et al., 1994, Cell 76:933-945; Staudt et al., 1988, Science 241:577-580; Bock et al., 1992, Nature 355:564-566; Tuerk et al., 1992, Proc. Natl. Acad. Sci. USA 89:6988-6992; Ellington et al., 1992, Nature 355:850-852; Rebar and Pabo, 1993, Science 263:671-673; Ladner et al., U.S. Pat. No. 5,096,815; Ladner et al., U.S. Pat. No. 5,223,409; Ladner et al., U.S. Pat. No. 5,198,346; and PCT Publication No. WO 94/18318.

[0158] In a specific embodiment, screening can be carried out by contacting the library members with a WOL protein or peptide (or derivative or analog) immobilized on a solid phase and harvesting those library members that bind to the peptide (or derivative or analog). Examples of such screening methods, termed “panning” techniques are described by way of example in Parmley & Smith, 1988, Gene 73:305-318; Fowlkes et al., 1992, BioTechniques 13:422-427; PCT Publication No. WO 94/18318; and in references cited herein above.

[0159] In another embodiment, the two-hybrid system for selecting interacting proteins or peptides in yeast (Fields & Song, 1989, Nature 340:245-246; Chien et al., 1991, Proc. Natl. Acad. Sci. USA 88:9578-9582) can be used to identify molecules that specifically bind to a WOL protein or peptide.

[0160] Binding interactions between two or more components can be measured in a variety of ways. One approach is to label one of the components with an easily detectable label, place it together with the other component(s) in conditions under which they would normally interact, perform a separation step which separates bound labeled component from unbound labeled component, and then measure the amount of bound component. The effect of a test agent included in the binding reaction can be determined by comparing the amount of labeled component which binds in the presence of this agent to the amount which binds in its absence.

[0161] The separation step in this type of procedure can be accomplished in various ways. In one approach, (one of) the binding partner(s) for the labeled component can be immobilized on a solid phase prior to the binding reaction, and unbound labeled component can be removed after the binding reaction by washing the solid phase. Attachment of the binding partner to the solid phase can be accomplished in various ways known to those skilled in the art, including, but not limited to, chemical cross-linking, non-specific adhesion to a plastic surface, interaction with an antibody attached to the solid phase, interaction between a ligand attached to the binding partner (such as biotin) and a ligand-binding protein (such as avidin or streptavidin) attached to the solid phase, and so on.

[0162] Alternatively, the separation step can be accomplished after the labeled component had been allowed to interact with its binding partner(s) in solution. If the size differences between the labeled component and its binding partner(s) permit such a separation, the separation can be achieved by passing the products of the binding reaction through an ultrafilter whose pores allow passage of unbound labeled component but not of its binding partner(s) or of labeled component bound to its partner(s). Separation can also be achieved using any reagent capable of capturing a binding partner of the labeled component from solution, such as an antibody against the binding partner, a ligand-binding protein which can interact with a ligand previously attached to the binding partner, and so on.

[0163] Screening procedures should use appropriately stringent conditions. For guidance regarding such conditions see, for example, Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N.Y.; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Greene Publishing Associates and Wiley Interscience, N.Y.

[0164] The above methods will isolate library members which bind the WOL protein or peptide. Stringency conditions can be varied to determine the specificity and strength of the interaction.

5.6. WOL Promoters

[0165] According to the present invention, WOL promoters and functional portions thereof described herein refer to regions of genomic DNA associated with the WOL gene which are capable of promoting expression of an operably linked coding sequence in plants, such that the resulting expression pattern is specific to vascular tissue and pericycle in embryos and vascular tissue in roots and other mature organs. The WOL promoter described herein refers to the regulatory elements of WOL genes, i.e., regulatory regions of genes which are capable of selectively hybridizing to the nucleic acids described in Section 5.1, or regulatory sequences contained, for example, in the region between the translational start site of the Arabidopsis WOL gene and the T23K3/3 marker 4 kb upstream of the translational start site. In one embodiment, the regulatory region is 2.5 kb upstream of the translational start site. Homologous nucleotide sequences are also part of the invention and refer to nucleotide sequences including, but not limited to, WOL promoters in diverse plant species (e.g., promoters of orthologs of Arabidopsis WOL) as well as genetically engineered derivatives of the promoters described herein.

[0166] The present invention also provides to variants of the promoters of the invention. Such variants have an altered nucleic acid sequence that can function similarly to the WOL promoter. Using methods well-known in the art, one may screen for equivalent functionality and variation in specificity of expression pattern among natural variants or experimentally-induced variants. In this manner it is possible to choose and design primers based on the desired specificity of expression.

[0167] Methods used for the synthesis, isolation, molecular cloning, characterization and manipulation of WOL promoter sequences are well known to those skilled in the art. See, e.g., the techniques described in Sambrook et al., 1989, Molecular Cloning A Laboratory Manual, 2nd. ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.

[0168] According to the present invention, WOL promoter sequences or portions thereof described herein may be obtained from appropriate plant sources from cell lines or recombinant DNA constructs containing WOL promoter sequences, and/or by chemical synthetic methods. WOL promoter sequences can be obtained from genomic clones containing sequences 5′ upstream of WOL coding sequences. Such 5′ upstream clones may be obtained by screening genomic libraries using WOL protein coding sequences, particularly those encoding WOL -terminal sequences, from WOL gene clones obtained as described in Sections 5.1 and 6. Standard methods that may used in such screening include, for example, the method set forth in Benton & Davis, 1977, Science 196:180 for bacteriophage libraries; and Grunstein & Hogness, 1975, Proc. Nat. Acad. Sci. U.S.A. 72:3961-3965 for plasmid libraries.

[0169] The full extent and location of WOL promoters within such 5′ upstream clones may be determined by the functional assay described below. In the event a 5′ upstream clone does not contain the entire WOL promoter as determined by the functional assay, the insert DNA of the clone may be used to isolate genomic clones containing sequences further 5′ upstream of the WOL coding sequences. Such further upstream sequences can be spliced on to existing 5′ upstream sequences and the reconstructed 5′ upstream region tested for functionality as a WOL promoter (i.e., promoting specific expression in vascular tissue and pericycle of embryos and/or roots of an operably linked gene in plants). This process may be repeated until the complete WOL promoter is obtained.

[0170] The location of the WOL promoter within genomic sequences 5′ upstream of the WOL gene isolated as described above may be determined using any method known in the art. For example, the 3′-end of the promoter may be identified by locating the transcription initiation site, which may be determined by methods such as RNase protection (e.g., Liang et al., 1989, J. Biol. Chem. 264:14486-98), primer extension (e.g., Weissenborn & Larson, 1992, J. Biol. Chem. 267:6122-31), and/or reverse transcriptase/PCR. The location of the 3′-end of the promoter may be confirmed by sequencing and computer analysis, examining for the canonical AGGA or TATA boxes of promoters that are typically 50-60 bp and 25-35 bp 5′-upstream of the transcription initiation site. The 5′-end promoter may be defined by deleting sequences from the 5′-end of the promoter containing fragment, constructing a transcriptional or translational fusion of the resected fragment and a reporter gene, and examining the expression characteristics of the chimeric gene in transgenic plants. Reporter genes that may be used to such ends include, but are not limited to, GUS, CAT, luciferase, β-galactosidase and C1 and R gene controlling anthocyanin production.

[0171] According to the present invention, a WOL promoter is one that confers to an operably linked gene in a transgenic plant tissue-specific expression in the presumptive pericycle tissue and the presumptive vascular tissue of embryonic hypocotyl, and/or in the pericyle and vascular tissue of the mature organs, especially the root. A WOL promoter comprises the region between about −7,000 bp and +1 bp upstream of the transcription initiation site of the WOL gene (SEQ ID NO:33). In one embodiment, a WOL promoter fragment which comprises nucleotides 3025 to 7025 of SEQ ID NO:33 (SEQ ID NO:34) is capable of tissue specific expression in the presumptive pericycle tissue and the presumptive vascular tissue of embryonic hypocotyl, and/or in the pericyle and vascular tissue of the mature root organs, especially the root. In another embodiment, a WOL promoter fragment which comprises nucleotides 4508 to 7025 of SEQ ID NO:33 (SEQ ID NO:35) is capable of tissue specific expression in the presumptive pericycle tissue and the presumptive vascular tissue of embryonic hypocotyl, and/or in the pericycle and vascular tissue of the mature root and hypocotyl. Additional cis-regulatory elements may also be located in the intronic or 3′ downstream sequences. In these embodiments, the expression patterns of gene products driven by WOL promoter fragments are not only tissue-specific, but are in part organ-specific at defined developmental stages.

[0172] A chimeric WOL promoter is within the scope of the present invention. As used herein, a “chimeric promoter” refers to a promoter that comprises functional portions of two different plant promoters. In one embodiment a native WOL promoter or portion thereof is modified by a regulatory elements from a heterologous promoter. Alternatively, a heterologous promoter is modified by the attachment of regulatory elements derived from the WOL promoter. In one embodiment the regulatory elements may be cis-regulatory elements (see Section 5.7). One example of a heterologous promoter is the SCARECROW promoter as identified in United States patent application of Benfey et al. for “Scarecrow Gene, Promoter and Uses Thereof”(WO97/41152, published Nov. 6, 1997), which is incorporated herein by reference in its entirety for its relevant teaching.

[0173] The manner of chimeric promoter constructions may be any well known in the art. For examples of approaches that can be used in such constructions, see Fluhr et al., 1986, Science 232:1106-12; Ellis et al., 1987, EMBO J. 6:11-16; Strittmatter & Chua, 1987, Proc. Natl. Acad. Sci. USA 84:8986-90; Poulsen & Chua, 1988, Mol. Gen. Genet. 214:16-23; Comai et al., 1991, Plant Mol. Biol. 15:373-81; Aryan et al., 1991, Mol. Gen. Genet. 225:65-71.

[0174] According to the present invention, where a WOL promoter or a recombinant WOL promoter is used to express a desired protein, the DNA construct is designed so that the protein coding sequence is ligated in phase with the translational initiation codon downstream of the promoter. Where the promoter fragment is missing 5′ leader sequences, a DNA fragment encoding both the protein and its 5′ RNA leader sequence is ligated immediately downstream of the transcription initiation site. Alternatively, an unrelated 5′ RNA leader sequence may be used to bridge the promoter and the protein coding sequence. In such instances, the design should be such that the protein coding sequence is ligated in phase with the initiation codon present in the leader sequence, or ligated such that no initiation codon is interposed between the transcription initiation site and the first methionine codon of the protein.

[0175] Further, it may be desirable to include additional DNA sequences in the protein expression constructs. Examples of additional DNA sequences include, but are not limited to, those encoding: a 3′ untranslated region; a transcription termination and polyadenylation signal; an intron; a signal peptide (which facilitates the secretion of the protein); or a transit peptide (which targets the protein to a particular cellular compartment such as the nucleus, chloroplast, mitochondria, or vacuole).

5.7. Cis-Regulatory Elements Of WOL Promoters

[0176] According to the present invention, the cis-regulatory elements within a WOL promoter may be identified using any method known in the art. For example, the location of cis-regulatory elements within an inducible promoter may be identified using methods such as DNase or chemical footprinting (e.g., Meier et al., 1991, Plant Cell 3:309-15) or gel retardation (e.g., Weissenborn & Larson, 1992, J. Biol. Chem. 267-6122-31; Beato, 1989, Cell 56:335-44; Johnson et al., 1989, Ann. Rev. Biochem. 58:799-839). Additionally, resectioning experiments may also be employed to define the location of the cis-regulatory elements. For example, an inducible promoter-containing fragment may be resected from either the 5′ or 3′-end using restriction enzyme or exonuclease digests.

[0177] To determine the location of cis-regulatory elements within the sequence containing the inducible promoter, the 5′- or 3′-resected fragments, internal fragments to the inducible promoter containing sequence, or inducible promoter fragments containing sequences identified by footprinting or gel retardation experiments may be fused to the 5′-end of a truncated plant promoter, and the activity of the chimeric promoter in transgenic plant examined. Useful truncated promoters to these ends comprise sequences starting at or about the transcription initiation site and extending to no more than 150 bp 5′ upstream. These truncated promoters generally are inactive or are only minimally active. Examples of such truncated plant promoters may include, among others, a “minimal” CaMV 35S promoter whose 5′ end terminates at position −46 bp with respect to the transcription initiation site (Skriver et al., 1991, Proc. Natl. Acad. Sci. USA 88:7266-70); the truncated “−90 35S” promoter in the X-GUS-90 vector (Benfey & Chua, 1989, Science 244:174-81); a truncated “−101 nos” promoter derived from the nopaline synthase promoter (Aryan et al., 1991, Mol. Gen. Genet. 225:65-71); and the truncated maize Adh-1 promoter in pADcat 2 (Ellis et al., 1987, EMBO J. 6:11-6).

[0178] According to the present invention, a cis-regulatory element of a WOL promoter is a sequence that confers tissue-specific expression in embryos and/or roots to a truncated promoter. Expression may or may not be organ exclusive.

5.8. WOL Promoter-Driven Expression Vectors

[0179] The properties of the nucleic acid sequences are varied as are the genetic structures of various potential host plant cells. In the preferred embodiments of the present invention, described herein, a number of features which an artisan may recognize as not being absolutely essential, but clearly advantageous are used. These include methods of isolation, synthesis or construction of nucleic acid constructs, the manipulation of the nucleic acid constructs to be introduced into plant cells, certain features of the nucleic acid constructs, and certain features of the vectors associated with the nucleic acid constructs.

[0180] Further, the nucleic acid constructs of the present invention may be encoded on DNA or RNA molecules. According to the present invention, it is preferred that the desired, stable genotypic change of the target plant be effected through genomic integration of exogenously introduced nucleic acid construct(s), particularly recombinant DNA constructs. Nonetheless, according to the present invention, such genotypic changes can also be effected by the introduction of episomes (DNA or RNA) that can replicate autonomously and that are somatically and germinally stable. Where the introduced nucleic acid constructs comprise RNA, plant transformation or gene expression from such constructs may proceed through a DNA intermediate produced by reverse transcription.

[0181] The present invention provides for use of recombinant DNA constructs which contain tissue-specific and developmental-specific promoter fragments and functional portions thereof. As used herein, a functional portion of a WOL promoter is capable of functioning as a tissue-specific promoter in the embryo and/or root vasculature of a plant, or in the developing vascular tissues of other organs. The functionality of such sequences can be readily established by any method known in the art. Such methods include, for example, constructing expression vectors with such sequences and determining whether they confer tissue-specific expression in the embryo and/or root vasculature to a marker gene operably linked to the above-mentioned sequences.

[0182] The WOL promoters of the invention may be used to direct the expression of any desired protein, or to direct the expression of a RNA product, including, but not limited to, an “antisense” RNA or ribozyme. Such recombinant constructs generally comprise a native WOL promoter or a recombinant WOL promoter derived therefrom, ligated to the nucleic acid sequence encoding a desired heterologous gene product.

[0183] A recombinant WOL promoter is used herein to refer to a promoter that comprises a functional portion of a native WOL promoter or a promoter that contains native promoter sequences that is modified by a regulatory element from a WOL promoter. Alternatively, a recombinant inducible promoter derived from the wol promoter may be a chimeric promoter, comprising a full-length or truncated plant promoter modified by the attachment of one or more WOL cis-regulatory elements.

[0184] The manner of chimeric promoter constructions may be any well known in the art. For examples of approaches that can be used in such constructions, see Fluhr et al., 1986, Science 232:1106-12; Ellis et al., 1987, EMBO J. 6:11-6; Strittmatter & Chua, 1987, Proc. Natl. Acad. Sci. USA 84:8986-90; Poulsen & Chua, 1988, Mol. Gen. Genet. 214:16-23; Comai et al., 1991, Plant Mol. Biol. 15:373-81; Aryan et al., 1991, Mol. Gen. Genet. 225:65-71.

[0185] According to the present invention, where a WOL promoter or a recombinant WOL promoter is used to express a desired protein, the DNA construct is designed so that the protein coding sequence is ligated in phase with the translational initiation codon downstream of the promoter. Where the promoter fragment is missing 5′ RNA leader sequences, a DNA fragment encoding both the protein and its 5′ RNA leader sequence is ligated immediately downstream of the transcription initiation site. Alternatively, an unrelated 5′ RNA leader sequence may be used to bridge the promoter and the protein coding sequence. In such instances, the design should be such that the protein coding sequence is ligated in phase with the initiation codon present in the leader sequence, or ligated such that no initiation codon is interposed between the transcription initiation site and the first methionine codon of the protein.

[0186] Further, it may be desirable to include additional DNA sequences in the protein expression constructs. Examples of additional DNA sequences include, but are not limited to, those encoding: a 3′ untranslated region; a transcription termination and polyadenylation signal; an intron; a signal peptide (which facilitates the secretion of the protein); or a transit peptide (which targets the protein to a particular cellular compartment such as the nucleus, chloroplast, mitochondria, or vacuole).

5.9. Production Of Transgenic Plants And Plant Cells

[0187] According to the present invention, a desirable plant or plant cell may be obtained by transforming a plant cell with the nucleic acid constructs described herein. In some instances, it may be desirable to engineer a plant or plant cell with several different gene constructs. In one embodiment, a heterologous protein may also be expressed to produce transgenic plants with altered expression at two loci. An example of a heterologous protein includes, but is not limited to, the SCARECROW protein which has been described in U.S. patent application of Benfey et al. for “Scarecrow Gene Promoter and Uses Thereof”, filed Nov. 5, 1998 (identified as docket number 5914-0075), which is incorporated herein by reference in its entirety for its relevant teaching. Thus, for example, and not by way of limitation, a WOL/SCARECROW double mutant can be produced and may have only protoxylem and a cell layer with the characteristics of endodermis and cortex. Such engineering may be accomplished by transforming a plant or plant cell with all of the desired nucleic acid constructs simultaneously. Alternatively, the engineering may be carried out sequentially. That is, transforming with one nucleic acid construct, obtaining the desired transformant after selection and screening, transforming the transformant with a second nucleic acid construct, and so on.

[0188] In an embodiment of the present invention, Agrobacterium is employed to introduce the nucleic acid constructs into plants. Such transformations preferably use binary Agrobacterium T-DNA vectors (Bevan, 1984, Nuc. Acid Res. 12:8711-21), and the co-cultivation procedure (Horsch et al., 1985, Science 227:1229-31). Generally, the Agrobacterium transformation system is used to engineer dicotyledonous plants (Bevan et al., 1982, Ann. Rev. Genet. 16:357-84; Rogers et al., 1986, Methods Enzymol. 118:627-41). The Agrobacterium transformation system may also be used to transform, as well as transfer, DNA to monocotyledonous plants and plant cells (see Hernalsteen et al., 1984, EMBO J. 3:3039-41; Hooykass-Van Slogteren et al., 1984, Nature 311:763-4; Grimsley et al., 1987, Nature 325:1677-79; Boulton et al., 1989, Plant Mol. Biol. 12:31-40.; Gould et al., 1991, Plant Physiol. 95:426-34).

[0189] In other embodiments, various alternative methods for introducing recombinant nucleic acid constructs into plants and plant cells may also be utilized. These other methods are particularly useful where the target is a monocotyledonous plant or plant cell. Alternative gene transfer and transformation methods include, but are not limited to, protoplast transformation through calcium-, polyethylene glycol (PEG)- or electroporation-mediated uptake of naked DNA (see Paszkowski et al., 1984, EMBO J. 3:2717-22; Potrykus et al., 1985, Mol. Gen. Genet. 199:169-177; Fromm et al., 1985, Proc. Natl Acad. Sci. USA 82:5824-8; Shimamoto, 1989, Nature 338:274-6), and electroporation of plant tissues (D'Halluin et al., 1992, Plant Cell 4:1495-1505). Additional methods for plant cell transformation include microinjection, silicon carbide mediated DNA uptake (Kaeppler et al., 1990, Plant Cell Reporter 9:415-8), and microprojectile bombardment (Klein et al., 1988, Proc. Natl. Acad. Sci. USA 85:4305-9; Gordon-Kamm et al., 1990, Plant Cell 2:603-18).

[0190] According to the present invention, a wide variety of plants may be engineered for the desired physiological and agronomic characteristics described herein using the nucleic acid constructs of the instant invention and the various transformation methods mentioned above. In preferred embodiments, target plants for engineering include, but are not limited to, crop plants such as maize, wheat, rice, soybean, tomato, tobacco, carrots, peanut, potato, sugar beets, sunflower, yam, Arabidopsis, rape seed, petunia, and spruce, as well as species of the genera Betula, Populus, Pinus, and Eucalyptus.

[0191] According to the present invention, desired plants and plant cells may be obtained by engineering the nucleic acid constructs described herein into a variety of plant cell types, including, but not limited to, protoplasts, tissue culture cells, tissue and organ explants, pollen, embryos as well as whole plants. In an embodiment of the present invention, the engineered plant material is selected or screened for transformants (i.e., those that have incorporated or integrated the introduced nucleic acid construct or constructs) following the approaches and methods described below. An isolated transformant may then be regenerated into a plant. Alternatively, the engineered plant material may be regenerated into a plant, or plantlet, before subjecting the derived plant, or plantlet, to selection or screening for the marker gene traits. Procedures for regenerating plants from plant cells, tissues or organs, either before or after selecting or screening for marker gene or genes, are well known to those skilled in the art.

[0192] A transformed plant cell, callus, tissue or plant may be identified and isolated by selecting or screening the engineered plant material for traits encoded by the marker genes present on the transforming DNA. For instance, selection may be performed by growing the engineered plant material on media containing inhibitory amounts of the antibiotic or herbicide to which the transforming marker gene construct confers resistance. Further, transformed plants and plant cells may also be identified by screening for the activities of any visible marker genes (e.g., the β-glucuronidase, luciferase, GFP, B or C1 genes) that may be present on the recombinant nucleic acid constructs of the present invention. Such selection and screening methodologies are well known to those skilled in the art.

[0193] Physical and biochemical methods may also be used to identify a plant or plant cell transformant containing the nucleic acid constructs of the present invention. These methods include but are not limited to: 1) detection and determination of the structure of the recombinant DNA insert by Southern blot or PCR amplification; 2) detection and examination of RNA transcripts of the nucleic acid constructs by Northern blot, S-1 RNase protection, primer-extension or reverse transcriptase-PCR amplification; 3) detection of enzyme or ribozyme activity (where such gene products are encoded by the nucleic acid construct) by enzymatic assays; 4) detection of protein products of the nucleic acid construct by protein gel electrophoresis, western blot, immunoprecipitation, or enzyme-linked immunoassays; and 5) measurement of compounds produced as a consequence of the expression of the introduced nucleic acid constructs by biochemical methods. Additional techniques, such as in situ hybridization, enzyme staining, and immunostaining, may also be used to detect the presence or expression of the recombinant construct in specific plant organs and tissues. Methods of performance of the above-mentioned assays are well known to those skilled in the art.

5.9.1. Transgenic Plants That Ectopically Express WOL

[0194] In accordance to the present invention, a plant that expresses a recombinant WOL nucleic acid may be engineered by transforming a plant cell with a nucleic acid construct comprising a plant promoter operably associated with a sequence encoding a WOL protein or a fragment thereof. Operably associated is used herein to mean that transcription controlled by the associated promoter would produce a functional mRNA, whose translation would produce the WOL protein. The plant promoter may be constitutive or inducible. Useful constitutive promoters include, but are not limited to, the CaMV 35S promoter, the T-DNA mannopine synthetase promoter, and their various derivatives. Useful inducible promoters include, but are not limited to, the promoters of ribulose bisphosphate carboxylase (RUBISCO) genes, chlorophyll a/b binding protein (CAB) genes, heat shock genes, the defense responsive gene (e.g., phenylalanine ammonia lyase genes), wound induced genes (e.g., hydroxyproline rich cell wall protein genes), chemically-inducible genes (e.g., nitrate reductase genes, gluconase genes, chitinase genes, PR-1 genes etc.), dark-inducible genes (e.g., asparagine synthetase gene as described by U.S. Pat. No. 5,256,558), and developmentally regulated genes (e.g., Shoot Meristemless gene).

[0195] In yet another embodiment of the present invention, it may be advantageous to transform a plant with a nucleic acid construct operably linking a modified or artificial promoter to a sequence encoding a WOL protein or a fragment thereof. Such promoters typically have unique expression patterns and/or expression levels not found in natural promoters because they are constructed by recombining structural elements from different promoters. See, e.g., Salina et al., 1992, Plant Cell 4:1485-93, for examples of artificial promoters constructed from combining cis-regulatory elements with a promoter core.

[0196] In a preferred embodiment of the present invention, the associated promoter is a strong root and/or embryo-specific plant promoter such that the WOL protein is overexpressed in the transgenic plant.

[0197] In yet another preferred embodiment of the present invention, the overexpression of WOL protein in root vasculature may be engineered by increasing the copy number of the WOL gene. One approach to producing such transgenic plants is to transform with nucleic acid constructs that contain multiple copies of the complete WOL gene (i.e., with its own native wol promoter). Another approach is repeatedly transform successive generations of a plant line with one or more copies of the complete WOL gene. Yet another approach is to place a complete WOL gene in a nucleic acid construct containing an amplification-selectable marker (ASM) gene such as the glutamine synthetase or dihydrofolate reductase gene. Cells transformed with such constructs is subjected to culturing regimes that select cell lines with increased copies of complete WOL gene. See, e.g., Donn et al., 1984, J. Mol. Appl. Genet. 2:549-62, for a selection protocol used to isolate of a plant cell line containing amplified copies of the GS gene. Cell lines with amplified copies of the WOL gene can then be regenerated into transgenic plants.

5.9.2. Transgenic Plants That Suppress Endogenous WOL Expression

[0198] In accordance with the present invention, a desired plant may be engineered by suppressing WOL activity. In one embodiment, the suppression may be engineered by transforming a plant with a nucleic acid construct encoding an antisense RNA or ribozyme complementary to a segment or the whole of WOL RNA transcript, including the mature target mRNA. In another embodiment, WOL gene suppression may be engineered by transforming a plant cell with a nucleic acid construct encoding a ribozyme that cleaves the WOL mRNA transcript. In another embodiment, the WOL mRNA transcript can be suppressed through the use of RNA interference (RNAi). In yet another embodiment, antisense technology can be used to inhibit WOL mRNA expression. Alternatively, the plant can be engineered, e.g., via targeted homologous recombination to inactive or “knock-out” expression of the plant's endogenous WOL.

[0199] For all of the aforementioned suppression constructs, it is preferred that such nucleic acid constructs express specifically in the embryonic tissues and/or the vascular tissue of the root. Alternatively, it may be preferred to have the suppression constructs expressed constitutively. Thus, constitutive promoters, such as the nopaline, CaMV 35S promoter, may also be used to express the suppression constructs. A most preferred promoter for these suppression constructs is a WOL promoter.

[0200] In accordance with the present invention, desired plants with suppressed target gene expression may also be engineered by transforming a plant cell with a co-suppression construct. A co-suppression construct comprises a functional promoter operatively associated with a complete or partial WOL nucleic acid sequence. It is preferred that the operatively associated promoter be a strong, constitutive promoter, such as the CaMV 35S promoter. Alternatively, the co-suppression construct promoter can be one that expresses with the same tissue and developmental specificity as the wol gene.

[0201] According to the present invention, it is preferred that the co-suppression construct encodes an incomplete WOL mRNA, although a construct encoding a fully functional WOL mRNA or enzyme may also be useful in effecting co-suppression.

[0202] In accordance with the present invention, desired plants with suppressed target gene expression may also be engineered by transforming a plant cell with a construct that can effect site-directed mutagenesis of the WOL gene. For discussions of nucleic acid constructs for effecting site-directed mutagenesis of target genes in plants see, e.g., Offringa et al., 1990, EMBO J. 9:3077-84; and Kanevskii et al., 1990, Dokl. Akad. Nauk. SSSR 312:1505-7. It is preferred that such constructs effect suppression of WOL genes by replacing the endogenous WOL gene sequence through homologous recombination with either an inactive or deleted WOL protein coding sequence.

5.9.3. Transgenic Plants That Express A Transgene Controlled By The WOL Promoter

[0203] In accordance with the present invention, a desired plant may be engineered to express a nucleic acid encoding a gene product of interest under the control of the WOL promoter. WOL promoters and functional portions thereof refer to regions of the nucleic acid sequence which are capable of promoting tissue-specific transcription of a gene of interest when operably linked to that gene. In the case of WOL, tissue-specific expression exists in the embryo and/or root vasculature of a plant, or in the developing vascular tissue of other organs. The WOL promoter described herein refers to the regulatory elements of WOL genes as described in Sections 5.7 and 5.8.

[0204] Genes that may be beneficially expressed in the embryo and/or root vasculature of a plant include genes involved in nitrogen fixation or cytokines or auxins, or genes which regulate growth, or growth of roots. In addition, genes encoding proteins that confer on plants herbicide, salt, or pest resistance may be engineered for tissue specific expression. The nutritional value of root crops may also be enhanced through WOL promoter driven expression of nutritional proteins (such as starch, lignin, or cellulose). Alternatively, therapeutically useful proteins may be expressed specifically in root crops.

[0205] Genes that may be beneficially expressed in the stems of plants include those involved in starch, lignin, cellulose biosynthesis, pest resistance, and cell expansion genes controlling fibre formation.

[0206] In other embodiments properties of wood in trees are altered. In one such embodiment, overexpression of a WOODEN LEG protein or polypeptide in a transgenic plant is used to increase layers of wood (vascular) tissues in trees. In another embodiment, ectopic expression of a WOODEN LEG protein or polypeptide in a transgenic plant is driven by a promoter other than the WOL promoter in order to increase vascular development in certain tissue layers, thus resulting in the formation of more wood. In still other embodiments, the WOL promoters of the invention are linked to a heterologous gene known to be involved in aspects of wood formation and genetically engineered into a plant. Such heterologous genes include, but are not limited to, genes known to have an effect on lignin production and/or composition such as the Caffeic Acid O-Methyltransferase (cOMT) gene of Moyle, et al., 1999. Plant Physiol. 119: 1147 and the SAM gene of Meng and Campbell,1995. Plant Physiol. 108: 1749. Genes related to cellulose production and degradation are also of great interest such as the cellulose synthase gene of Arioli et al., 1998. Science 279:717-720. In still other embodiments, a gene controlling pigmentation and aspects of vascular patterning effecting wood grain appearance is expressed under the control of a WOL promoter incorporated into the invention. Thus, the invention provides methods that utilize WOL promoters to improve the quality of wood and/or adjust the characteristics of wood to meet specific, e.g. commercial, specifications.

[0207] In accordance with the present invention, desired plants which express a heterologous gene of interest under the control of the WOL promoter may be engineered by transforming a plant cell with WOL promoter driven constructs using those techniques described in this Section 5.9.

5.9.4. Screening Of Transformed Plants For Those Having Desired Altered Traits

[0208] It will be recognized by those skilled in the art that in order to obtain transgenic plants having the desired engineered traits, screening of transformed plants (i.e., those having an nucleic acid construct of the invention) having those traits may be required. For example, where the plants have been engineered for ectopic overexpression of a WOL nucleic acid, transformed plants are examined for those expressing a WOL gene product at the desired level and in the desired tissues and developmental stages. Where the plants have been engineered for suppression of a WOL gene product, transformed plants are examined for those expressing a WOL gene product (e.g., RNA or protein) at reduced levels in various tissues. The plants exhibiting the desired physiological changes, e.g., ectopic WOL overexpression or WOL suppression, may then be subsequently screened for those plants that have the desired structural changes at the plant level (e.g., transgenic plants with overexpression or suppression of the WOL gene having the desired altered root or stem structure). Altered root structure can include, but is not limited to longer roots, shorter roots, thicker roots, thinner roots, and roots with a predominantly adventitious origin. Altered stem structure can include, but is not limited to, thicker or thinner stems. The same principle applies to obtaining transgenic plants having tissue-specific expression of a heterologous gene in embryos and/or roots by the use of a WOL promoter driven expression construct.

[0209] Alternatively, the transformed plants may be directly screened for those exhibiting the desired structural and functional changes. In one embodiment, such screening may be for the size, length or pattern of the root of the transformed plants. In other embodiments, the screening of the transformed plants may be for improved agronomic characteristics (e.g., faster growth or deeper root growth, more extensive wood production, etc.), as compared to unengineered progenitor plants, when cultivated under various growth conditions (e.g., soils or media containing different amount of nutrients, water content).

[0210] According to the present invention, plants engineered with WOL overexpression may exhibit improved vigorous growth characteristics when cultivated under conditions where large and thicker roots are advantageous. Plants engineered for WOL suppression may exhibit improved vigorous growth characteristics when cultivated under conditions where thinner roots are advantageous.

[0211] Engineered plants and plant lines possessing such improved agronomic characteristics may be identified by examining any of following parameters: 1) the rate of growth, measured in terms of rate of increase in fresh or dry weight; 2) vegetative yield of the mature plant, in terms of fresh or dry weight; 3) the seed or fruit yield; 4) the seed or fruit weight; 5) the total nitrogen content of the plant; 6) the total nitrogen content of the fruit or seed; 7) the free amino acid content of the plant; 8) the free amino acid content of the fruit or seed; 9) the total protein content of the plant; and 10) the total protein content of the fruit or seed. The procedures and methods for examining these parameters are well known to those skilled in the art.

[0212] According to the present invention, a desired plant is one that exhibits improvement over the control plant (i.e., progenitor plant) in one or more of the aforementioned parameters. In an embodiment, a desired plant is one that shows at least 5% increase over the control plant in at least one parameter. In a preferred embodiment, a desired plant is one that shows at least 20% increase over the control plant in at least one parameter. Most preferred is a plant that shows at least 50% increase in at least one parameter.

6. EXAMPLE 1

Characterization Of WOL

[0213] This example shows the identification of WOL, a gene involved in the control of asymmetric cell divisions and xylem differentiation through a specific signal transduction pathway. Sequence analysis shows that the WOL protein is a novel two component signal transducer and is required for asymmetric cell divisions during vascular tissue morphogenesis. In situ studies show that WOL is expressed in the vascular cylinder and pericycle in embryogenesis through at least five days after germination. These findings indicate that the WOL gene regulates key events that establish the asymmetric division that generate vascular patterning.

6.1. Introduction

[0214] The WOL locus was previously identified by a recessive mutation that resulted in reduced cell number and exclusive xylem differentiation within the vascular tissue (Scheres et al., 1995, Development 121:53-62). This reduced cell number was first observed during embryogenesis, when a cell division process failed to take place in the root and lower hypocotyl region soon after the torpedo stage. Subsequently, this pattern was elaborated by the procambial initials during primary root development (Scheres et al. 1995, supra).

6.2. WOL Is Essential For Vascular Asymmetric Cell Division

[0215] The WOL-dependent divisions that resulted in the patterning of xylem and phloem of the root were identified by determining the vascular cell lineage relationships in the primary root of wildtype and wol Arabidopsis (FIG. 1, Table 1). Examination of primary root meristem serial sections was conducted to ascertain the effects of wol mutant on this tissue. Seedlings were fixed according to Scheres et al. (1994, Development 120:2475-87) and embedded using Leica Historesin (Heidelberg, Germany). Sections (2-3 mm) were made on a Leica RM2165 rotary microtome, using a Leica microtome knife. Sections were stained in a 0.05% toluidine blue solution in water and photographed on an Olympus Provis microscope using a Sensicam 12 bit cooled camera (PCO, ccd imaging). Images were processed with Adobe Photoshop 4.0.1.

[0216] In serial sections of the primary root meristem (FIG. 1), xylem cell lineages formed an axis composed of 4-5 cell files very close to the underlying quiescent center (FIG. 1C, schematic). Two domains of initials (2-5 cells each; FIGS. 1B-C) that gave rise to the phloem cell lineages and to the undifferentiated procambial cell lineages through asymmetric cell divisions (FIGS. 1C-G; schematic) flanked this axis. The number and exact pattern of these procambial divisions showed some variability between individual seedlings, which is in contrasted to the invariant pattern of cell lineages in the endodermis and outer layers (Scheres et al., 1994, supra). These divisions were asymmetric in the sense that they give rise to multiple cell lineages with different fates (Horvitz & Herskowitz, 1992, Cell 68:237-55). The histologically early phloem differentiation as compared to xylem differentiation (FIGS. 1H-I) was consistent with previous descriptions in other species (Esau, K. 1977. Anatomy of seed Plants. John Wiley & Sons, New York, N.Y., ed. 2).

[0217] In wol, the periclinal cell divisions described above are absent (FIGS. 1J-K, schematic) with the exception of a few divisions that slightly increased cell number in the vascular cylinder (Table 1). Furthermore, the number of vascular initials in wol was slightly lower than in wild-type, which indicated that some of the embryonic divisions required to form the initials did not occur. Taken together, WOL activity was associated with a set of formative divisions that first took place during the late stages of embryogenesis (Scheres et al. 1995, supra) and that continued to propagate the pattern in the root meristem.

	TABLE 1
	Initial cells	Differentiated cells
	wt	11 ± 1.49	31 ± 1.71
	wol	8 ± 2.23	9 ± 2.07

[0218] Cell numbers in the primary root of Arabidopsis (wt n=8; wol n=6). Numbers of initial cells were counted in sections made directly above the quiescent center, numbers of differentiated cells were made approximately 200 mm above the quiescent center. Mean cell numbers and ±SD are indicated.

6.3. WOL Is Required For Vascular Morphogenesis

[0219] The role of WOL in phloem specification was analyzed previously in the context of a double mutant of wol and fass (a mutation resulting in supernumerary cell layers). The double mutants from the cross described in Scheres et al. (1995, supra) were isolated by analysis of the fass-looking plants of the F3 segregating in the wol background. Wol x fass double mutant seedlings were cleared with acidified methanol (20% MeOH; 4% concentrated HCl in H2O) and incubated at 55°-57° C. for 15 minutes. The acidified methanol was then replaced with a basic solution (7% NaOH in 60% EtOH) and incubated for 15 minutes at room temperature. The seedlings were rehydrated in several steps by incubation in varying concentrations of EtOH (40%, then 20% and finally in 10% EtOH). The seedlings were stained for 5 minutes in 0.01% basic fuchsin solution, destained in 70% ethanol and rehydrated to 10% ethanol solution. An equal amount of 50% glycerol was added and then incubated another 30 minutes. Seedlings were mounted in 50% glycerol. CLSM images were taken on an Axiovert 135M confocal microscope with an argon ion laser (568+488 nm emission). Image processing consisted of Kalman filtering during image acquisition (Bio-Rad software). Optical sections were projected together to form a composite image of the vascular bundle.

[0220] In the wol x fass double mutant, there was an increase in the number of vascular cell layers with phloem markers observed in the vascular cylinder, indicating that WOL is not essential for phloem development. A model was proposed, in which xylem specification temporally precedes phloem development. Because the wol mutant had a reduced number of vascular precursor cells, all the available cells were specified as xylem (Scheres et al. 1995, supra). More recently, it was shown that xylem organization is also altered in wol (Cano-Delgado et al., 2000, Development 127:3395-3405). The xylem axis in wildtype consists of two types of cells: protoxylem, the two outermost cells with predominantly annular (ring like) cell wall thickenings which differentiates early, and metaxylem, the central cells with reticulate (more continuous) wall thickenings, which differentiates later (FIG. 2A). In contrast, the vascular cylinder of the wol primary root consists solely of protoxylem (FIG. 2B). Therefore, the status of xylem in the wol x fass background was investigated. Both protoxylem and metaxylem were found to be present (FIG. 2C). Thus, WOL was not necessary for metaxylem differentiation, but did have an indirect influence on xylem differentiation by controlling the number of cells in the vascular cylinder.

6.4. Cloning And Description Of The Arabidopsis WOL Gene

[0221] The WOL locus of Arabidopsis was characterized genetically and molecularly. WOL, a putative two component histidine kinase with a receptor domain similar to that of the DhkA receptor of Dictyostelium discoideum, is shown to be required for a set of asymmetric cell divisions that establish the morphogenesis of vascular tissue in the root and hypocotyl region. The deduced domain structure of WOL suggests it represents a novel class among the two hybrid molecules characterized to date from plants, some other eukaryotes and bacteria. The WOL protein is a component of the signal transduction pathway regulating vascular cell proliferation and differentiation.

[0222] The molecular nature of the WOL gene product was identified through positional cloning of the WOL gene (FIG. 3A). WOL locus was cloned using chromosome walking techniques. CAPS (cleaved amplified polymorphic sequences, see Konieczny & Ausubel, 1993, Plant J. 4:403-10) markers T23K3/3 (SEQ ID NO:21) and Kin2/4 (SEQ ID NO:22) (and six other markers, see Table 2) between pre-existing markers RNS1 and rga were created by detecting polymorphism between Landsberg and Columbia ecotypes. Complementation vector pCOM32 was created by cloning a 13.8 kb Msc1 fragment into the SmaI of the pBIN19 derivative pRD400 (Datla et al., 1992, Gene 122:383-4). The construct was transformed into Agrobacterium tumefaciens strain C58C1 pGV2260) (essentially as in Bevan, 1984, Nucleic Acid Res. 12:8711-21). wol plants were transformed with pCOM32 (Clough & Bent, 1998, Plant J. 16:735-43). Transgenic seedlings (T1) with long roots were selected by resistance to kanamycin. Presence of the transgene in these plants was confirmed by PCR. Segregation of the transgene in T2 generation was confirmed.

[0223] An Arabidopsis wol mutant was also rescued by inserting a transgene containing a fragment of pCOM32.

TABLE 2
CAPS Markers
Marker	Location (in BAC)	Primers	Length	Restriction enzyme cutting sites (col and ler)
RGA	(F219)	GTTTAAGCAAGCGAGTATGC	263	Rsa1: col 1 (143,120);
(CAPS)		TTCGATTCAGTTCGGTTTAG		ler 0 (263)
		(SEQ ID NO: 28)
T8O11/1	4854-5743 (T8O11)	gaa ttc ttg ttt tag agt tcc	890	Hind2: col 0 (890);
(CAPS)		tga gta gag tgt tct ttc tcc		ler 1 (725,165)
		(SEQ ID NO: 37)
Kin2/4	6274-7511 (T23K3)	ACTGAGAACCGAAGAAATCTGGG	1238	Sac1: col 0 (1238);
(CAPS)		AGTCCGAAAAATGCCGAAATAC		ler 1 (973,265)
		(SEQ ID NO: 22)
Kin2-3	7993-9253 (T23K3)	AGA GAG ACG CCG TGA AAT CC	1261	Dde1: col 3: (572,421,219,49);
(CAPS)		TAT TAA TCC CAC GGG ATC G		ler 2 (572,470,219)
		(SEQ ID NO: 38)
T23K3/2	13547-14655 (T23K3)	ctt gat gat tgt tga gtg ccc	1109	Ksp632I: col 1 (611,498);
(CAPS)		gtt cgg tgc gga tct tcc		ler 0 (1109)
		(SEQ ID NO: 39)
T23K3/3	17173-18127 (T23K3)	caa aat gtg tgt gtg tcg gcc	955	Hph1: col 1 (577,377);
(CAPS)		gta cca aag tcc aca cga ttc c		ler 2 (577,275,102)
		(SEQ ID NO: 21)
T23K3/4	66322-67455 (T23K3)	ggc tga ctt gac tct ctt ttc c	1134	Hinf1: col 6 (463,295,200,100,36,30,10);
(CAPS)		ccg agt gct ttt tag agc c		ler 5: (463,295,236,100,30,10)
		(SEQ ID NO: 40)
T23K3/7	33713-34944 (T23K3)	tga tca cac atg gta cct ttc g	1232	Dra1 + Hind3 (SSLP): col 4 (379,323,217,
(SSLP)		gca agc tct tga tct ctc tag c		273,40); ler 4 (379,323,202,273,40)
		(SEQ ID NO: 41)
F504/1	78313-78632 (F504)	gtg tga tga aac tgt ctc gcc	319	StyI: col 0 (319)
(dCAPS)		gtg taa gct tgt taa gag ttt acc		ler 1: (25,294)
		(SEQ ID NO: 42)
nga1145	(T8K22)	cct tca cat cca aaa ccc ac	85-89	ler (89); col (85)
(SSLP)		gtg ata gac ttt gaa gaa ag
		(SEQ ID NO: 43)
RNS1	(T17M13)	tat cca tct aac tgt gat gcc	n.550	Ava1: col 0 (n.550); ler 1 (n. 300,250)
		act ttg aca tca aaa cgt acc
		(SEQ ID NO: 27)
ler = ecotype Landsberg erecta
col = ecotype Columbia

[0224] The wol locus was mapped to an 11 kb region between two CAPS markers in the BAC clone T23K3 (GenBank Accession Number AC007069) (FIG. 3A). The annotation (Lin et al., 1999, Nature 402:761-8) predicted only one gene (T23K3.2, a putative two component histidine kinase) in this region. The region between the CAPS markers was completely sequenced in wol and only one point mutation was found, converting T278 to I278 in the deduced amino acid sequence. The identity of the two component hybrid molecule was confirmed as WOL by complementation of the mutation with a 13.8 kb fragment of genomic DNA (pCOM32, FIG. 3A). Homozygous wol plants which contained the transgene had indeterminate root growth, normal cell number and a wild-type pattern of xylem, phloem and procambial cells (FIGS. 3C-D).

[0225] The WOL coding region was identified by sequencing the longest (T20648) of several ESTs (GenBank Accession Numbers AA586219, SEQ ID NO:14; AI992824, SEQ ID NO:15; and T20648, SEQ ID NO:16) homologous to the WOL locus. Gene specific primers were used in the RobusT RT-PCR Kit (Finnzymes Oy, Espoo, Finland) according to the manufacturer's instructions. To determine the 5′-UTR of the WOL mRNA the 5′ RACE System for Rapid Amplifications of cDNA Ends version 2.0 (Life Technologies, Paisley, Scotland) was used according to the manufacturer's instructions. The major amplification products that resulted from the 5′RACE were cloned. Three different cDNA species (GenBank Accession Numbers AJ278528, AJ278529, and AJ278530) corresponding to three different transcription start sites and alternative splicing schemes were detected (FIG. 3B). All resulted in an identical longest ORF of 1057 amino acid residues, which indicated that the alternative splicing did not have an impact on the amino acid sequence of the gene product.

6 .5. WOL Is A Member Of A Novel Family Of Two Component Hybrid Molecules

[0226] The predicted WOL protein showed extensive similarity to two component hybrid molecules, and thus suggested that it functioned as a signal transducer (FIG. 3E). The WOL protein was shown to have a short N-terminal cytoplasmic domain (residues 1-105, SEQ ID NO:6) followed by an extracellular receptor (R) domain (residues 127-400, SEQ ID NO:8) flanked by two transmembrane regions (residues 106-126, SEQ ID NO:7 and residues 401-421, SEQ ID NO:9) and the C-terminal phosphorelay domain system with a histidine kinase domain (H) (residues 449-737, SEQ ID NO:10) and two receiver domains (DA and DB) (residues 762-893, SEQ ID NO:11 and 922-1044, SEQ ID NO:12, respectively).

[0227] The WOL domain organization and receptor domain structure place it in a distinct subclass among previously identified plant two component receptors. The other receptors have been shown to function in ethylene or cytokinin signal transduction or in osmosensing (Chang et al., 1993, Science 262:539-44; Kakimoto, 1996, Science 274:982-5; Urao et al., 1999, Plant Cell 11:1743-54; Urao et al., 2000, Trends Plant Sci. 5: 67-74). The tandem arrangement of two putative receiver domains has been previously reported for an uncharacterized gene slr0322 of Synechochystis (Mizuno et al., 1996, DNA Res. 3:407-14). However, this gene does not exhibit significant homology to the WOL genes and may not be very closely related functionally. Among the two component molecules of bacteria, plants and some other eukaryotes characterized to date, the putative receptor domain, the histidine kinase domain and one of the two receiver domains (DB) of WOL are most similar to DhkA receptor of Dictyostelium discoideum (SEQ ID NO:17). DhkA is essential for cellular organization during fruiting body development (Mizuno et al. 1996, supra) and its ligand may be a peptide (Wang et al., 1999, Mol Cell Biol. 7:4750-6). It is therefore possible that a homologous receptor-ligand interaction is specifying development both in slime molds and plants.

6.6. WOL Expression Is Specific For The Vascular Cylinder

[0228] Specificity of WOL expression was determined using a gene specific probe (FIG. 3B). Genomic DNA preparation (Doyle & Doyle, 1990, Focus 12:13-5) was performed from 17-day-old seedlings. Southern blot analysis was performed with 15 mg of DNA and the 32P-labeled 256 bp PCR fragment (corresponding to nucleotides 10143 to 10398 of the BAC clone T23K3, SEQ ID NO:13) of WOL or a 1067 bp cDNA fragment (corresponding to nucleotides 10055 to 11204 of SEQ ID NO:1) of WOL genomic sequence as a probe (Maniatis et al., 1982, Molecular Cloning, a Laboratory Manual Cold Spring Harbor Laboratory Press, New York, N.Y.). Both probes were specific for the WOL gene. Southern blot analysis indicated that hybridization was specific for the WOL gene under the conditions used.

[0229] WOL expression was monitored by Northern blot analysis. Briefly, total RNA was isolated from 17-day-old Arabidopsis thaliana ecotype Columbia root and shoot (Martinez-Zapater & Salinas, 1998, in Methods in Molecular Biology: Arabidopsis Protocols, Humana Press Inc., Totowa, N.J., Vol 82). Northern blot analysis was carried out with 15 mg of total RNA. The membrane was hybridized with a 32P-labeled gene specific WOL probe (described above). A single major band of about 3.7 kb which was more abundant in root than shoot was detected in the RNA blot analysis(FIG. 3G), thus demonstrating highly localized expression in the root, though expression was not entirely exclusive to the root.

[0230] In an embodiment of the present invention, RNA in situ hybridization can be employed to analyze expression patterns of WOL genes as well as expression patterns of heterologous gene products driven by WOL promoters. Numerous alternative methods, adjustments, and variations on portions of the RNA in situ hybridization procedure are well known to those practiced in the art (Di Laurenzio et al. 1996, Cell 86: 423-33). The following procedure for RNA in situ hybridization has been optimized by the inventors for Arabidopsis roots and siliques. It is important to conduct the procedure in a RNase free work environment prior to the posthybridization washes.

[0231] Sample preparation consists of three stages: fixation, dehydration, and clearing. Roots are first cut so that 2-3 mm of hypocotyl remain contacted to the root. This helps to orient the tissue later. Siliques are cut about 1 mm of tissue away from the both ends of each silique. After cutting, the tissue is immediately immersed in a freshly prepared fixative (4% paraformaldehyde solution in 1×PBS). Sections remain in the fixative for 2-4 hours at room temperature during which time the samples are vacuum infiltrated 3-4 times for 5 minute periods.

[0232] After fixation, the fixative is replaced (optional for roots) and the samples are left to incubate overnight at 4° C. The following day all fixative is removed and the tissue samples are rinsed twice with 1×PBS, each time for 30 min. Roots are next embedded in 1% agarose (in PBS) and trimmed into a block, while silique samples are left free. The tissue samples are then dehydrated in a graded ethanol series (ethanol+water): 30% ethanol for 30 min, 50% ethanol for 30 min, 70% ethanol for 30 min (can go overnight), 85% ethanol for 30 min, 95% ethanol for 30 min, 100% ethanol for 30 min, 100% ethanol for 30 min, and 100% ethanol for 30 min. The tissue samples are then cleared by passing them through the through the following solution series:50% ethanol/50% xylene for 30 min, 100% xylene for 30 min, 100% xylene for 30 min, and 100% xylene for 30 min.

[0233] To infiltrate the samples, the xylene is removed and fresh molten Histoplast (Shandon) is added to the samples which are then allowed to incubate overnight at 60° C. The Histoplast is changed at least once a day over the next 1-4 days. The solidified blocks from the molds should be stored at 4° C. The tissue blocks are trimmed into 7-10 um thick microtome sections (Leica: Disposable microtome blade 819) and the ribbon pieces are floated on a Superfrost plus slide (Menzel-Glässer/KEBO 113.720-0) covered with DEPC-H2O. The slides are warmed (50° C.) allowing the ribbon to flatten out. The water is removed and the slides are dried completely at room temperature. In order to bake the sections, slides are incubated overnight at 37-42° C. The sections are then stored at 4° C.

[0234] To synthesize probes, it is recommended to start with about 200-300 bp long single-stranded RNA probes. Template DNA can be cloned into a vector containing SP6/T7 promoters of the DIG RNA Labeling Kit (BM 1 175 025) and the RNA synthesized by using in vitro transcription system. The plasmid is linearized for making both antisense and sense (negative control) “run-off” transcripts. It is preferable to use an enzyme that leaves 5′-overhangs or blunt ends. DNA is purified by phenol/chloroform extraction, precipitated, then the pellet is resuspended in DEPC-H2O. A master mix is made for the number of reactions using the BM: DIG RNA Labeling Kit (SP6/T7) (BM 1 175 025). Exactly 9 ul of the master mix and 2 ul of appropriate RNA-polymerase are combined and allowed to incubate for 2 hours at 37° C. The DNA is then removed from the mixture (BM: DIG RNA Labeling Kit). After incubate the mixture for 15 min at 37° C., the reaction is stopped and the RNA is precipitated by adding 2 ul 0.5 M EDTA, 6 ul 4 M LiCl, and 180 ul cold 100% ethanol. The mixture is then incubated overnight at −80° C. The RNA is spun down at 13 000 rpm for 20-30 min at 4° C. and the pellet rinsed with 70% ethanol and spun for and additional 5 min. The pellet is dried and resuspend in 95 ul of DEPC- H2O and 1 ul of RNase inhibitor was added for an incubation period of 30 min at 37° C.

[0235] In order to reduce the size of long probes, they are hydrolyzed chemically in alkaline carbonate buffer at 60° C. The carbonate hydrolysis buffer (pH 10.2) is prepared by mixing 8.5 ml of 1M Na2CO3 with 1 ml of 1M NaHCO3. The hydrolysis time is calculated as follows: time (min)=(starting length in kb−final length in kb)/(rate constant)(starting length in kb)(final length in kb), where the rate constant=0.11 kb/1 min. 10 ul of the carbonate buffer are added to the probe (90 ul) and incubated at 60° C. for the calculated time.

[0236] Following incubation, 12.5 ul 5% acetic acid is added to each probe sample. To precipitate the RNA, 12.5 ul 3 M NaOAC pH 5.2, 310 ul ethanol, and 10 ug tRNA (optional) is added and the resulting mixture is allowed to incubate overnight at −80° C. The following day the RNA is spun down at 13 000 rpm for 20-30 min at 4° C. and the resulting pellet is rinsed with 70% ethanol and spun for an additional 5 min. The pellet is dried and resuspended in DEPC-H2O and 1 ul of RNase inhibitor is added to the mixture for an incubation period of 30 min at 37° C. The probe is then quantified using the protocol in “The DIG system user's guide for filter hybridization” DIG RNA Labeling Kit (BM 1 175 025).

[0237] To pretreat the slides, they are placed in a slide rack and passed through the following solution series: Xylene for 10 min, Xylene for 10 min, Methanol for 15 min, 100% ethanol for 1 min, 100% ethanol for 1 min, 95% ethanol for 1 min, 85% ethanol: 0.85% NaCl for 1 min, 70% ethanol: 0.85% NaCl for 1 min, 50% ethanol: 0.85% NaCl for 1 min, 30% ethanol: 0.85% NaCl for 1 min, 0.85% NaCl for 2 min, 1×PBS for 2 min, 0.2 M HCl for 20 min, H2O for rinse, 2×SSC for 20 min, a H20 rinse, 10 ug/ml Proteinase K (Sigma P-2308) in 100 mM Tris pH 7.5; 50 mM EDTA for 30 min at 37° C. (prewarmed), 1×PBS for 2 min, fixative (4% paraformaldehyde) for 10 min, 0.5% acetic anhydride in 0.1 M triethanolamine pH 8.0 for 10 min (done in fume hood), 1×PBS for 2 min, and 0.85% NaCl for 2 min.

[0238] In order to dehydrate the samples, the slides are passed through a second series of solutions: 30% ethanol: 0.85% NaCl for 1 min, 50% ethanol: 0.85% NaCl for 1 min, 70% ethanol: 0.85% NaCl for 1 min, 85% ethanol: 0.85% NaCl for 1 min, 95% ethanol for 1 min, 100% ethanol for 1 min, and 100% ethanol for 1 min. After this extensive washing, the rack of slides are placed into a jar with a small amount of 100% ethanol (not touching slides) which is then sealed with parafilm.

[0239] Prehybridization and hybridization were carried out in a formamide atmosphere chamber. Slides are then placed in the chamber and each was covered with 250 ul of prehybridization solution (50% formamide,1×salts, 1×Denhardt's, 200 ug/ml tRNA, 10 U/ml RNase inhibitor). A piece of parafilm slightly smaller than the slide is placed on top of the solution and the slides, in the enclosed chamber, are allowed to incubate for 1 hour at room temperature and for at least 1 hour at 45° C.

[0240] During this time the hybridization solution is prepared and warmed to 45° C. First, the probe is readied by adding 0.05-0.5 ug/ml/kb of the probe complex to 25 ul of DEPC-H2O and incubating the mixture for 1 min at 80° C., followed by immediate cooling on ice. Second, 25 ul of formamide is added to 200 ul of hybridization solution. The parafilm is removed and the prehybridization solution is drain off completely. The slides are placed back to the same chamber and the probe is then added to the hybridization solution and the resulting solution is placed over the samples on each slide. The slides are again covered with parafilm and allowed to hybridize overnight at 45° C.

[0241] Posthybrization washes are performed by removing the parafilm and allowing the hybridization solution to drain off completely. Each slide is then rinsed in 5×SSC/50% formamide by dipping the slide couple of times in the solution. Slides are then placed in a slide rack standing in a jar containing 5×SSC/50% formamide. Slides are not allowed to dry out at any time during the washes. Slides are incubated for 4-5 hours at 45° C., rinsed shortly with NTE solution, and incubated again in 10 ug/ml RNase A (Sigma R-5503) in 0.5 M NaCl; 10 mM Tris pH 8.0; 5 mM EDTA (=NTE solution) for 30 min at 37° C. The slides are twice washed in NTE solution for 5 min at 37° C. and allowed to incubate in 0.5×SSC/50% formamide for 1 hour at 45° C., after which each slide is rinsed in 1×PBS for 5 min. Slides are then stored overnight in 1×PBS at 4° C.

[0242] In order to detect probes, Slides are first incubated with gentle agitation for 45 min in blocking solution. Following the incubation, the solution is replaced with buffer A and the incubation is continued for 45 min. The slides are placed in a same kind of chamber that is used in the hybridization step in preparation of addition of antibodies. Approximately 500 ul of antibody solution (antibody conjugate 1:1000) is spread over each slide and a piece of parafilm is put on the top of the solution. The slides are allowed to incubate for 1 hour in room temperature, after which the parafilm is removed and the slides are placed in a slide rack standing in ajar containing buffer A (1% BSA (fraction V, Sigma A-3912), 0.3% Triton X-100, 100 mM Tris pH 7.5,150 mM NaCl). The slides are washed three times with gentle agitation for 20 min. followed by a brief wash in detection buffer (2×5 min) before placing the slides back to the chamber. About 500 ul of color substrate solution is added to each slide. Each slide is then immediately covered with parafilm and kept protected from the light.

[0243] The slides are incubated for 1-2 days in room temperature taking care not to shake the slides and disrupt color development. The reaction is then stopped by removing the parafilm and dipping the slides in 1×TE-buffer (pH 8.0) for a couple of minutes. The buffer is drained off and 2-3 drops of aqueous mountant (for example 50% glycerol) are added to each slide. Finally, a coverslip is placed on each slide and if necessary sealed in place with clear nail polish.

[0244] The tissue specificity of WOL expression at the cellular level was determined by in situ localization of WOL mRNA on embryonic and root sections and images were taken using differential interference contrast (DIC) settings (FIG. 4).

[0245] In the wild-type primary root, WOL was expressed in the vascular cylinder and pericycle (FIGS. 4A-B). The expression pattern of WOL was established during the early stages of embryogenesis. At the globular stage of embryogenesis, WOL mRNA was detected in the four innermost cells, which are the precursors of the vascular tissue (procambium) (FIG. 4D). During the heart, torpedo, and nearly mature stages of embryogenesis (FIGS. 4E-G) expression was apparent in the procambium of the cotyledon shoulders, prospective hypocotyl and embryonic root (FIGS. 4E-G). WOL expression in the wol mutant primary root was detected in the vascular cells, indicating that wildtype WOL function is not necessary for its own expression (FIG. 4C).

[0246] WOL expression both spatially and temporally coincides with the divisions of the procambial cells of the embryonic and primary root which are defective in the wol mutant. The WOL gene product is a receptor molecule that controls the asymmetric cell divisions of the vascular initials through a specific signal transduction pathway involving a phosphotransfer reaction characteristic of the two component receptors. In the root tip, WOL expression can be detected both in the region of asymmetric cell divisions and in the zone of differentiation immediately above it. WOL expression during pericycle development may also be related to its role in regulating asymmetric cell divisions, since the pericycle is ontogenetically part of the vascular cylinder (Scheres et al. 1994; 1995, supra) and WOL expression can be detected prior to the separation of the pericycle cell lineages. Otherwise the pericycle appears anatomically normal in wol.

[0247] The exclusive differentiation of protoxylem in wol precludes the possibility of determining if WOL is required for division of the cambium found between xylem and phloem. The pattern of the wol-dependent procambial cell divisions around the developing xylem provides an intriguing parallel to the pattern of the cambial cell divisions between phloem and xylem, which are very prominent in wood and storage root development (Esau, 1977, Anatomy of seed Plants. John Wiley & Sons, New York, N.Y., ed. 2.). It is therefore possible that at least some aspects of developmental regulation are common to the procambial and cambial cell divisions and that WOL genes contribute to the diversity of vascular patterns found in plants.

6.7. WOL Genes, Orthologs And Paralogs

[0248] Two other WOL paralogs (F17L21.11, SEQ ID NO:18 GenBank No. AC004557; and MXH1.16, SEQ ID NO:19 GenBank No. AB011485) with a similar deduced protein domain structure were found, which indicated that WOL belonged to a small protein family (FIG. 3F). The deduced sequence of the WOL protein was 57% identical to F17L21.11 (GenBank Accession Number AC004557, SEQ ID NO:18) and 54% identical to MXH1.16 (GenBank Accession Number AB011485, SEQ ID NO:19). To compare deduced amino acid sequences, SeqWeb Software (a web-based interface to the GCG Wisconsin Package: Gap program) was utilized with the default algorithm and parameter settings of the program: blosum62, gap weight 8, length weight 2. Furthermore, a WOL ortholog sequence was reported in the genome of Hordeum vulgare (GenBank Accession Number AJ234550, SEQ ID NO:20). Among the characterized two component receptor molecules, WOL proteins and protein products of WOL orthologs and paralogs are unique in having at least one, and preferably two, putative D domains. The closest homologue of WOL-like genes is DhkA (GenBank Accession Number U42597, SEQ ID NO:17; see Wang et al., 1996, EMBO J. 15:3890-8 and Wang et al., 1999, Mol Cell Biol. 7:4750-6) of the slime mold Dictyostelium discoideum (FIG. 3F). WOL and DhkA are 24% identical in the R domain, 44% identical in the H domain, and 39% identical in the DB domains. However, the DA domain (with the absolutely conserved aspartic acid residues at positions 768 and 825, and a lysine residue at position 882 characteristic to the receiver domains) is absent in DhkA (SEQ ID NO:17). The functional role of the phosphorelay domains remains to be determined. The mutation in wol results in a non-conservative change of an amino acid of the putative receptor domain that is conserved within the WOL protein family (FIG. 3F). This indicates that the fully recessive wol mutation may reduce the ability of the molecule to bind a ligand or transmit the information of ligand binding to the C-terminal part of the molecule.

[0249] WOL genes are also active in the cambial zone of a trunk of a birch tree (Betula pendula). Using degenerate oligonucleotides (forward primer is SEQ ID NO:31; reverse primer is SEQ ID NO:32) based on the sequence conservation within the WOL genes of Arabidopsis, two different WOL genes from a cDNA library representing the wood forming tissue of birch tree (Betula pendula) were isolated (WOL gene 1 is SEQ ID NO:25 and 29; WOL gene 2 is SEQ ID NO:26 and 30) (FIG. 6). Because of its expression during wood development in trees, WOL has a more general role in vascular development and regulates vascular development both during the primary and secondary phases of plant development.

6.8. Expression Of Heterologous Gene Products Driven By the 2.7 kb WOL Promoter

[0250] This example demonstrates that the 2.7 kb WOL promoter (SEQ ID NO: 36) can drive expression of a heterologous gene product in a tissue specific manner. The 2.7 kb WOL promoter was incorporated into the heterologous expression constructs WOLpro::GUS and WOLpro:GFP. The promoter sequence corresponds to 2688 base pairs, 13574-16262, of Arabidopsis BAC clone T23K3 (SEQ ID NO: 13) (GenBank Accession number AC007069 Chromosome II section 5; Clone available from: Arabidopsis Biological Resource Center, The Ohio State University, 039 Rightmire Hall, 1060 Carmack Rd., Columbus, Ohio 43210 USA). The 5′ UTR end of the promoter sequence corresponds to base pair number 13575 of the T23K3 clone, immediately upstream of the first methionine of the WOL gene coding sequence found at base pairs 13572-13574 of the T23K3 clone (SEQ ID NO: 13). Both ends of the promoter were modified in order to insert XbaI and BamHI restriction sites into the 5′ end and the 3′ end, respectively.

[0251] The promoter was cloned into GUS gene fusion vector pBI101 T-DNA region (GenBank No. U12639). The WOL promoter::GUS construct was transformed into the Columbia ecotype background according to the methods of Clough and Bent (1998, Plant J 16:735-43), using transformation methods commonly known to those skilled in the art. Seedlings were stained to reveal promoter-driven expression of GUS six days after germination. The GUS expression patterns observed indicate that the WOL promoter drives expression in a tissue-specific manner (developing vasculature and progenitor cells of vascular tissue, particularly xylem). Tissue-specific expression was observed in hypocotyl (FIG. 9B), vasculature basal to the apical meristem (FIGS. 9C and 9B), and at the base of the cotyledons (FIG. 9D). Separate preparations were made of roots of five day old plants generated in the same background (Columbia) with the same transformed construct. In roots, GUS staining was limited to the pericycle/vascular initial and in developing vasculature throughout the root tip (FIG. 9G).

[0252] The WOLpromoter::GUS construct was next transformed into a homozygous recessive wol mutant background. The resultant seedlings were stained for GUS six days after germination by methods known to those skilled in the art. The observed GUS patterns again indicated that the 2.7 kb WOL promoter drives expression in a tissue-specific manner as described in the instant application. Expression was observed in developing vasculature in the stipe, basal to the silique (FIG. 9A), vasculature basal to the apical meristem (FIG. 9F), and developing vasculature at the base of the embryonic leaves (FIG. 9E).

[0253] Another construct was utilized that consisted of the 2.7 kb WOL promoter fused to the GFP reporter gene. The promoter was cloned into a “GFP-link” vector. The GFP-link vector is modified from the binary vector pBIN m-gfp5-ER (GenBank Number X77672) by removing the 35S promoter. This GFP-containing vector also has XbaI and BamHI sites upstream of the GFP gene. The green fluorescence patterns observed in the roots five days after germination indicate that the WOL promoter drives expression in a tissue-specific manner. Expression was observed in the pericycle/vascular initial and developing vasculature tissue in the roots.

[0254] The expression patterns of the GUS and GFP reporter genes that were driven by the 2.7 kb WOL promoter strongly correlate with the expression pattern of the WOL gene obtained utilizing RNA in situ hybridization techniques, the results of which are described in Section 6 of the instant application. The results described in Section 6 below show that WOL is expressed in the vascular cylinder and pericycle of roots in embryogenesis through at least five days after germination.

[0255] In summary the observed expression patterns matched those observed in experiments where in situ.

[0256] Although the invention is described in detail with reference to specific embodiments thereof, it will be understood that variations which are functionally equivalent are within the scope of this invention. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and accompanying drawings such modifications are intended to fall within the scope of the appended claims.

[0257] All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

Claims

1. An isolated nucleic acid molecule selected from the group consisting of: a) a nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to the nucleotide sequence of SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof; b) a nucleic acid molecule comprising a fragment of at least 300 nucleotides of the nucleotide sequence of SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof; c) a nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30; d) a nucleic acid molecule which encodes a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30, wherein the fragment comprises at least 15 contiguous amino acids of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30; and e) a nucleic acid molecule which encodes a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule comprising SEQ ID NOs:1, 2, 3, 4, 25 or 29, or a complement thereof, under stringent conditions.

2. A vector containing the nucleic acid molecule of claim 1.

3. A vector of claim 2, that is an expression vector containing transcriptional or translational regulatory elements that control expression of the nucleotide sequence.

4. The nucleic acid molecule of claim 1 further comprising nucleic acid sequences encoding a heterologous polypeptide.

5. A genetically-engineered host cell which contains the nucleic acid molecule of claim 1.

6. An isolated polypeptide selected from the group consisting of: a) a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30, wherein the fragment comprises at least 15 contiguous amino acids of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30; b) a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30, wherein the polypeptide is encoded by a nucleic acid molecule which hybridizes to a nucleic acid molecule comprising SEQ ID NOs: 1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof under stringent conditions; and c) a polypeptide which is encoded by a nucleic acid molecule comprising a nucleotide sequence which is at least 95% identical to a nucleic acid comprising the nucleotide sequence of SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof.

7. The polypeptide of claim 6 further comprising heterologous amino acid sequences.

8. An antibody which selectively binds to a polypeptide of claim 6.

9. An anti-idiotypic antibody that mimics an epitope of WOODEN LEG protein.

9. A method for producing a polypeptide selected from the group consisting of: a) a polypeptide comprising the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30; b) a polypeptide comprising a fragment of the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30, wherein the fragment comprises at least 15 contiguous amino acids of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30; and c) a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NOs:5, 6, 7, 8, 9, 10, 11, 12, 29, or 30, wherein the polypeptide is encoded by a nucleic acid molecule which hybridizes to a nucleic acid molecule comprising SEQ ID NOs:1, 2, 3, 4, 25, 26, 33, 34, or 35, or a complement thereof under stringent conditions; comprising culturing the host cell of claim 4 under conditions in which the nucleic acid molecule is expressed.

10. A method for detecting the presence of a polypeptide of claim 6 in a sample, comprising: a) contacting the sample with a compound which selectively binds to a polypeptide of claim 6; and b) determining whether the compound binds to the polypeptide in the sample.

11. The method of claim 10, wherein the compound which binds to the polypeptide is an antibody.

12. A method for detecting the presence of a nucleic acid molecule of claim 1 in a sample, comprising the steps of: a) contacting the sample with a nucleic acid probe or primer which selectively hybridizes to the nucleic acid molecule; and b) determining whether the nucleic acid probe or primer binds to a nucleic acid molecule in the sample.

13. The method of claim 12, wherein the sample comprises mRNA molecules and is contacted with a nucleic acid probe.

14. A method for identifying a compound which binds to a polypeptide of claim 6 comprising the steps of: a) contacting a polypeptide, or a cell expressing a polypeptide of claim 6 with a test compound; and b) determining whether the polypeptide binds to the test compound.

15. The method of claim 14, wherein the binding of the test compound to the polypeptide is detected by a method selected from the group consisting of: a) detection of binding by direct detecting of test compound/polypeptide binding; b) detection of binding using a competition binding assay; c) detection of binding using an assay for WOODEN LEG-mediated signal transduction.

16. A method for modulating the activity of a polypeptide of claim 6 comprising contacting a polypeptide or a cell expressing a polypeptide of claim 6 with a compound which binds to the polypeptide in a sufficient concentration to modulate the activity of the polypeptide.

17. A method for identifying a compound which modulates the activity of a polypeptide of claim 6, comprising: a) contacting a polypeptide of claim 6 with a test compound; and b) determining the effect of the test compound on the activity of the polypeptide to thereby identify a compound which modulates the activity of the polypeptide.

18. A transgenic plant containing a transgene having the nucleic acid molecule of claim 1.

19. A transgenic plant containing a transgene having the nucleic acid molecule of claim 1 operatively associated with a regulatory sequence containing transcriptional and translational regulatory elements that control expression of the nucleotide sequence in a transgenic plant cell.

20. The transgenic plant of claim 19, in which the transgene encodes an antisense nucleotide sequence that suppresses expression of endogenous WOODEN LEG gene product, resulting in thinner or shorter root development.

21. A method for altering root development by modifying the expression of a WOODEN LEG protein or polypeptide.

22. The method of claim 21, wherein said root development is altered by decreasing root length by decreasing WOODEN LEG protein or polypeptide expression.

23. The method of claim 21, wherein said root development is altered by increasing root length by overexpressing WOODEN LEG protein or polypeptide.

24. A plant genetically-engineered to modify expression of a WOODEN LEG protein or polypeptide, so that root development is altered.

25. A plant genetically-engineered to overexpress a WOODEN LEG protein or polypeptide, resulting in thicker or longer root development.

26. A genetically-engineered plant in which the endogenous WOODEN LEG gene is disrupted or inactivated, resulting in thinner or shorter root development.

27. A method of screening for a genetically engineered plant of claim 25 wherein the roots are examined for increased thickness or length as compared to a wild type untransformed plant.

28. A method of screening for a genetically engineered plant of claim 26 wherein the roots are examined for decreased thickness or length as compared to a wild type untransformed plant.

29. A transgenic plant containing a transgene encoding a gene of interest operatively associated with a WOODEN LEG promoter, so that the gene of interest is expressed in roots.

30. The transgenic plant of claim 29, in which the gene of interest encodes a gene product that confers herbicide, salt, pathogen, or insect resistance.

31. A method for directing expression of a gene in the pericycle and vascular tissue in the hypocotyl region of a plant comprising: a) placing said gene under the control of the WOODEN LEG promoter in a transgenic plant; and b) assaying for the expression of said gene in said transgenic plant.

32. A method for directing expression of a gene in the root structures of a plant comprising: a) placing said gene under the control of the WOODEN LEG promoter in a transgenic plant; and b) assaying for the expression of said gene in said transgenic plant.

33. An isolated WOL protein.

34. The WOL protein of claim 33 having the amino acid sequence shown in FIG. 5D (SEQ ID NO:5).

35. A WOL protein lacking one to seven of the following domains: a short N-terminal domain, a transmembrane domain, an extracellular receptor domain, a transmembrane domain, a histidine kinase domain, receiver domain DA, and a receiver domain DB.

36. A polypeptide corresponding to the short N-terminal domain, transmembrane domain, extracellular receptor domain, transmembrane domain, histidine kinase domain, receiver domain DA, or the receiver domain DB of the WOL protein.

37. An isolated nucleic acid molecule comprising SEQ ID NOs:25 or 26 or both SEQ ID NOs:25 and 26, wherein the nucleic acid encodes a protein that has the ability to regulate the set of asymmetric cell divisions that establish vascular tissue during root and hypocotyl development, and that indirectly regulates xylem differentiation by controlling the number of cells in the vascular cylinder.

38. A fragment of the isolated nucleic acid molecule of claim 37.

39. A polypeptide comprising the amino acid sequence of SEQ ID Nos: 29 or 30 or both SEQ ID Nos: 29 and 30, wherein the polypeptide has the ability to regulate the set of asymmetric cell divisions that establish vascular tissue during root and hypocotyl development, and that indirectly regulates xylem differentiation by controlling the number of cells in the vascular cylinder.

40. A fragment of the polypeptide of claim 39.

41. A plant genetically-engineered to overexpress a WOODEN LEG protein or polypeptide, resulting in increased cell layers in vascular tissues, such that wood production in increased.

42. A plant genetically-engineered to modify expression of a WOODEN LEG protein or polypeptide, so that development of vascular tissue is altered.

43. A plant genetically-engineered to overexpress a WOODEN LEG protein or polypeptide, so that development of vascular tissue is altered.

44. A genetically-engineered plant in which the endogenous WOODEN LEG gene is disrupted or inactivated, so that development of vascular tissue is altered.

45. A transgenic plant containing a transgene encoding a gene of interest operatively associated with a WOODEN LEG promoter, so that the gene of interest is expressed in developing vascular tissue.

46. A transgenic plant containing a transgene encoding a gene of interest operatively associated with a WOODEN LEG promoter, so that lignin or cellulose production is altered.

47. The transgenic plant of claim 46 wherein the gene of interest is SAM or the gene of interest encodes cellulose synthase or caffeic acid O-methyltransferase.