Non-pathogen induced systemic acquired resistance (SAR) in plants

Abstract

The present invention discloses the production of transgenic plants that exhibit a systemic acquired resistance (SAR) response even in the absence of an infecting pathogen. The invention encompasses such plants, methods and biological molecules useful for producing the plants, and methods for increasing the disease resistance of plants.

Description

FIELD OF THE INVENTION

[0002] This invention relates to nucleic acid molecules useful for producing plants having enhanced pathogen resistance characteristics, transgenic plants expressing these nucleic acid molecules, methods of making such plants, and methods for increasing the resistance of plants to pathogens.

BACKGROUND OF THE INVENTION

[0003] Plants are hosts to thousands of infectious diseases caused by a vast array of phytopathogenic fungi, bacteria, viruses, and nematodes. These pathogens are responsible for significant crop losses worldwide, resulting from both infection of growing plants and destruction of harvested crops (Baker et al., 1997).

[0004] Plants recognize and resist many invading phytopathogens by inducing a rapid defense response, termed the hypersensitive response (HR). HR results in localized cell and tissue death at the site of infection, which constrains further spread of the infection. This local response often triggers non-specific resistance throughout the plant, a phenomenon known as systemic acquired resistance (SAR). Once triggered, SAR provides resistance for days to a wide range of pathogens. The generation of the HR and SAR in a plant depends upon the interaction between a dominant or semi-dominant resistance (R) gene product in the plant and a corresponding dominant avirulence (Avr) gene product expressed by the invading phytopathogen. It has been proposed that phytopathogen Avr products function as ligands, and that plant R products function as receptors. Thus, in the widely accepted model of phytopathogen/plant interaction, binding of the Avr product of an invading pathogen to a corresponding R product in the plant initiates the chain of events within the plant that produces HR and SAR and ultimately leads to disease resistance. A detailed review of the current understanding of Avr/R gene product interactions is presented in Baker et al. (1997).

[0005] Because the systemic acquired resistance (SAR) response acts nonspecifically throughout the plant to provide enhanced resistance to many pathogens, it has been extensively studied as a possible mechanism for conferring broad-spectrum pathogen resistance. The SAR response is characterized by the induction of at least nine gene families (known as SAR genes) in uninfected leaves of the plant. Some of the SAR genes encode proteins that have antimicrobial activity, including glucanases, chitinases and the pathogenesis-related (PR) proteins such as PR-1. A number of chemicals are known to trigger SAR, including salicylic acid, 2,6-dichloroisonicotinic acid (INA), 1,2,3-benzothiadiazole-7-thiocarboxylic acid-S-methyl ester, and arachidonic acid when applied through the roots, sprayed onto leaves or injected into stems. These and other chemicals are being investigated as candidate agents for inducing SAR in crop plants on an agricultural scale. For a more detailed discussion of the SAR response, see Agrios (1997), Chapter 5.

[0006] While efforts to utilize the SAR response to enhance resistance to phytopathogens have largely been based on the external application of inducing agents, molecular genetic research has focused on isolating and manipulating plant resistance (R) genes. Since the cloning of the first R gene, Pto from tomato, which confers resistance to Pseudomonas syringae pv. tomato (Martin et al., 1993), a number of other R genes have been reported (for reviews see Hammond-Kosack and Jones, 1997 and Baker et al., 1997). Sequence analyses of the proteins encoded by these R genes have revealed a number of motifs that are conserved between various R proteins; including leucine rich repeats (LRR), nucleotide binding site (NBS), Toll-IL-1R homology (TIR), leucine zipper (LZ) and transmembrane (TM) domains (Baker et al., 1997).

[0007] Much effort is currently being directed towards using R genes to engineer pathogen resistance in plants. The production of transgenic plants carrying a heterologous gene sequence is now routinely practiced by plant molecular biologists, and methods for incorporating an isolated gene (such as an R gene) into an expression cassette, producing plant transformation vectors, and transforming many types of plants are well known. Examples of the production of transgenic plants having modified characteristics as a result of the introduction of a heterologous transgene include: U.S. Pat. No. 5,719,046 to Guerineau (production of herbicide resistant plants by introduction of bacterial dihydropteroate synthase gene); U.S. Pat. No. 5,231,020 to Jorgensen (modification of flavenoids in plants); U.S. Pat. No. 5,583,021 to Dougherty (production of virus resistant plants); and U.S. Pat. No. 5,767,372 to De Greve and U.S. Pat. No. 5,500,365 to Fischoff (production of insect resistant plants by introducing Bacillus thuringiensis genes).

[0008] In conjunction with such techniques, the isolation of plant R genes has similarly permitted the production of plants having enhanced resistance to certain pathogens. A number of these genes have been used to introduce the encoded resistance characteristic into plant lines that were previously susceptible to the corresponding pathogen. For example, U.S. Pat. No. 5,571,706 to Baker and Whitham describes the introduction of the N gene into tobacco lines that are susceptible to Tobacco Mosaic Virus (TMV) in order to produce TMV-resistant tobacco plants. WO 95/28423 describes the creation of transgenic plants carrying the Rps2 gene from Arabidopsis thaliana, as a means of creating resistance to bacterial pathogens including Pseudomonas syringae, and WO 98/02545 describes the introduction of the Prf gene into plants to obtain enhanced pathogen resistance. Cao et al. (1998) describes the introduction into Arabidopsis of the NPR1 cDNA expressed under the control of the 35S promoter to produce enhanced resistance to multiple bacterial pathogens.

[0009] The first R gene conferring virus resistance to be isolated from plants was the N gene of Nicotiana glutinosa tobacco (Whitham et al., 1994). The N gene (or homologs of this gene) is present in some but not all types of tobacco, and confers resistance to Tobacco Mosaic Virus (TMV). TMV is an important pathogen of not only tobacco, but also of other crop plants including tomato (Lycopersicon sp.) and pepper (Capsicum sp.). A review of the wide range of host species that serve as hosts to TMV is presented in Holmes (1946). TMV is the type virus of the genus Tobamovirus, which includes a number of closely related viral pathogens of commercially important plants. For example, the Tobamovirus group includes tomato mosaic virus, pepper green mottle virus and ondontoglossum ringspot virus, which is a pathogen of orchids (Agrios, 1997).

[0010] The N. glutinosa N gene is described in detail in U.S. Pat. No. 5,571,706 (“Plant Virus Resistance Gene and Methods”) to Baker & Whitham, which is incorporated herein by reference. The sequence of this gene is available on GenBank under accession number U558886. U.S. Pat. No. 5,571,706 discloses the sequence of the N gene, as well as two cDNAs corresponding to the gene. The N gene (including the 5′ and 3′ regulatory regions) is over 12 kb in length and comprises five exons and four introns, encoding a full-length N protein of 1144 amino acids, with a deduced molecular mass of 131.4 kDa. cDNA-N is a cDNA encoded by the N gene; it is approximately 3.7 kb in length and encodes the full-length N protein. A second cDNA, cDNA-N-tr, is approximately 3.8 kb in length. It results from an alternative splicing pattern and encodes a truncated protein, N-tr, that is 652 amino acids in length and has a deduced molecular mass of 75.3 kDa. The N protein include TIR, NBS and LRR domains (Whitham et al., 1994, Baker et al., 1997). U.S. Pat. No. 5,571,706, and Whitham et al. (1994) describe the production of transgenic tobacco plants carrying a full-length N transgene; these plants show the HR response following TMV challenge.

[0011] While molecular genetic approaches that focus on individual R genes are promising, such approaches may be somewhat limited since each individual R gene will likely confer resistance to a relatively narrow range of pathogens. In contrast, exploitation of the SAR response could produce plants that are resistant to a broad range of pathogens of different types. The present invention is directed to a molecular genetic approach for producing plants that display an SAR response even in the absence of a plant pathogen, and which consequently show enhanced resistance to a broad spectrum of plant pathogens.

SUMMARY OF THE INVENTION

[0012] A molecular-genetic approach for producing a constitutive systemic acquired resistance (SAR) response in plants is provided. The SAR response in these plants is described as “constitutive” since it occurs even in the absence of an infecting pathogen. Plants that exhibit this SAR response show enhanced resistance to a broad range of phytopathogens, including viruses such as TMV, bacteria and fungi. Among other things, the invention encompasses nucleic acid molecules that are used to produce plants that show such an SAR response, the plants themselves and methods of making such plants.

[0013] The invention is founded on the discovery that a non-pathogen induced SAR response is exhibited by transgenic plants that comprise the following elements:

[0014] (1) an R gene (or a cDNA encoding the R gene product(s)); and

[0015] (2) a transgene that expresses the R gene product (or an effective portion thereof).

[0016] Typically, element (1) is a native R gene, but it may also be a transgene comprising the R gene, a corresponding R cDNA, or a recombinant construct that otherwise expresses the R protein(s). (As described in more detail below, while most R genes have only a single reading frame and therefore encode a single R protein product, some R genes, including the tobacco N gene and the flax L6 gene, contain alternatively spliced exons, and therefore encode two R protein products.) The nucleic acid molecule of element (1) is, by itself, ordinarily sufficient to confer enhanced resistance to a pathogen that carries the corresponding Avr gene when expressed in an otherwise susceptible plant. Expression of this nucleic acid molecule is typically, but not necessarily, controlled by regulatory elements (promoter and terminator regions) that are associated with the native R gene.

[0017] Element (2) is typically a cDNA form of the R gene, and is generally expressed in the plant under the control of a promoter that produces expression levels that are greater than the native R gene promoter. High-level promoters suitable for use in this application are well known in the art, and include inducible and constitutive promoters. Inducible promoters may be employed in situations where it is advantageous to control expression of the non-pathogen induced SAR response. For example, it may be beneficial to turn on the SAR response once plants have reached a certain developmental stage, or when the likelihood of pathogen infection is highest. As described in more detail below, element (2) need not necessarily encode a complete R gene product but, in some circumstances, may encode only a portion of the R protein. The inventors have shown, for example, that element (2) may encode one or more domains of an R protein, but need not encode a complete R protein. For example, in certain embodiments, element (2) may encode all or part of a TIR domain of an R protein.

[0018] R genes and R gene products that may be employed in the invention include, but are not limited to, R genes encoding proteins having a TIR domain, such as: the N gene of tobacco (described in U.S. Pat. No. 5,571,706); the RPP5 gene of Arabidopsis (described in Parker et al., 1997) the RPP1 gene of Arabidopsis (described in Botella et al., 1998); the L6 gene of flax (described in Lawrence et al., 1995); and the M gene of flax (described in Anderson et al., 1997). Transgenic plants produced according to the invention (referred to as constitutive SAR plants for convenience) exhibit an SAR response and, as a result, shown enhanced resistance to a wide range of pathogens, including bacterial, viral and fungal pathogens.

[0019] In one embodiment of the invention, the invention provides transgenic plants comprising:

[0020] (1) a first nucleic acid molecule encoding one or more protein products of an R gene sufficient to confer resistance to a phytopathogen; and

[0021] (2) a second nucleic acid molecule encoding a protein comprising at least one polypeptide encoded by the R gene, wherein co-expression of the first and second nucleic acid molecules is sufficient to produce a systemic acquired resistance response in the plant.

[0022] The term “a protein comprising at least one polypeptide encoded by the R gene” refers to a protein that includes at least one amino acid region (typically at least 10 contiguous amino acids) of the R protein. In other words, the polypeptide may be a sub-part of the R protein. Typically, such a polypeptide will be a domain of the R protein, such as a TIR domain, although less than an entire domain may also be employed.

[0023] The invention also encompasses a method of producing a plant that exhibits an SAR response in the absence of a pathogen infection. The method comprises introducing into a plant having an R gene a nucleic acid molecule that expresses a polypeptide component of a protein encoded by the R gene, wherein co-expression of the R gene and the polypeptide component produces an SAR response in the plant.

[0024] In another embodiment, the invention provides transgenic plants comprising a first nucleic acid molecule encoding an R gene product having a TIR domain, and a second nucleic acid molecule encoding a polypeptide comprising the TIR domain of the R gene product or an effective portion thereof, wherein co-expression of the first and second nucleic acid molecules produces a constitutive SAR response in the plant. In particular cases, the R gene product may be a product of a gene selected from the group consisting of the N gene of tobacco, the M and L6 genes of flax and the RPP5 and RPP1 genes of Arabidopsis.

[0025] In another embodiment of the invention, the R gene is the tobacco N gene, and the transgenic plants comprise the following elements:

[0026] (1) a first nucleic acid molecule encoding an N and an N-tr protein; and

[0027] (2) a second nucleic acid molecule encoding a protein comprising an N protein TIR domain.

[0028] The first nucleic acid molecule may be any molecule that encodes an N protein and an N-tr protein. Thus, for example, the first nucleic acid molecule may be a native N gene, an N transgene, or a cDNA-N/intron construct.

[0029] In one embodiment, the second nucleic acid molecule comprises cDNA-N or cDNA-N-tr. In another embodiment, the second nucleic acid molecule comprises a recombinant molecule encoding the N protein TIR region or a sufficient part of the TIR region to produce the SAR response when the first and second nucleic acid molecules are co-expressed in the plant.

[0030] Plants produced by the methods disclosed herein exhibit a constitutive SAR response and, consequently, enhanced broad-spectrum pathogen resistance. Parts of such plants, including seeds, fruit, stems, leaves and roots, may be utilized in conventional ways as food sources etc. The present invention is applicable to any plant type, but is expected to be particularly useful in plant types from which the corresponding R gene is obtained, and closely related plants. By way of example, application of the invention based on the tobacco N gene is expected to be particularly beneficial with respect to solanaceaous plants such as tobacco, tomato, potato and pepper.

[0031] The invention also encompasses methods for increasing or enhancing the disease resistance of plants. Such methods for increasing the disease resistance of plants involve plants having a first and second nucleic acid molecule as described supra. The methods comprise obtaining a plant having a first nucleic acid molecule encoding one or more protein products of an R gene sufficient to confer resistance to a phytopathogen; and then introducing into the genome of said plant a second nucleic acid molecule comprising at least one polypeptide encoded by the R gene, wherein co-expression of the first and second nucleic acid molecules is sufficient to produce a systemic acquired resistance response in the plant. The R gene of the first nucleic acid molecule can be native to the plant or can be introduced into the genome of the plant that lacks the R gene.

BRIEF DESCRIPTION OF THE DRAWINGS

[0032] FIG. 1 shows an alignment of the TIR domains of N, M, L6, RPP5 and RPP1. The consensus sequence (the lower line of the figure) represents amino acids that are conserved between 3 or more of the 5 proteins.

[0033] FIG. 2 is a composite figure showing data obtained with lesion mimic plants. The data shows Northern blot analyses of PR-1a expression, and the presence or absence of constitutive lesions and SAR response (the lower panel shows ribosomal RNA staining showing the even loading of RNA gels). Eight lines of NN tobacco transformed with the 35S-cDNA-N construct are shown. The phenotype observations and RNA collection from these samples were performed in the absence of TMV infection. The right-hand three lanes represent analyses of non-transgenic NN plants. The first two of these were infected with TMV approximately 10 days prior to sampling, the last was not infected. I=infected with TMV, U.I.=uninfected.

[0034] FIG. 3 shows the constitutive HR phenotype in TIR::Samsun NN transgenic plants overexpressing TIR after 8-10 weeks; expression occurred in the absence of TMV infection.

[0035] FIG. 4 shows a Northern analysis of TIR expression in TIR::Samsun NN transgenic plants and wild-type N gene containing Samsun NN plants.

[0036] FIG. 5 compares replication of potato virus (PVX) and tobacco rattle virus (TRV) in TIR::Samsun NN transgenic plants and wild-type N gene containing Samsun NN plants.

DETAILED DESCRIPTION OF THE INVENTION

[0037] I. Sequence Listing

[0038] SEQ ID NO:1 shows the nucleic acid sequence of the N. glutinosa N gene. The sequence comprises the following regions:

Nucleotide numbers Feature
1-4281             5′ regulatory sequence (pN)
4282-4760          exon 1 (last codon split between exon 1 and exon 2)
4761-4990          intron 1
4991-6086          exon 2
6087-6928          intron 2
6929-7201          exon 3
7202-9019          intron 3
9020-10588         exon 4
10589-10921        intron 4
10922-10939        exon 5
10940-12286        3′ regulatory region (3′-GRS)

[0039] SEQ ID NO:2 shows the nucleic acid sequence of the N. glutinosa cDNA-N.

[0040] SEQ ID NO:3 shows the amino acid sequence of the N. glutinosa N protein.

[0041] SEQ ID NO:4 shows the nucleic acid sequence of the N. glutinosa cDNA-N-tr.

[0042] SEQ ID NO:5 shows the amino acid sequence of the N. glutinosa N-tr protein.

[0043] II. Definitions

[0044] Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology may be found in Benjamin Lewin, Genes V, published by Oxford University Press, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8).

[0045] In order to facilitate review of the various embodiments of the invention, the following definitions of terms are provided:

[0046] R gene: A plant disease resistance gene which, when expressed in a plant, confers enhanced resistance to one or more phytopathogens. R genes typically encode one or more R proteins, the production of which is required for pathogen resistance. In the gene-for-gene model of plant disease resistance, R genes provide resistance against pathogens that carry a corresponding avirulence (Avr) gene. Examples of plant R genes include, but are not limited to, those shown in Table 1.

TABLE 1
Examples of cloned R genes
		Confers	Conserved
R Gene	Isolated from	resistance to	domains	Citation
N	tobacco	TMV	TIR-NBS-LRR	Whitham
				et al. 1994
Hm1	maize	Cochliobolus	—	Johal and
		carbonum		Briggs
				(1992)
Pto	tomato	Pseudomonas	—	Martin et al.
		syringae pv.		(1993)
		tomato
RPS2	Arabidopsis	Pseudomonas	LZ-NBS-LRR	Bent et al.
		syringae pv.		(1994)
		tomato
RPM1	Arabidopsis	Pseudomonas	LZ-NBS-LRR	Grant et al.
		syringae pv.		(1995)
		maculicula
I2	tomato	Fusarium	NBS-LRR	Ori et
		oxysporum		al. 1997
M	flax	Melampsora lini	TIR-NBS-LRR	Anderson
				et al. 1997
L6	flax	Melampsora lini	TIR-NBS-LRR	Lawrence
				et al. 1995
RPP1	Arabidopsis	Peronospora	TIR-NBS-LRR	Botella et al.
		parasitica		1998
RPP5	Arabidopsis	Peronospora	TIR-NBS-LRR	Parker et al.
		parasitica		1997
Xa21	rice	Xanthamonas	LRR	Song et al.
		oryzae pv. oryzae		1995
Cf2	tomato	Cladosporium	LRR-TM	Dixon et al.
		fulvum		1995
Cf9	tomato	Cladosporium	LRR-TM	Jones et al.
		fulvum		1994
HSIpro-1	sugar beet	Heterodera	LRLR-TM	Cal et al.
		schachtii		1997

[0047] Detailed descriptions of these and other R genes are presented in Hammond-Kosack and Jones, 1996, Baker et al., 1997, and references cited therein.

[0048] The various R gene sequences known in the art may be regarded as prototypical sequences; homologs or variants of each of these sequences may be isolated or produced by recombinant means and used in the present invention. Such homologous and variant R genes encode homologous and variant R proteins that share specified levels of sequence identity with the relevant prototypical R gene sequence and retain R gene function. By way of example, R gene homologs and variants typically encode R proteins that share at least 40% sequence identity with the relevant prototypical R protein, and confer enhanced disease resistance when expressed in an otherwise pathogen-susceptible host plant. By way of example, variants or homologs of the prototypical flax L6 gene disclosed in Lawrence et al. (1995) will encode an L6 protein that shares at least 40% amino acid sequence identity with the prototypical L6 protein, and retain L6 gene function, i.e., retain the ability to confer enhanced resistance to the pathogen Melampsora lini when expressed in otherwise susceptible flax plants.

[0049] In view of this, it will be apparent to one of ordinary skill in the art that the invention is not limited to use of the prototypical R gene sequences, but that it may be practiced using variants and homologs of the sequences. Accordingly, where reference is made herein to molecules relating to an R gene, for example the flax L6 gene, the L6 cDNA or the L6 protein, it will be understood that such reference includes not only the prototypical sequences of these molecules as reported in the scientific literature, but also corresponding sequences of L6 gene homologs and variants. Also included within the scope of such terms are molecules that differ from the disclosed prototypical molecules by minor variations, such as nucleic acid molecules that vary from the disclosed sequences by virtue of the degeneracy of the genetic code, and nucleic acid sequences that have been modified to encode R proteins having conservative amino acid substitutions. Such variant sequences may be produced by manipulating the nucleotide sequence of a selected prototypical R gene using standard procedures such as site-directed mutagenesis or the polymerase chain reaction.

[0050] R protein: a protein encoded by an R gene. While most R genes encode a single protein, some R genes, including N and L6, show alternative splicing patterns, producing two mRNAs that are translatable into two different (but closely related) R proteins (see Whithamn et al., 1994; Parker et al., 1997). Expression in a plant of the R protein(s) encoded by an R gene produces resistance to pathogens carrying the corresponding Avr gene.

[0051] cDNA-R: a cDNA molecule that encodes an R protein.

[0052] TIR domain: The amino terminus of certain R proteins, including the proteins encoded by the N gene of tobacco, the M and L6 genes of flax and the RPP5 and RPP1 genes of Arabidopsis, contain a region that shows similarity to the cytoplasmic domains of the Drosophila Toll protein (amino acids 848-999) and human IL-1R protein (amino acids 352-527) (Hammond-Kosack and Jones, 1996; Whitham et al., 1994; Baker et al., 1997; Parker et al., 1997). The TIR domain has been suggested to be associated with a signaling function. The TIR domain of R genes is defined by sequence similarity (see, for example, Hammond-Kosack et al., 1997) and is generally found in the first approximately 150 amino acids of the amino terminus of the protein. FIG. 1 shows an alignment of the TIR domains of N, M, L6, RPP5 and RPP1. The consensus sequence (the lower line of the figure) represents amino acids that are conserved between 3 or more of the 5 proteins. Table 2 below shows the percentage sequence similarities and identities of the TIR regions of 4 R genes using the N gene as the reference sequence. The first 150 N-terminal amino acids of each R protein were compared for this analysis. The percentages were obtained by comparing the sequences with the GCG software package (GCG version 9, Genetics Computer Group, Madison, Wisconsin, a subsidiary of Oxford Molecular Group, Inc.) using the Bestfit alignment set to default parameters (gap creation penalty=12, gap extension penalty=4). Typically, an R protein TIR region will have at least 45% sequence similarity to the N protein TIR region when compared using this method.

TABLE 2
Percentage similarity/identity of TIR domains to the N TIR domain
N	RPP5	L6	M	RPP1
100/100	57/53	53/43	55/46	53/44

[0053] Systemic Acquired Resistance (SAR): SAR is a non-specific defense response of plants that is usually triggered following the induction of a hypersensitive response (HR; localized necrotic lesions around the site of a pathogen infection) by an invading pathogen. SAR has been observed in both monocotyledenous and dicotyledenous plants and may be triggered by any type of invading pathogen (bacteria, virus or fungus). The SAR response is non-specific in that it produces enhanced resistance to a broad spectrum of pathogens, regardless of the type of invading pathogen that triggered the response. It generally occurs throughout the plant, regardless of where the pathogen infection occurred. The SAR response usually begins within 2-10 days after the triggering pathogen invasion, and lasts for anywhere from several days to several weeks.

[0054] The SAR response is typically characterized at the molecular level by the induction of families of genes termed SAR genes. These genes encode products including glucanases, chitinases, csyteine-rich proteins related to thaumatin and pathogenesis-related (PR) proteins. For a more detailed discussion of the SAR response, see Agrios et al. (1997), Chapter 5, and Ryals et al. (1994). Methods for detecting the SAR response are discussed in more detail below.

[0055] The present invention is directed to plants that exhibit a “constitutive SAR response.” This term indicates that the SAR response is exhibited by a plant even in the absence of the conventional triggering event, i.e., pathogen invasion. However, the term does not require that the plant exhibit the SAR response at all times in development, simply that the response is exhibited without the need for the pathogen trigger.

[0056] N gene: A gene that encodes an N and an N-tr protein and which, when introduced into a plant such as tobacco, enhances the resistance of that plant to TMV infection. The prototypical N gene is the gene isolated from N. glutinosa and disclosed in U.S. Pat. No. 5,571,706. The sequence of this gene, including 5′ and 3′ regulatory regions, is shown in SEQ ID NO:1. The ability of an N gene to confer TMV resistance may readily be determined by scoring the HR and SAR responses to TMV infection in transgenic plants, and by monitoring systemic spread of the virus, as described below.

[0057] The disclosed N gene sequence is designated as the prototypical N gene since it is the first N gene to have been isolated. As discussed above, the present invention is not limited to use of prototypical R genes, but may be practiced using homologs and sequence variants. For example, U.S. Pat. No. 5,571,706, discusses how functional homologs of the N gene may be obtained from other plant species, such as from other Solanaceous species. Such homologs encode proteins having specified levels of sequence identity with the prototype N protein (e.g., at least 60% sequence identity), and retain N gene function, i.e., retain the ability to confer TMV resistance when introduced into plants. Similarly, the disclosed N and N-tr proteins are the prototypes of such proteins, and homologs of these proteins are encoded by N gene homologs. Accordingly, where reference is made herein to molecules relating to the N gene, for example, cDNA-N, N or N-tr proteins and introns of the N gene (such as 13), it will be understood that such reference includes not only the prototypical sequences of these molecules disclosed herein, but also corresponding sequences from N gene homologs. Also included within the scope of such terms are molecules that differ from the disclosed prototypical molecules by minor variations, such as nucleic acid molecules that vary from the disclosed sequences by virtue of the degeneracy of the genetic code, and nucleic acid sequences that have been modified to encode N or N-tr proteins having conservative amino acid substitutions. Such variant sequences may be produced by manipulating the nucleotide sequence of the tobacco cDNA-N or N gene using standard procedures such as site-directed mutagenesis or the polymerase chain reaction.

[0058] N tobacco: A tobacco line that carries at least one copy of an N gene. A plant that is homozygous for the N gene is designated NN, while a plant lacking a functional N gene is designated nn.

[0059] N protein/N-tr protein: Proteins encoded by an N gene. The N protein encoded by the prototypical N gene is shown in SEQ ID NO:3. The N-tr protein is a truncated form of the N protein and is encoded by an alternatively spliced form of the N gene; the prototypical sequence of N-tr is shown in SEQ ID NO:5. Expression of both forms of the protein in a plant cell is required for TMV resistance.

[0060] cDNA-N: A cDNA molecule that encodes an N protein. The nucleic acid sequence of the prototypical cDNA-N is shown in SEQ ID NO:2.

[0061] cDNA-N-tr: A cDNA molecule that encodes an N-tr protein. The nucleic acid sequence of the prototypical cDNA-N-tr is shown in SEQ ID NO:4.

[0062] pN/cDNA-N/intron 3/3′-GRS: While nn transgenic plants that contain an N-gene transgene show enhanced resistance to TMV infection, it has been shown that nn plants expressing cDNA-N or cDNA-N-tr transgene constructs do not. However, the expression of a construct comprising the N gene promoter (pN) operably linked to a form of cDNA-N that retains the third intron (I3) of the N gene, and in turn linked to the N gene 3′ regulatory region (3′-GRS), does confer TMV resistance. Because intron 3 (I3) includes the alternatively spliced exon of the N gene (see Whitham et al., 1994), such constructs express both the N and N-tr proteins. Hence a construct of this arrangement (referred to as a pN/cDNA-N/intron 3/3′-GRS construct) may be used in this application in place of an N gene.

[0063] Sequence identity: The similarity between two nucleic acid sequences, or two amino acid sequences is expressed in terms of the similarity or identity between the sequences. Sequence identity is frequently measured in terms of percentage; the higher the percentage, the more alike the two sequences are. Homologs of prototype R proteins will possess a relatively high degree of sequence identity when aligned using standard methods.

[0064] Methods of alignment of sequences for comparison are well known in the art. Various programs and alignment algorithms are described in: Smith and Waterman (1981); Needleman and Wunsch (1970); Pearson and Lipman (1988); Higgins and Sharp (1988); Higgins and Sharp (1989); Corpet et al. (1988); Huang et al. (1992); and Pearson et al. (1994). Altschul et al. (1994) presents a detailed consideration of sequence alignment methods and homology calculations.

[0065] The NCBI Basic Local Alignment Search Tool (BLAST) (Altschul et al., 1990) is available from several sources, including the National Center for Biotechnology Information (NCBI, Bethesda, Md.) and on the Internet, for use in connection with the sequence analysis programs blastp, blastn, blastx, tblastn and tblastx. It can be accessed at http://www.ncbi.nlm.nih.gov/BLAST/. A description of how to determine sequence identity using this program is available at http://www.ncbi.nlm.nih.gov/BLAST/blast_help.html.

[0066] Homologs of prototype R proteins are typically characterized by possession of at least 50% sequence identity counted over the full-length alignment with the amino acid sequence of the selected prototype R protein using the NCBI Blast 2.0, gapped blastp set to default parameters. Proteins with even greater similarity to the reference sequences will show increasing percentage identities when assessed by this method, such as at least 60%, at least 70%, at least 75%, at least 80%, at least 90% or at least 95% sequence identity. When less than the entire sequence is being compared for sequence identity, homologs will typically possess at least 75% sequence identity over short windows of 10-20 amino acids, and may possess sequence identities of at least 85% or at least 90% or 95% depending on their similarity to the reference sequence. Methods for determining sequence identity over such short windows are described at http://www.ncbi.nlm.nih.gov/BLAST/blast_FAQs.html. One of skill in the art will appreciate that these sequence identity ranges are provided for guidance only; it is entirely possible that strongly significant homologs could be obtained that fall outside of the ranges provided.

[0067] Oligonucleotide: A linear polynucleotide sequence of up to about 100 nucleotide bases in length.

[0068] Vector: A nucleic acid molecule as introduced into a host cell, thereby producing a transformed host cell. A vector may include nucleic acid sequences that permit it to replicate in a host cell, such as an origin of replication. A vector may also include one or more selectable marker genes and other genetic elements known in the art.

[0069] Transformed: A transformed cell is a cell into which has been introduced a nucleic acid molecule by molecular biology techniques. As used herein, the term transformation encompasses all techniques by which a nucleic acid molecule might be introduced into such a cell, including transfection with viral vectors, transformation with plasmid vectors, and introduction of naked DNA by electroporation, lipofection, and particle gun acceleration.

[0070] Isolated: An “isolated” biological component (such as a nucleic acid or protein or organelle) has been substantially separated or purified away from other biological components in the cell of the organism in which the component naturally occurs, i.e., other chromosomal and extra-chromosomal DNA and RNA, proteins and organelles. Nucleic acids and proteins that have been “isolated” include nucleic acids and proteins purified by standard purification methods. The term also embraces nucleic acids and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.

[0071] Purified: The term purified does not require absolute purity; rather, it is intended as a relative term. Thus, for example, a purified N protein preparation is one in which the N protein is more enriched than the protein is in its natural environment within a plant cell. Generally, a preparation of N protein is purified such that the N protein represents at least 5% of the total protein content of the preparation. For particular applications, higher purity may be desired, such that preparations in which the N protein represents at least 20% or at least 50% of the total protein content may be employed.

[0072] Ortholog: Two nucleotide or amino acid sequences are orthologs of each other if they share a common ancestral sequence and diverged when a species carrying that ancestral sequence split into two species. Orthologous sequences are also homologous sequences.

[0073] Operably linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Alternatively, two protein coding sequences can be operably linked such that the sequences are placed in the same reading frame so as to produce a single open reading frame comprising the two protein coding sequences. Generally, operably linked DNA sequences are contiguous and, where necessary to join two protein-coding regions, in the same reading frame.

[0074] Recombinant: A recombinant nucleic acid is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques.

[0075] cDNA (complementary DNA): A piece of DNA generally lacking internal, non-coding segments (introns) and regulatory sequences that determine transcription. cDNA is synthesized in the laboratory by reverse transcription from messenger RNA extracted from cells. It is recognized, however, that certain embodiments of the invention involve the use of nucleic acid constructs comprising cDNA sequences and the sequences of one or more introns, such as, for example, the pN/cDNA-N/intron 3/3′-GRS construct described, supra. Thus, the use herein of the term “cDNA” is not intended to exclude such constructs.

[0076] ORF (open reading frame): A series of nucleotide triplets (codons) coding for amino acids without any termination codons. These sequences are usually translatable into a peptide.

[0077] Transgenic plant: As used herein, this term refers to a plant that contains recombinant genetic material not normally found in plants of this type and which has been introduced into the plant in question (or into progenitors of the plant) by human manipulation. Thus, a plant that is grown from a plant cell into which recombinant DNA is introduced by transformation is a transgenic plant, as are all offspring of that plant that contain the introduced transgene (whether produced sexually or asexually).

[0078] Transgene: As used herein, the term transgene refers to recombinant genetic material residing in cells of a plant.

[0079] III. Design of Genetic Constructs

[0080] The following sections and Examples provide detailed guidance on the design, and use of nucleic acid constructs for producing constitutive SAR plants. Standard molecular biology methods are used to practice the present invention, unless otherwise described. Such standard methods are described in Sambrook et al. (1989), Ausubel et al (1987) and Innis et al (1990).

[0081] Generally speaking, constitutive SAR plants produced according to the present invention comprise two genetic elements that together produce the SAR response. These elements are:

[0082] (1) an R gene or a cDNA encoding the R gene product(s); and

[0083] (2) a transgene comprising a coding sequence for a product of the R gene or a portion thereof that is effective to produce the SAR response when co-expressed in the plant with element (1).

[0084] The first element may be a native R gene or a transgene, or a cDNA encoding the protein product(s) of the R gene (cDNA-R). Generally, this element will be expressed under the regulatory control of the native R gene promoter and 3′ regulatory sequences, although other regulatory sequences known in the art may also be employed. Expression of this first genetic element in the plant will ordinarily confer enhanced resistance to one or more phytopathogens. Where the first element is a transgene, plant transformation methods (as described further in the following section) are used to introduce the transgene. It will be appreciated by one of skill in the art that where this element is a native R gene, transformation will be required only to introduce the second genetic element.

[0085] The second genetic element is a transgene that expresses either a product of the R gene (i.e., an R protein), or a portion thereof that is effective to produce the SAR response when co-expressed with the product of the first genetic element. This transgene may thus be an R gene, a cDNA derived from the R gene and encoding the R gene product(s) (i.e., cDNA-R), or another construct expressing an effective portion of the R protein. The term “effective portion” of the R protein refers to any part of the R protein that, when co-expressed in the plant with the product(s) of the first genetic element, produces an SAR response even in the absence of pathogen infection. By way of example, when the first genetic element is the tobacco N gene, the TIR domain of the N protein is an effective portion of the N protein. Thus, the second genetic element may be a genetic construct that expresses the TIR domain of the N protein.

[0086] One of skill in the art will appreciate that the determination of whether a particular portion of the R protein constitutes an “effective portion” may readily be determined using standard experimental procedures. Briefly, a plant carrying the selected R gene (the first genetic element) is transformed with a genetic construct encoding the region of the R protein to be tested. To plants are selected, and assayed for the presence of the SAR response (in the absence of infecting pathogen) using standard techniques (such as detecting the expression of PR-1 proteins in the absence of pathogen infection) as described below. The presence of the SAR response indicates that the region of the R protein encoded by the genetic construct does constitute an effective portion of the R protein.

[0087] Typically, the second genetic element is designed such that the encoded protein is expressed under the control of regulatory regions or promoter known to produce high-level protein expression. Such regulatory regions may confer constitutive expression of the second genetic element, or may be inducible, such that the expression is turned on only in certain tissues, at defined developmental stages, or in response to application of an inducing agent. In general, the promoter of the second genetic element is a heterlogous promoter. Such a heterologous promoter is a promoter that is not native to the nucleotide sequence that is transcribed. In this instance, a heterologous promoter is any promoter that is not the native promoter of R gene which encodes the R protein, or portion thereof, of the second genetic element.

[0088] In particular embodiments, the R gene used, or from which the cDNA-R is derived, is an R gene having a TIR domain (see Table 1 for examples of R genes having a TIR domain). In this instance, the first genetic element may be the R gene, and the second genetic element may be a construct that expresses a protein or polypetide comprising the TIR domain, or an effective portion of the TIR domain.

[0089] In other particular embodiments, the second genetic element is a trangene that comprises a coding sequence for a polypeptide consisting essentially of a TIR domain, or an effective portion. By “polypeptide consisting essentially of a TIR domain, or an effective portion thereof” is intended a polypeptide consisting of: an amino acid sequence of a TIR domain or an effective portion thereof and optionally includes additional amino acids adjacent to the TIR domain or effective portion thereof. The additional amino acids can be adjacent to the N-terminal end and/or the C-terminal end of the TIR domain or effective portion thereof. While the additional amino acids can include those that are found adjacent to the TIR domain or effective portion thereof in a native R protein, the polypetide, in this instance, does not possess the amino acid sequence of the full-length, native R-protein. Furthermore, the presence of the additional amino acids in the polypeptide will not affect the capability of the polypeptide to produce a SAR response in the absence of an infecting pathogen, when co-expressed in a plant comprising the first and second genetic elements as described supra.

[0090] In yet other embodiments of the invention, the R gene selected is the tobacco N gene. Where the N gene is used as the basis for embodiments of the invention, it should be noted that introduction of either cDNA-N or cDNA-N-tr into TMV susceptible tobacco does not produce resistance to TMV infection. Thus, these forms of the cDNA are not generally useful as the first genetic element. However, introduction of a cDNA construct comprising pN/cDNA-N/intron 3/3′-GRS does produce TMV resistance. As described above, this construct includes the alternatively spliced exon, and thus encodes both of the N gene products-the N protein and the N-tr protein. Therefore, where the selected R gene is the tobacco N gene, the first genetic element may be, for example, the N gene, pN/cDNA-N/intron 3/3′-GRS, or another form of the N cDNA that includes the alternatively spliced exon and which, when expressed in TMV susceptible tobacco produces enhanced TMV resistance. The second genetic element may be, for example, cDNA-N, cDNA-N-tr, or a construct that expresses the N protein TIR domain, or an effective portion thereof.

[0091] The transgenic plants of the invention find use in methods for increasing the disease resistance of plants. Such plants display increased resistance to plant pathogens. The methods of the invention for increasing the disease resistance of plants involve plants having a first and second genetic element or nucleic acid molecule as described supra. The methods comprise obtaining a plant having a first nucleic acid molecule encoding one or more protein products of an R gene sufficient to confer resistance to a phytopathogen; and then introducing into the genome of said plant a second nucleic acid molecule comprising at least one polypeptide encoded by the R gene, wherein co-expression of the first and second nucleic acid molecules is sufficient to produce a systemic acquired resistance response in the plant. The R gene of the first nucleic acid molecule can be native to the plant. That is the R gene occurs as part of a native nucleic acid molecule of the plant, such as, for example, a nucleic acid molecule of a chromosome. Alternatively, if the plant lacks a desired R gene, the methods of the invention additionally involve introducing into the genome of the plant a first nucleic acid molecule comprising the desired R gene.

[0092] IV. Plant Transformation

[0093] Plant transformation techniques are now routinely performed and are well known in the art. The nucleic acid molecules, transgenes, or genetic elements of the invention can be introduced into the genome of a plant using plant transformation methods known in the art. As discussed above, the second genetic element is typically a transgene and so is introduced into the plant species in question using such techniques. The first genetic element may be a native gene or a transgene.

[0094] Where the first genetic element is a transgene, it too is introduced into the plant species by transformation. When the first genetic element is introduced by transformation, it may be co-transformed with the second genetic element, or each element may be separately transformed, such that plant lines separately carrying each of the elements are produced. The elements may then be brought together by conventional plant breeding techniques.

[0095] Where the first genetic element is a native gene, the second genetic element may be introduced into a plant carrying the first genetic element. Alternatively, the second genetic element may be transformed into a plant of the same species, and the two elements may be brought together by crossing plants carrying the (native) first genetic element and the second (transgenic) element.

[0096] Constructs to be transformed into the plant lines are typically cloned into a suitable transformation vector, which is then introduced into plant cells by one of a number of techniques (e.g., electroporation). Progeny plants are regenerated from the transformed plant material, and those progeny plants containing the introduced construct are selected.

[0097] Selection of progeny plants containing the introduced transgene may be made based upon the detection of an altered phenotype. Such a phenotype may result directly from the introduced transgene (e.g., a constitutive SAR response) or may be manifested as enhanced resistance to a chemical agent (such as an antibiotic) as a result of the inclusion of a dominant selectable marker gene incorporated into the transformation vector.

[0098] Successful examples of the modification of plant characteristics by transformation with cloned nucleic acid sequences are replete in the technical and scientific literature. Selected examples, which serve to illustrate the knowledge in this field of technology include, but are not limited to, U.S. Pat. No. 5,571,706 (“Plant Virus Resistance Gene and Methods”); U.S. Pat. No 5,677,175 (“Plant Pathogen Induced Proteins”); U.S. Pat. No. 5,510,471 (“Chimeric Gene for the Transformation of Plants”); U.S. Pat. No. 5,750,386 (“Pathogen-Resistant Transgenic Plants”); U.S. Pat. No. 5,597,945 (“Plants Genetically Enhanced for Disease Resistance”); U.S. Pat. No. 5,589,615 (“Process for the Production of Transgenic Plants with Increased Nutritional Value Via the Expression of Modified 2S Storage Albumins”); U.S. Pat. No. 5,750,871 (“Transformation and Foreign Gene Expression in Brassica Species”); U.S. Pat. No. 5,268,526 (“Overexpression of Phytochrome in Transgenic Plants”).

[0099] These examples include descriptions of transformation vector selection, transformation techniques and the construction of constructs designed to over-express an introduced transgene. In light of the foregoing and the teaching herein of genetic constructs designed to produce a constitutive SAR response, one of skill in the art will be able to introduce these constructs into plants in order to produce plants having a constitutive SAR response and therefore enhanced broad-spectrum disease resistance.

[0100] a. Plant Types

[0101] Because all plant types are susceptible to one or more plant pathogens, the present invention may be usefully applied to produce broad-spectrum resistance in any plant type. Thus, the invention may be applied to both monocotyledonous and dicotyledenous plants, including, but not limited to maize, wheat, rice, barley, soybean, cotton, sorghum, beans in general, rape/canola, alfalfa, flax, sunflower, safflower, millet, rye, sugarcane, sugar beet, cocoa, tea, Brassica, cotton, coffee, sweet potato, flax, peanut, clover; vegetables such as lettuce, tomato, cucurbits, cassava, potato, carrot, radish, pea, lentils, cabbage, cauliflower, broccoli, Brussels sprouts, peppers, and pineapple; tree fruits such as citrus, apples, pears, peaches, apricots, walnuts, avocado, banana, and coconut; and flowers such as orchides, carnations and roses.

[0102] By way of example, TMV is a serious pathogen of Solanaceous species such as tobacco (Nicotiana sp.), tomato (Lycopersicon sp.) and pepper (Capsicum sp.) and is able to infect potato (Solanum sp.). Thus, the use of N gene-based constructs as described herein to produce constitutive SAR plants of these species will be particularly valuable to provide enhanced resistance against not only TMV, but also a broad range of other viruses and bacteria and fungal pathogens that infect these species.

[0103] b. Vector Construction

[0104] A number of recombinant vectors suitable for stable transfection of plant cells or for the establishment of transgenic plants have been described including those described in Weissbach and Weissbach, (1989), and Gelvin et al., (1990). Typically, plant transformation vectors include one or more cloned plant genes (or cDNAs) under the transcriptional control of 5′ and 3′ regulatory sequences, together with a dominant selectable marker. Such plant transformation vectors typically also contain a promoter regulatory region (e.g., a regulatory region controlling inducible or constitutive, environmentally or developmentally regulated, or cell- or tissue-specific expression), a transcription initiation start site, a ribosome binding site, an RNA processing signal, a transcription termination site, and/or a polyadenylation signal. As described above, the first genetic element according to the present invention may be a native R gene, in which case the gene is already present in the plant genome to be transformed. In cases where the first genetic element is a heterologous R gene, it may be introduced into the plant tissue using a transformation vector, but will typically be used with its own regulatory sequences.

[0105] The second genetic element is generally constructed using regulatory sequences that produce expression levels that are higher than expression levels produced by the regulatory sequences of the corresponding R gene. Such regulatory sequences may provide constitutive expression (i.e., expression regardless of triggering stimulus) or expression that is inducible (i.e., expression in response to a triggering stimulus) or expression that is tissue-specific (i.e., expression that is restricted to, or enhanced in, certain tissues of the plant).

[0106] Examples of constitutive plant promoters that may be useful for expressing the second genetic element include: the cauliflower mosaic virus (CaMV) 35S promoter, which confers constitutive, high-level expression in most plant tissues (see, e.g., Odel et al., 1985, Dekeyser et al., 1990, Terada and Shimamoto, 1990; Benfey and Chua, 1990); the nopaline synthase promoter (An et al., 1988); and the octopine synthase promoter (Fromm et al., 1989).

[0107] A variety of plant gene promoters that are regulated in response to environmental, hormonal, chemical, and/or developmental signals, also can be used for expression of the cDNA in plant cells, including promoters regulated by (a) heat (Callis et al, 1988; Ainley, et al. 1993; Gilmartin et al 1992); (b) light (e.g., the pea rbcS-3A promoter, Kuhlemeier et al., 1989, and the maize rbcS promoter, Schaffner and Sheen, 1991); (c) hormones and other signaling molecules, such as abscisic acid (Marcotte et al., 1989), methyl jasmonate or salicylic acid (see also Gatz et al., 1997); and (d) wounding (e.g., wunI, Siebertz et al., 1989).

[0108] Chemical-regulated promoters can be used to modulate the expression of a nucleic acid construct of the invention in a plant through the application of an exogenous chemical regulator. Depending upon the objective, the promoter may be a chemical-inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression. Chemical-inducible promoters are known in the art and include, but are not limited to, the maize In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR-1a promoter, which is activated by salicylic acid. Other chemical-regulated promoters of interest include steroid-responsive promoters (see, for example, the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis et al. (1998) Plant J. 14(2):247-257) and tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet. 227:229-237, and U.S. Pat. Nos. 5,814,618 and 5,789,156), herein incorporated by reference.

[0109] Alternatively, tissue specific (root, leaf, flower, and seed for example) promoters (Carpenter et al. 1992, Denis et al. 1993, Opperman et al. 1993, Yamamoto et al. (1991) Plant Cell 3:371-82, Stockhause et al 1997; Roshal et al., 1987; Schernthaner et al., 1988; and Bustos et al., 1989) can be fused to the coding sequence to obtained particular expression in respective organs.

[0110] Plant transformation vectors may also include RNA processing signals, for example, introns, which may be positioned upstream or downstream of the ORF sequence in the transgene. In addition, the expression vectors may also include additional regulatory sequences from the 3′-untranslated region of plant genes, e.g., a 3′ terminator region to increase mRNA stability of the mRNA, such as the PI-II terminator region of potato or the octopine or nopaline synthase (NOS) 3′ terminator regions.

[0111] Finally, as noted above, plant transformation vectors may also include dominant selectable marker genes to allow for the ready selection of transformants. Such genes include those encoding antibiotic resistance genes (e.g., resistance to hygromycin, kanamycin, bleomycin, G418, streptomycin or spectinomycin) and herbicide resistance genes (e.g., phosphinothricin acetyltransferase).

[0112] c. Transformation and Regeneration Techniques

[0113] Transformation and regeneration of both monocotyledonous and dicotyledonous plant cells is now routine, and the appropriate transformation technique will be determined by the practitioner. The choice of method will vary with the type of plant to be transformed; those skilled in the art will recognize the suitability of particular methods for given plant types. Suitable methods may include, but are not limited to: electroporation of plant protoplasts; liposome-mediated transformation; polyethylene glycol (PEG) mediated transformation; transformation using viruses; micro-injection of plant cells; micro-projectile bombardment of plant cells; vacuum infiltration; and Agrobacterium tumefaciens (AT) mediated transformation. Typical procedures for transforming and regenerating plants are described in the patent documents listed at the beginning of this section.

[0114] d. Selection of Transformed Plants

[0115] Following transformation and regeneration of plants with the transformation vector, transformed plants are usually selected using a dominant selectable marker incorporated into the transformation vector. Typically, such a marker will confer antibiotic resistance on the seedlings of transformed plants, and selection of transformants can be accomplished by exposing the seedlings to appropriate concentrations of the antibiotic.

[0116] After transformed plants are selected and grown to maturity, they can be assayed using the methods described below to assess whether a constitutive SAR phenotype is expressed.

[0117] V. Assessment of Systemic Acquired Resistance (SAR) Response

[0118] The SAR response can be distinguished from other disease resistance responses both functionally and at the molecular level. Functionally, the SAR provides enhanced resistance against a broad spectrum of pathogens. At the molecular level, the SAR response is associated with the expression of a number of SAR-specific proteins.

[0119] SAR proteins are proteins that are closely associated with the maintenance of a resistance response; many of these proteins belong to the class of pathogenesis-related (PR) proteins. PR proteins were originally identified in tobacco as novel proteins that accumulate after TMV infection (Ryals et al., 1996). In tobacco, SAR proteins fall into about nine families: acidic forms of PR-1 (PR-1a, PR-1b and PR-1c); beta-1,3-glucanase (PR-2a, PR-2b and PR-2c); class II chitinases (PR-3a and PR-3b, also termed PR-Q); hevein-like protein (PR-4a and PR-4b); thaumatin-like protein (PR-5a and PR-5b); acidic and basic isoforms class III chitinase; an extracellular beta-1,3-glucanase (PR-Q′); and the basic isoform of PR-1 (Ward et al., 1991). In Arabidopsis, the SAR marker proteins are PR-1, PR-2 and PR-5 (Uknes et al., 1992). The genes encoding these SAR markers have been cloned and characterized and used extensively to evaluate the onset of SAR (see Ward et al., 1991, and Uknes et al., 1992). The relative expression of the various SAR proteins vary between species. For example, acidic PR-1 is weakly expressed in the SAR response in cucumber, but is the predominant SAR protein in tobacco and Arabidopsis. Conserved homologs of SAR proteins, including PR-1, have been identified in monocotyledenous species, including maize and barley.

[0120] The PR-1 proteins are highly conserved and so represent a good molecular marker for detecting SAR. A constitutive SAR response may thus be detected by growing plants in the absence of pathogen, and then assaying for the expression of PR-1 RNA or protein. Plants carrying the R gene that are either exposed or not exposed to the pathogen may be used as positive and negative controls, respectively. Because PR-1 proteins are highly conserved, antibodies that raised against the tobacco PR-1 proteins, including the PR-1c protein, also recognize PR-1 proteins from other plant species (see Takahashi et al., 1994). Therefore, anti-PR-1 antibodies may conveniently be used across a range of plant species to detect SAR proteins.

[0121] At the functional level, the SAR response provides enhanced resistance to a wide range of pathogens. While the individual assays for detecting such resistance will vary depending on the particular pathogen, the general observation of enhanced resistance against a number of pathogens (compared to a control R plant) in the absence of a prior triggering infection is indicative of a constitutive SAR response.

[0122] By “disease resistance” is intended that the plants avoid the disease symptoms that are the outcome of plant-pathogen interactions. That is, pathogens are prevented from causing plant diseases and the associated disease symptoms, or alternatively, the disease symptoms caused by the pathogen is minimized or lessened. While the invention does not depend of any particular reduction in the severity of disease symptoms, the methods and plants of the invention will generally reduce the disease symptoms resulting from a pathogen challenge by at least about 5% to about 50%, at least about 10% to about 60%, at least about 30% to about 70%, at least about 40% to about 80%, or at least about 50% to about 90% or greater. Hence, the methods of the invention can be utilized to protect plants from disease, particularly those diseases that are caused by plant pathogens.

[0123] The transgenic plants of the invention display enhanced resistance to plant pathogens or phytopathogens, including but are not limited to, viruses or viroids, bacteria, insects, nematodes, fungi, and the like. Viruses include any plant virus, for example, TMV, tobacco or cucumber mosaic virus, ringspot virus, necrosis virus, maize dwarf mosaic virus, etc. Specific fungal and viral pathogens for the major crops include: Soybeans: Phytophthora megasperma fsp. glycinea, Macrophomina phaseolina, Rhizoctonia solani, Sclerotinia sclerotiorum, Fusarium oxysporum, Diaporthe phaseolorum var. sojae (Phomopsis sojae), Diaporthe phaseolorum var. caulivora, Sclerotium rolfsii, Cercospora kikuchii, Cercospora sojina, Peronospora manshurica, Colletotrichum dematium (Colletotichum truncatum), Corynespora cassuicola, Septoria glycines, Phyllosticta sojicola, Alternaria alternata, Pseudomonas syringae p.v. glycinea, Xanthomonas campestris p.v. phaseoli, Microsphaera diffusa, Fusarium semitectum, Phialophora gregata, Soybean mosaic virus, Glomerella glycines, Tobacco Ring spot virus, Tobacco Streak virus, Phakopsora pachyrhizi, Pythium aphanidermatum, Pythium ultimum, Pythium debaryanum, Tomato spotted wilt virus, Heterodera glycines Fusarium solani; Canola: Albugo candida, Alternaria brassicae, Leptosphaeria maculans, Rhizoctonia solani, Sclerotinia sclerotiorum, Mycosphaerella brassiccola, Pythium ultimum, Peronospora parasitica, Fusarium roseum, Alternaria alternata; Alfalfa: Clavibater michiganese subsp. insidiosum, Pythium ultimum, Pythium irregulare, Pythium splendens, Pythium debaryanum, Pythium aphanidermatum, Phytophthora megasperma, Peronospora trifoliorum, Phoma medicaginis var. medicaginis, Cercospora medicaginis, Pseudopeziza medicaginis, Leptotrochila medicaginis, Fusarium, Xanthomonas campestris p.v. alfalfae, Aphanomyces euteiches, Stemphylium herbarum, Stemphylium alfalfae; Wheat: Pseudomonas syringae p.v. atrofaciens, Urocystis agropyri, Xanthomonas campestris p.v. translucens, Pseudomonas syringae p.v. syringae, Alternaria alternata, Cladosporium herbarum, Fusarium graminearum, Fusarium avenaceum, Fusarium culmorum, Ustilago tritici, Ascochyta tritici, Cephalosporium gramineum, Collotetrichum graminicola, Erysiphe graminis f.sp. tritici, Puccinia graminis f.sp. tritici, Puccinia recondita f.sp. tritici, Puccinia striuformis, Pyrenophora tritici-repentis, Septoria nodorum, Septoria tritici, Septoria avenae, Pseudocercosporella herpotrichoides, Rhizoctonia solani, Rhizoctonia cerealis, Gaeumannomyces graminis var. tritici, Pythium aphanidermatum, Pythium arrhenomanes, Pythium ultimum, Bipolaris sorokiniana, Barley Yellow Dwarf Virus, Brome Mosaic Virus, Soil Borne Wheat Mosaic Virus, Wheat Streak Mosaic Virus, Wheat Spindle Streak Virus, American Wheat Striate Virus, Claviceps purpurea, Tilletia tritici, Tilletia laevis, Ustilago tritici, Tilletia indica, Rhizoctonia solani, Pythium arrhenomannes, Pythium gramicola, Pythium aphanidermatum, High Plains Virus, European wheat striate virus; Sunflower: Plasmophora halstedii, Sclerotinia sclerotiorum, Aster Yellows, Septoria helianthi, Phomopsis helianthi, Alternaria helianthi, Alternaria zinniae, Botrytis cinerea, Phoma macdonaldii, Macrophomina phaseolina, Erysiphe cichoracearum, Rhizopus oryzae, Rhizopus arrhizus, Rhizopus stolonifer, Puccinia helianthi, Verticillium dahliae, Erwinia carotovorum pv. carotovora, Cephalosporium acremonium, Phytophthora cryptogea, Albugo tragopogonis; Corn: Fusarium moniliforme var. subglutinans, Erwinia stewartii, Fusarium moniliforme, Gibberella zeae (Fusarium graminearum), Stenocarpella maydi (Diplodia maydis), Pythium irregulare, Pythium debaryanum, Pythium graminicola, Pythium splendens, Pythium ultimum, Pythium aphanidermatum, Aspergillusflavus, Bipolaris maydis O, T (Cochliobolus heterostrophus), Helminthosporium carbonum I, II & III (Cochliobolus carbonum), Exserohilum turcicum I, II & III, Helminthosporium pedicellatum, Physoderma maydis, Phyllosticta maydis, Kabatiella maydis, Cercospora sorghi, Ustilago maydis, Puccinia sorghi, Puccinia polysora, Macrophomina phaseolina, Penicillium oxalicum, Nigrospora oryzae, Cladosporium herbarum, Curvularia lunata, Curvularia inaequalis, Curvulariapallescens, Clavibacter michiganense subsp. nebraskense, Trichoderma viride, Maize Dwarf Mosaic Virus A & B, Wheat Streak Mosaic Virus, Maize Chlorotic Dwarf Virus, Claviceps sorghi, Pseudonomas avenae, Erwinia chrysanthemi pv. zea, Erwinia carotovora, Corn stunt spiroplasma, Diplodia macrospora, Sclerophthora macrospora, Peronosclerospora sorghi, Peronosclerospora philippinensis, Peronosclerospora maydis, Peronosclerospora sacchari, Sphacelotheca reiliana, Physopella zeae, Cephalosporium maydis, Cephalosporium acremonium, Maize Chlorotic Mottle Virus, High Plains Virus, Maize Mosaic Virus, Maize Rayado Fino Virus, Maize Streak Virus, Maize Stripe Virus, Maize Rough Dwarf Virus; Sorghum: Exserohilum turcicum, Colletotrichum graminicola (Glomerella graminicola), Cercospora sorghi, Gloeocercospora sorghi, Ascochyta sorghina, Pseudomonas syringae p.v. syringae, Xanthomonas campestris p.v. holcicola, Pseudomonas andropogonis, Puccinia purpurea, Macrophomina phaseolina, Perconia circinata, Fusarium moniliforme, Alternaria alternata, Bipolaris sorghicola, Helminthosporium sorghicola, Curvularia lunata, Phoma insidiosa, Pseudomonas avenae (Pseudomonas alboprecipitans), Ramulispora sorghi, Ramulispora sorghicola, Phyllachara sacchari, Sporisorium reilianum (Sphacelotheca reiliana), Sphacelotheca cruenta, Sporisorium sorghi, Sugarcane mosaic H, Maize Dwarf Mosaic Virus A & B, Claviceps sorghi, Rhizoctonia solani, Acremonium strictum, Sclerophthona macrospora, Peronosclerospora sorghi, Peronosclerospora philippinensis, Sclerospora graminicola, Fusarium graminearum, Fusarium oxysporum, Pythium arrhenomanes, Pythium graminicola, etc.

[0124] Nematodes include parasitic nematodes such as root-knot, cyst, and lesion nematodes, including Heterodera and Globodera spp; particularly Globodera rostochiensis and globodera pailida (potato cyst nematodes); Heterodera glycines (soybean cyst nematode); Heterodera schachtii (beet cyst nematode); and Heterodera avenae (cereal cyst nematode).

[0125] VI. Obtaining R Gene Homologs and Sequence Variants

[0126] The Examples provided below utilized the prototypical tobacco N gene and related cDNA molecules as described by Whitham et al. (1994). However, as described above, the invention is not limited to the use of prototypical R genes, but may be practiced using R gene homologs and sequence variants that differ in exact sequence from the prototype sequences.

[0127] R Gene Homologs

[0128] R gene homologs may be obtained from closely or distantly related plant species by conventional molecular biology methods, including polymerase chain reaction-based techniques and nucleic acid hybridization.

[0129] By way of example, homologs of the N gene are present in a number of plant species including tomato and other varieties of tobacco. Such homologs may also be used to produce constitutive SAR plants as described herein. As described above, homologs of the disclosed N gene confer TMV resistance when introduced into otherwise susceptible plants and encode N and N-tr that are typically characterized by possession of at least 50% sequence identity counted over the full-length alignment with the amino acid sequence of the prototype N and N-tr sequences using the NCBI Blast 2.0, gapped blastp set to default parameters. Proteins with even greater similarity to the reference sequences will show increasing percentage identities when assessed by this method, such as at least about 60%, 65%, 70%, generally at least about 75%, 80%, 85%, preferably at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, and more preferably at least about 98%, 99% or more sequence identity to the reference sequence.

[0130] Both conventional hybridization and PCR amplification procedures may be utilized to clone sequences encoding N and N-tr homologs. Common to both of these techniques is the hybridization of probes or primers derived from the prototype cDNA-N or N gene sequence to a target nucleotide preparation, which may be, in the case of conventional hybridization approaches, a cDNA or genomic library or, in the case of PCR amplification, a cDNA or genomic library, or an mRNA preparation. Amplification of, or hybridization to, a cDNA library in order to obtain N homologs should preferably be performed on a cDNA library made from a plant infected with TMV so that the N homolog is actively expressed in the cells from which the library is made.

[0131] Direct PCR amplification may be performed on cDNA or genomic libraries prepared from the plant species in question, or RT-PCR may be performed using mRNA extracted from the plant cells using standard methods. PCR primers will typically, but not necessarily, comprise at least about 10 consecutive nucleotides of the tobacco cDNA-N or N gene. One of skill in the art will appreciate that sequence differences between the tobacco cDNA-N or N gene and the target nucleic acid to be amplified may result in lower amplification efficiencies. To compensate for this, longer PCR primers or lower annealing temperatures may be used during the amplification cycle. Where lower annealing temperatures are used, sequential rounds of amplification using nested primer pairs may be necessary to enhance specificity.

[0132] Degenerate PCR primers, which are well known to those of ordinary skill in the art, can also be employed for PCR amplification. A degenerate primers is not a primer consisting of a single nucleotide sequence, but rather is a mixture of primers of different nucleotide sequences which are capable of encoding for an amino acid sequence that corresponds to a particular portion of the coding sequence of a gene interest. Because of the degeneracy of the genetic code, a particular amino acid can be specified by more than one codon. A degenerate primers is thus synthesized to take in to account the degeneracy of the genetic code and will typically include all possible nucleotide sequences that could encode the amino acid sequence of that portion of the protein to which the primer corresponds. In producing such degenerate primers, it is recognized that not all organisms use all possible codons to specify a particular amino acid, and some organisms, and some particular genomes in an organism, such as, for example, the mitochondrial genome, do not follow the universal genetic code. Accordingly, it will typically be preferable to synthesize a degenerate oligonucleotide primer based on the genetic code and codon usage in an organism or within a particular genome of an organism. Such genetic codes, codon usage, and methods for their determination are known in the art.

[0133] For conventional hybridization techniques the hybridization probe is preferably conjugated with a detectable label such as a radioactive label, and the probe is preferably of at least 20 nucleotides in length. As is well known in the art, increasing the length of hybridization probes tends to give enhanced specificity. The labeled probe derived from the tobacco cDNA-N or N gene sequence may be hybridized to a plant cDNA or genomic library and the hybridization signal detected using means known in the art. The hybridizing colony or plaque (depending on the type of library used) is then purified and the cloned sequence contained in that colony or plaque isolated and characterized.

[0134] Homologs of the tobacco cDNA-N or N gene may alternatively be obtained by immunoscreening of an expression library. With the provision of the disclosed N gene and encoded proteins, the N or N-tr proteins may be expressed and purified in a heterologous expression system (e.g., E. coli) and used to raise antibodies (monoclonal or polyclonal) specific for the N or N-tr protein. Antibodies may also be raised against synthetic peptides derived from the tobacco N or N-tr amino acid sequences. Methods of raising antibodies are well known in the art and are described in Harlow and Lane (1988). Such antibodies can then be used to screen an expression cDNA library produced from the plant from which it is desired to clone the N homolog using routine methods. The selected cDNAs can be confirmed by sequencing and enzyme activity.

[0135] Parallel approaches may be employed to obtain homologs of other R genes, such as Prf and L6.

[0136] Variant Sequences

[0137] Variant R proteins include proteins that differ in amino acid sequence from the selected prototypical R protein sequence. Such proteins may be produced by manipulating the nucleotide sequence of the prototype cDNA-R or R gene using standard procedures such as site-directed mutagenesis or the polymerase chain reaction. The simplest modifications involve the substitution of one or more amino acids for amino acids having similar biochemical properties. These so-called conservative substitutions are likely to have minimal impact on the activity of the resultant protein. Table 3 shows amino acids that may be substituted for an original amino acid in a protein and which are regarded as conservative substitutions.

TABLE 3
Original Residue Conservative Substitutions
Ala              ser
Arg              lys
Asn              gln; his
Asp              glu
Cys              ser
Gln              asn
Glu              asp
Gly              pro
His              asn; gln
Ile              leu; val
Leu              ile; val
Lys              arg; gln; glu
Met              leu; ile
Phe              met; leu; tyr
Ser              thr
Thr              ser
Trp              tyr
Tyr              tip; phe
Val              ile; leu

[0138] More substantial changes in biological function or other features may be obtained by selecting substitutions that are less conservative than those in Table 3, i.e., selecting residues that differ more significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain. The substitutions that in general are expected to produce the greatest changes in protein properties will be those in which (a) a hydrophilic residue, e.g., seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g., leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histadyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine. The effects of these amino acid substitutions or deletions or additions may be assessed for R protein derivatives by analyzing the ability of a nucleic acid molecule encoding the derivative proteins to produce a constitutive SAR response when used in conjunction with the techings of this invention.

[0139] Variant R cDNAs or R genes may be produced by standard DNA mutagenesis techniques, for example, M13 primer mutagenesis. Details of these techniques are provided in Sambrook et al. (1989), Ch. 15. By the use of such techniques, variants may be created which differ in minor ways from the prototypical R gene nucleic acid sequences, yet which still retain R gene function. In their simplest form, such variants may differ from the disclosed sequences by alteration of the coding region to fit the codon usage bias of the particular organism into which the molecule is to be introduced.

[0140] Alternatively, the coding region may be altered by taking advantage of the degeneracy of the genetic code to alter the coding sequence in such a way that, while the nucleotide sequence is substantially altered, it nevertheless encodes proteins having amino acid sequences identical or substantially identical to the prototype R protein sequences. For example, the second amino acid residue of the prototype N protein is alanine. This is encoded in the prototype N gene open reading frame (ORF) by the nucleotide codon triplet GCA. Because of the degeneracy of the genetic code, three other nucleotide codon triplets—GCT, GCC and GCG—also code for alanine. Thus, the nucleotide sequence of the N ORF could be changed at this position to any of these three codons without affecting, the amino acid composition of the encoded protein or the characteristics of the protein. Based upon the degeneracy of the genetic code, variant DNA molecules may be derived from R cDNA and gene sequences using standard DNA mutagenesis techniques as described above, or by synthesis of DNA sequences.

[0141] The following Examples are offered by way of illustration and not by way of limitation.

EXAMPLES

Example 1

Overexpression of N cDNAs in NN Tobacco Plants Induces a Constitutive Systemic Acquired Resistance Phenotype, even in the Absence of TMV Infection

[0142] A. Vector Construction and Plant Transformation

[0143] cDNA-N and cDNA-N-tr were cloned into the T-DNA vector pOCA28 (Olszewski et al., 1988; gift from F. Ausubel, Harvard Medical School). These constructs place cDNA expression under the regulatory control of the 35S promoter and the NOS terminator. The resulting vectors were transformed into TMV resistant tobacco (Samsun::NN) or TMV susceptible tobacco (SR1::nn) by Agrobacterium-mediated transformation (Horsch et al., 1985).

[0144] B. Expression of SAR Response

[0145] The lower leaves of To transformants were inoculated with TMV (U 1 strain) approximately 4 weeks after transfer to soil as described by Takahashi (1956) and Klement (1990). Following such inoculation, resistance or susceptibility of a plant to TMV and virus spread was assessed using standard assays, including determining HR and SAR responses, and detecting the presence of TMV in the upper leaves of the plant. The plants were also analyzed at approximately 10 weeks after transfer to soil.

[0146] With respect to HR, the inoculated leaves of a resistant tobacco plant show localized regions of necrosis around the site of TMV infection within about 48 hours after inoculation; the lesions are generally about 0.1 cm in diameter and TMV is restricted to the region immediately surrounding the necrotic lesions. In contrast, leaves of susceptible plants generally show no lesions, the TMV spreads systemically, and the leaves develop mosaic symptoms characterized by intermittent areas of light and dark leaf tissue.

[0147] The SAR response was determined functionally about 7-10 days after inoculation of the lower leaves, by inoculating upper leaves of the plant in the same manner. A TMV resistant plant in which the SAR has been triggered by the earlier inoculation will show HR lesions on these upper leaves within about 48 hours of the second inoculation, but the lesions are typically fewer and significantly smaller (0.03-0.05 cm diameter) than the HR lesions on the lower leaves. A susceptible plant will again show no lesions, and the mosaic patterning signifying systemic infection will be observed on the upper leaves.

[0148] The SAR response was detected at the molecular level by detecting PR-i a RNA using a standard Northern Blot procedure. Total RNA was extracted from upper leaves of 4- or 10-week-old plants. Certain of the plants were first inoculated with TMV on their lower leaves, and the upper leaves were harvested approximately 10 days after inoculation. Following electrophoresis and Northern blotting of the RNA, the filters were hybridized with a probe comprising the tobacco PR-1a cDNA (Cornelissen et al., 1987).

[0149] Systemic spread of the virus can be detected in a number of ways. By visual inspection of the leaves, systemic infection can be detected by the appearance of the mosaic light and dark patches on the leaves away from the site of the initial inoculation. The presence of systemically spread virus can also be detected by a bioassay in which leaves of the inoculated test plant (taken from a part of the test plant distal from the initial inoculation (“distal leaves”)) are rubbed onto an indicator plant (e.g., N. tabacum Samsun NN). The development of an HR response on the indicator plant indicates the presence of systemic spread of the virus through the test plant. Additionally, systemic spread of the virus may be detected at the molecular level by removing distal leaves, extracting RNA using standard procedures and performing a Northern blot using a radiolabeled probe derived from the TMV genome. In this test, systemic spread is indicated by the presence of TMV-hybridizing bands on the Northern blot. Alternatively, systemic spread of the virus may be detected immunologically, for example by ELISA of protein extracted from distal leaves using an anti-TMV protein antibody.

[0150] TMV infection of 4-week-old cDNA-N::Samsun AN or cDNA-N-tr::Samsun NN transgenic plants was observed to induce an HR similar to that induced by TMV in wild type N plants. However, the HR continued to spread throughout the plant resulting in death of the plant within about 10 days. The induced HR and subsequent plant death was not associated with virus spread. Thus, it appears that cDNA-N::Samsun NN or cDNA-N-tr::Samsun NN overexpressing transgenic plants when challenged with pathogen show a hyperactive response. One possible explanation for this is that a diffusible systemic signal generated in the inoculated leaf may act as a signal to induce death in the TMV uninfected parts of the plant. Notably, several virus types other than TMV (including tobacco rattle virus and tobacco etch virus) did not trigger this early phenotype.

[0151] Surprisingly, at about 10 weeks of soil growth (about the time of flowering) transgenic AN plants overexpressing cDNA-N or cDNA-N-tr showed a constitutive lesion phenotype without TMV infection (this phenotype is referred to as “lesion mimic”). The lesions started at leaf tips, and spread throughout the leaf within about 5 days. Lesions appeared only in the lower half of the plant. Overexpressing transgenic plants showing these constitutive lesions displayed an increased resistance or immunity when challenged with TMV pathogen. In addition, these plants show increased expression of pathogen related protein 1a (PR1a) RNA, a well-characterized molecular marker of systemic acquired resistance (FIG. 2). Interestingly, PR-1a RNA levels appeared to be higher in overexpressing plants than in NN plants that had been triggered to produce SAR by prior inoculation with TMV (see FIG. 2).

[0152] The early (4 week) phenotype exhibited by the cDNA-N::Samsun NN and cDNA-N-tr::Samsun NN plants could be detrimental to crop plants grown in the field, since exposure to the triggering pathogen at this stage of development might be lethal. A number of approaches might be used to prevent this phenomenon. For example, since the early phenotype is apparently triggered only by the pathogen that corresponds to the particular R gene utilized, problems associated with the early phenotype could be minimized by selecting an R gene that confers resistance to a pathogen that does not typically cause significant disease in the plant type that is to be transformed (or in the geographic area in which the plant is to be grown). Alternatively, exposure of the plants to the triggering pathogen during early growth could be minimized by physical isolation (such as greenhouse growth). At the molecular level, the early phenotype may be avoided altogether by placing the expression of the second genetic element under the control of either an inducible promoter, or a promoter that is developmentally controlled. Thus, in the case of an inducible promoter, the inducing agent could be applied to the plants to turn on the SAR response later in development (for example, around 10 weeks). The use of an inducible promoter is also advantageous in that the SAR response need not be turned if there is no pathogen problem in the crop. In the case of a developmentally controlled promoter, the promoter used would preferably cause expression of the second genetic element only after the plants had reached a maturity level where the early phenotype no longer occurs (around 10 weeks of age).

Example 2

Overexpression of the N TIR Domain in NN Plants Induces a Constitutive Systemic Acquired Resistance Phenotype, even in the Absence of TMV Infection

[0153] To determine whether the entire N protein is required for this molecular-genetic activation of the SAR response, constructs were produced in which each of the three domains of the N protein—TIR, NBS and LRR—was independently expressed under the control of the 35S promoter and the NOS terminator. The constructs expressed the following sections of the N protein:

[0154] construct 1: amino acids 1-150 (including the TIR domain);

[0155] construct 2: amino acids 201-441 (including the NBS domain);

[0156] construct 3: amino acids 590-928 (including the LRR domain).

[0157] The constructs were transformed into Samsun::NN tobacco as described above, and the resulting transgenic plants were tested for SAR response in the absence of TMV infection, as well as following TMV infection.

[0158] TMV infection of 4-week-old NBS:Samsun AN and LRR:Samsun AN plants (i.e., Samsun NN plants transformed with the NBS and LRR domain constructs, respectively) produced the same response as TMV infection of 4-week-old untransformed Samsun NN plants, i.e., HR that contains the virus and prevents systemic spread. However, TMV infection of 4-week-old TIR:Samsun NN plants produced the same response as observed with cDNA-N::Samsun NN or cDNA-N-tr::Samsun NN plants, i.e., HR response followed by spread of the HR response (without corresponding systemic spread of the virus) and subsequent plant death.

[0159] Furthermore, at 10 weeks of age, and in the absence of TMV challenge, the TIR:Samsun NN plants also showed the constitutive SAR response seen with cDNA-N::Samsun NN or cDNA-N-tr::Samsun NN plants.

Example 3

Overexpression of the N-TIR Domain Induces a Constitutive HR Phenotype in the Absence of TMV Infection and Provides Resistance to Other Virulent Viral Pathogens

[0160] Different regions of N-cDNA were expressed to further define the region of N-cDNA that is sufficient to the initiate constitutive defense response (HR and SAR) in the absence of TMV. TIR, NBS, and LRR regions of N-cDNA were independently inserted between the 35S promoter and NOS terminator in a pMB4 T-DNA vector. These constructs were transformed into SR1 nn (TMV susceptible) and Samsun NN (TMV resistant, wild-type N gene) tobacco plants by Agrobacterium-mediated transformation (Horsch et al., 1985). Transgenic TIR::Samsun NN plants overexpressing the TIR domain showed constitutive HR after 8-10 weeks in the absence of TMV infection (FIG. 3). However, overexpression of the NBS or LRR region of the N gene failed to induce this response (data not shown). This suggests that the 450 bp N-TIR region is sufficient to induce constitutive defense response when overexpressed in the background of the N gene. Furthermore, this phenotype is similar to that of the phenotype induced when N-cDNA or N-tr-cDNA is overexpressed in the wild-type N gene background.

[0161] To assess 35S-TIR expression in these plants, Northern analysis was performed using one μg poly (A)+ RNA isolated from Samsun NN wild-type plants and two different TIR overexpressing 10- to 12-week-old sibling plants (FIG. 4, lanes 1 and 2). Wild-type N message in the Northern analysis was not detected, as it is expressed at a very low level. However, the wild-type N message was detected using RT-PCR (data not shown). These results indicate that the TIR message is overexpressed compared to the wild-type N gene containing Samsun NN plants (FIG. 4). Ongoing experiments will determine if the message expression correlates with TIR protein expression.

[0162] Whether the constitutive HR induced by TIR overexpression induces resistance to other virulent viral pathogens, such as tobacco rattle virus (TRV, strain Ppk20), potato virus X (PVX), and tobacco etch virus (TEV), was examined. TIR::Samsun NN transgenic plants (10 to 12 weeks old) overexpressing TIR and exhibiting the constitutive HR phenotype and the wild-type Samsun NN plants were infected with known amounts of TRV, PVX, and TEV on leaves younger than those displaying HR. Two weeks after virus infection, RNA was extracted from the inoculated leaves. About 5 μg of total RNA was used in the Northern analysis. PVX virus replication was detected by Northern hybridization analysis using the PVX coat protein as a probe. The TRV probe consisted of approximately 500 bps of the 5′ terminus of RNA1. Replication of TRV and PVX were reduced approximately 70-80% in the TIR::Samsun NN transgenic plants when compared to replication in the control Samsun NN plants (FIG. 5). These data suggest that TIR overexpressing plants resist replication of these viruses through TIR/N induced SAR.

[0163] All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications 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.

[0164] Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

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Claims

1. A transgenic plant comprising: (a) a first nucleic acid molecule encoding one or more protein products of an R gene sufficient to confer resistance to a phytopathogen; and (b) a second nucleic acid molecule comprising a transgene, said transgene comprising a heterologous promoter operably linked to a coding sequence for a protein comprising at least one polypeptide encoded by the R gene; wherein co-expression of the first and second nucleic acid molecules is sufficient to produce a systemic acquired resistance response in the plant.

2. The plant of claim 1, wherein the first nucleic acid molecule is an R gene expressed under the control of the native R gene promoter.

3. The plant of claim 1, wherein the R gene encodes a polypeptide comprising a TIR domain.

4. The plant of claim 3, wherein the R gene is selected from the group consisting of N, L6, M and RPP5, and functional homologs thereof.

5. The plant of claim 4, wherein the polypeptide encoded by the second nucleic acid comprises the TIR domain.

6. The plant of claim 1, wherein the first nucleic acid molecule encodes an N protein or an N-tr protein, and the second nucleic acid molecule encodes a protein comprising an N protein TIR region.

7. Transgenic seed of the plant of claim 1.

8. A method of producing a plant that exhibits an SAR response in the absence of a pathogen infection, comprising introducing a transgene into a plant having an R gene, said transgene comprising a heterologous promoter operably linked to a coding sequence for a protein comprising at least one polypeptide encoded by the R gene, wherein co-expression of the R gene and the polypeptide component produces an SAR response in the plant.

9. A plant produced by the method of claim 8.

10. Transgenic seed of a plant of claim 9.

11. A transgenic plant comprising: (a) a first nucleic acid molecule encoding an R gene product having a TIR domain; and (b) a second nucleic acid molecule comprising a transgene, said transgene comprising a heterologous promoter operably linked to a coding sequence for a polypeptide consisting essentially of a TIR domain, or an effective portion thereof; wherein co-expression of the first and second nucleic acid molecules produces a constitutive SAR response in the plant.

12. The transgenic plant of claim 11, wherein the R gene product is a product of a gene selected from the group consisting of the N gene of tobacco, the M gene of flax, the L6 gene of flax and the RPP5 gene of Arabidopsis.

13. A transgenic plant comprising: (a) a first nucleic acid molecule encoding an N protein and an N-tr protein; and (b) a second nucleic acid molecule comprising a transgene, said transgene comprising a heterologous promoter operably linked to a coding sequence for a polypeptide consisting essentially of an N protein TIR domain, or an effective portion thereof; wherein expression of the first and second nucleic acid molecules in the plant produces an increased resistance to at least one phytopathogen.

14. The plant of claim 13, wherein the first nucleic acid molecule is a native nucleic acid molecule.

15. The plant of claim 14, wherein the first nucleic acid molecule is a native N gene.

16. The plant of claim 13, wherein the N protein comprises an amino acid sequence as shown in SEQ ID NO:3.

17. The plant of claim 13, wherein the N-tr protein comprises an amino acid sequence as shown in SEQ ID NO:5.

18. The plant of claim 17, wherein the plant is selected from the group consisting of tobacco, tomato and pepper.

19. Transgenic seed of the plant of claim 13.

20. A method for increasing the disease resistance of a plant, said method comprising: (a) obtaining a plant comprising a first nucleic acid molecule encoding one or more protein products of an R gene sufficient to confer resistance to a phytopathogen; and (b) introducing into the genome of said plant a second nucleic acid molecule comprising a transgene, said transgene comprising a heterologous promoter operably linked to a coding sequence for a protein comprising at least one polypeptide encoded by the R gene; wherein co-expression of the first and second nucleic acid molecules is sufficient to produce a systemic acquired resistance response in the plant.

21. The plant of claim 20, wherein the first nucleic acid molecule is a native nucleic acid molecule.

22. The plant of claim 20, wherein said first nucleic acid molecule is introduced into said genome of said plant.