Tobacco rattle virus vectors and related compositions and methods

Abstract

The application provides, in part, vectors based on novel tobacco rattle virus replicons, as well as methods for using such vectors and transgenic plants.

Description

BACKGROUND OF THE INVENTION

[0003] Aided by high-throughput sequencing technology, plant biologists have identified large numbers of novel open reading frames (ORFs). Large-scale functional genomic approaches are needed in order to convert this sequence information into functional information. Traditionally, Agrobacterium Ti plasmid transfer DNA (T-DNA) and transposon-based insertional mutant populations have provided the resources for the analysis of phenotypes. Large collections of such insertion and deletion mutant populations have been generated for plants like Arabidopsis thaliana due to the ease of transformation. However, these mutant collections are not generally saturated, meaning that all ORFs have not been disrupted or tagged by an insertion or deletion. Saturation may be difficult to achieve because of bias in the insertion of T-DNA or transposons and because disruptions of essential genes often result in nonviable plants that are lost from the collection. In addition, many plant genomes have a high degree of gene duplication, and therefore a disruption of a gene will not yield any measurable phenotype because a duplicate copy of the gene compensates for the defect. Alternative methods for probing gene function have been developed, including dsRNA-mediated suppression of genes by vectors that produce sense and antisense transcripts. However, all of these approaches rely on the generation of transgenic lines. The generation of transgenic plant lines is a time consuming process, and is only practical for high throughput analyses in Arabidopsis.

[0004] Gene silencing approaches, such as virus induced gene silencing (VIGS), offer an attractive and quick alternative for knocking out expression of a gene without the need to genetically transform the plant. Using this method, recombinant virus carrying a partial sequence of a host gene is used to infect the plant. When the virus spreads systemically, the endogenous gene transcripts, which are homologous to the insert in the viral vector (VIGS-vector), are degraded by post-transcriptional gene silencing (PTGS). Vectors for carrying out gene silencing suffer from a variety of shortcomings, including inability to silence genes in proliferating or non-proliferating cells, inability to silence genes in a large area of the target plant, and poor rate of infection in target plants.

[0005] Improved vectors for use in plants, and particularly vectors for use in gene silencing and high-throughput gene analysis, are needed in the field of plant biology.

SUMMARY OF THE INVENTION

[0006] In certain aspects, the invention relates to the discovery of novel RNA1 and RNA2 sequences of tobacco rattle virus (TRV). TRV is a bipartite RNA virus that is useful in transforming plants. Novel RNA1 and RNA2 sequences disclosed herein, and portions thereof, can be used independently to transform plants and plant cells, and have also been incorporated into novel TRV-RNA1 and TRV-RNA2 vectors to achieve particularly efficient transformation of plants. In certain embodiments, the invention provides novel TRV-RNA2 vectors that can be engineered to carry a heterologous nucleic acid for delivery into a plant. The novel TRV RNAs and vectors can be used to achieve, for example, suppression of host plant gene expression or overexpression of the heterologous nucleic acid. In certain embodiments, the invention provides methods for making transgenic plants, as well as the resulting transgenic plants and plant products thereof. In certain embodiments, the invention provides methods for evaluating the function of novel or uncharacterized plant genes, and many of the vectors disclosed herein are particularly suitable for high-throughput analysis of plant gene function.

[0007] In certain aspects, the invention provides recombinant nucleic acids comprising a novel TRV-RNA1 nucleotide sequence of SEQ ID NO:1, and complementary sequences thereof. Certain embodiments of the invention also provide TRV-RNA1 nucleic acids that have one or more of the following nucleotides: A at nucleotide 1266, C at nucleotide 2291, T at nucleotide 3094, T at nucleotide 3130, G at nucleotide 3634, A at nucleotide 4123, T at nucleotide 4254, A at nucleotide 4642, and A at nucleotide 5559. The nucleotide positions are given in reference to the sequence of SEQ ID NO:1, but in certain embodiments, the invention also provides variants of the novel TRV-RNA1 nucleotide sequence, including truncations, rearrangements, insertions, deletions, and mutations, so long as one or more of the identified nucleotides is present at a position that discernibly corresponds to the cited position in SEQ ID NO: 1. For example, if the sequence of SEQ ID NO:1 is broken into a few pieces that are then reassembled in a different order, one of skill in the art will be able to discern that one or more of the above described nucleotides are still present in the same local sequence context as in SEQ ID NO: 1, despite the rearrangement, and accordingly, the rearranged nucleic acid is encompassed by certain embodiments of the present invention. In certain embodiments, the TRV-RNA1 nucleotide sequence is operably linked to a plant active promoter. In certain embodiments, a transcription terminator is positioned within about 10, 100 or 1000 bases downstream of the 3′ end of the TRV-RNA1 nucleotide sequence. In certain embodiments, a self-cleaving ribozyme is positioned within about 1, 10 or 100 bases of the 3′ end of the TRV-RNA1 nucleotide sequence. In certain embodiments, the TRV-RNA1 nucleic acid is an RNA or a DNA, particularly a cDNA of SEQ ID NO: 1. In certain embodiments, the TRV-RNA1 is connected to or contains as an insert a heterologous nucleic acid. Optionally, the heterologous nucleotide sequence includes one or more recombination sites that may be used for the insertion of a nucleic acid of interest (e.g. a nucleic acid to be expressed or a nucleic acid that mediates gene silencing). Examples of recombination sites include a restriction enzyme cleavage site, a multiple cloning site, an integrase recognition site, a transposase recognition site and a recombinase recognition site. In certain embodiments, the heterologous nucleotide sequence causes reduced expression (also referred to as “gene silencing” herein, whether partial or complete reduction of expression of the targeted gene is achieved) of one or more genes of a host plant cell.

[0008] In certain aspects, the invention provides TRV-RNA1 vectors comprising a novel TRV-RNA1 sequence of the invention. The vector may be designed, for example, for delivery to a plant by Agrobacterium-mediated transformation or microparticle bombardment. In certain embodiments, the TRV-RNA1 nucleic acid is flanked by (meaning positioned between, but not necessarily immediately adjacent to) a T DNA left border sequence and a T DNA right border sequence that mediate transfer into a chromosome of a host plant cell. The vector may be designed for expression of a heterologous gene, in which case it may be desirable to include an additional promoter to drive expression of the heterologous gene. The vector may also be designed for gene silencing. In certain embodiments, the TRV-RNA1 vector is designed for rapid cloning and testing of gene function by gene silencing. Such vectors may include one or more att sites characteristic of a modified phage lambda integrase cloning system, thereby allowing rapid cloning and analysis of a large number of nucleic acids of interest.

[0009] In certain aspects, the invention provides recombinant nucleic acids comprising a novel TRV-RNA2 nucleotide sequence of SEQ ID NO:5, and complementary sequences thereof. Certain embodiments of the invention also provide TRV-RNA2 nucleic acids that have one or more of the following nucleotides: base insertions at nucleotides 287, 380, 3490, 3662 and 3756; C at nucleotide 338, T at nucleotide 339, A at nucleotide 340, C at nucleotide 342, G at nucleotide)343, C at nucleotide 344, C at nucleotide 654, T at nucleotide 3509, G at nucleotide 3660. The nucleotide positions are given in reference to the sequence of SEQ ID NO:5, but in certain embodiments, the invention also provides variants of the novel TRV-RNA2 nucleotide sequence, including truncations, rearrangements, insertions, deletions, and mutations, so long as one or more of the identified nucleotides is present at a position that discernibly corresponds to the cited position in SEQ ID NO:5. In certain embodiments, a heterologous nucleic acid is also included in or attached to a TRV-RNA2 recombinant nucleic acid. Optionally, the heterologous nucleotide sequence includes one or more recombination sites that may be used for the insertion of a nucleic acid of interest (e.g. a nucleic acid to be expressed or a nucleic acid that mediates gene silencing). Examples of recombination sites include a restriction enzyme cleavage site, a multiple cloning site, an integrase recognition site, a transposase recognition site and a recombinase recognition site. In certain embodiments, the heterologous nucleotide sequence causes reduced expression (also referred to as “gene silencing” herein, whether partial or complete reduction of expression of the targeted gene is achieved) of one or more genes of a host plant cell. In certain embodiments, the TRV-RNA2 nucleotide sequence is operably linked to a plant active promoter. In certain embodiments, a transcription terminator is positioned within about 10, 100 or 1000 bases downstream of the 3′ end of the TRV-RNA2 nucleotide sequence. In certain embodiments, a self-cleaving ribozyme is positioned within about 1, 10 or 100 bases of the 3′ end of the TRV-RNA2 nucleotide sequence. In certain embodiments, the TRV-RNA2 nucleic acid is an RNA or a DNA, particularly a cDNA of SEQ ID NO:5.

[0010] In certain aspects, the invention provides novel TRV-RNA2 vectors comprising a TRV-RNA2 sequence of the invention. The vector may be designed, for example, for delivery to a plant by Agrobacterium-mediated transformation or microparticle bombardment. In certain embodiments, the TRV-RNA2 vector is flanked by a T DNA left border sequence and a T DNA right border sequence. The vector may be designed for expression of a heterologous gene, in which case it may be desirable to include an additional promoter to drive expression of the heterologous gene. The vector may also be designed for gene silencing. In certain embodiments, the TRV-RNA2 vector is designed for rapid cloning and testing of gene function by gene silencing. Such vectors may include one or more att sites characteristic of a modified phage lambda integrase cloning system, thereby allowing rapid cloning and analysis of a large number of nucleic acids of interest.

[0011] In certain aspects, the invention provides cells, plants and plant products comprising a TRV-RNA 1 nucleic acid or TRV-RNA2 nucleic acid of the invention. Plants, cells and plant products disclosed herein may also comprise both a TRV-RNA1 nucleic acid and a TRV-RNA2 nucleic acid. In certain embodiments, a cell is bacterial cell. In certain embodiments, a cell is a plant cell. Plants and plant cells may be stably or transiently transformed with one or more TRV-RNA1 or RNA2 replicons. In certain embodiments, the invention provides viruses or viral particles comprising a TRV-RNA1 or TRV-RNA2 nucleic acid of the invention.

[0012] In certain aspects, the invention provides methods for making transgenic plants. In certain embodiments, a method of the invention comprises introducing a novel TRV-RNA1 vector into one or more cells of host plant. In certain embodiments, a method of the invention comprises introducing a novel TRV-RNA2 vector into one or more cells of host plant. In certain embodiments, a method of the invention comprises introducing novel TRV-RNA1 and TRV-RNA2 vectors into one or more cells of a host plant. In certain embodiments, a method of the invention comprises introducing a novel TRV-RNA2 vector into one or more cells of a host plant, wherein the host plant is stably transformed with a TRV-RNA1 nucleic acid. Plant that are stably transformed with a TRV-RNA1 (novel or otherwise) are particularly suitable for use in high-throughput screening of TRV-RNA2 vectors containing many different gene silencing inserts. In certain embodiments, a method of the invention comprises introducing a novel TRV-RNA1 vector into one or more cells of a host plant, wherein the host plant is stably transformed with a TRV-RNA2. A TRV-RNA2 replicon is generally quiescent in the absence of a TRV-RNA1, and therefore plants stably transformed with a TRV-RNA2 may be maintained in a quiescent state until activation of the TRV-RNA2 is achieved by introducing the TRV-RNA1. A method may further comprise generating offspring of the initially transformed plant, e.g. by selfing or outcrossing. In certain embodiments, the invention provides methods for introducing a TRV vector into one or more cells of a tomato plant, the method comprising: spraying the tomato plant with a liquid mixture comprising Agrobacterium cells containing the TRV vector. In certain embodiments, the invention further provides the transgenic plants produced according to such methods, as well as plant products derived therefrom.

[0013] In certain aspects, the invention provides methods for decreasing the expression of a gene in one or more cells of a plant, the method comprising introducing a TRV-RNA2 (or optionally a TRV-RNA1) vector of the invention that includes a gene silencing insert into one or more cells of the plant, wherein expression of the gene silencing insert causes down-regulation of expression of the gene in the plant or portion of the plant. In certain embodiments, the invention provides methods for evaluating the function of a selected gene in a plant, the method comprising: introducing a TRV-RNA2 vector carrying a gene silencing insert into one or more cells of the plant and observing at least one phenotype of the plant. The phenotype may be compared to that of a plant in which the gene silencing insert is not expressed.

[0014] The embodiments and practices of the present application, other embodiments, and their features and characteristics, will be apparent from the description, figures and claims that follow.

BRIEF DESCRIPTION OF THE DRAWINGS

[0015] FIG. 1. TRV based VIGS system. (a) Genome organization of TRV. The TRV-RNA1 open reading frames (ORFs) correspond to 134 and 194 kDa replicase, movement protein (MP) and a 16-kDa cysteine-rich protein. The TRV-RNA2 ORFs corresponds to coat protein (CP), and the 29.4 and 32.8 kDa proteins. gRNA, genomic RNA; sgRNA, subgenomic RNA. Asterisks (*) indicate the readthrough of 134 kDa protein. (b) TRV based VIGS vectors. TRV cDNA clones were placed in between the duplicated CaMV 35S promoter (2 3 35S) and the nopaline synthase terminator (NOSt) in a T-DNA vector. LB and RB refer to left and right borders of T-DNA. Rz, self-cleaving ribozyme. MCS, multiple cloning sites. (c) Silencing of the PDS gene. Infection of recombinant TRV carrying the PDS sequence silences endogenous PDS in N. benthamiana plants and causes inhibition of carotenoid biosynthesis resulting in the photobleaching phenotype. On the left, whole plant and on the right, enlarged single leaf.

[0016] FIG. 2. Response to TMV and TMV-GFP in transgenic N containing MS4-5 and control N. benthamiana plants. (a,b) Hypersensitive response (HR) of transgenic MS4-5 line containing the N gene (a) and no HR in control N. benthamiana plants (b) 3 days after TMV infection. (c-f) Response of MS4-5 plants to TMV-GFP in the inoculated leaf (c) and upper uninoculated leaves (d). Response of control N. benthamiana plants to TMV-GFP in the inoculated leaf (e)and upper un-inoculated leaves (f). GFP pictures were taken under UV illumination. Inoculated leaf pictures were taken 1 day after infection and the pictures of upper leaves were taken 10 days later. (g) Northern blot analysis of TMV RNA accumulation in mock (M), infected (I) and upper un-inoculated (U) leaves of N. benthamiana (left) and MS4-5 (right) plants probed with the MP gene of TMV. Each lane contains 5 μg of total RNA. TMV RNA accumulation was measured 3 days after infection in the inoculated leaves and 10 days after infection in the upper uninoculated leaves. The picture of the ethidium bromide stained gel shown below the blot indicates equal loading of RNA. (h) PR1a message accumulation in infected (I) control N. benthamiana and mock (M) and infected (I) MS4-5 leaves 72 h after TMV infection blots were prepared using 10 μg of total RNA and probed with PR1a cDNA. The picture of the ethidium bromide stained gel shown below the blot indicates equal loading of RNA.

[0017] FIG. 3. Effect of TRV infection on resistant and susceptibility response to TMV-GFP. (a) Agrobacterium cultures containing pTRV1 and pTRV2 were mixed in 1:1 ratio and infiltrated on to 4-leaf stage plant using 1 ml needle-less syringe. Eight days after infiltration, these plants were infiltrated with Agrobacterium culture containing TMV-GFP construct. (b,c) TMV-GFP infection in TRV infected MS4-5 plants in the infiltrated leaf (b) and systemic upper leaves (c). (d,e) TMV-GFP infection in TRV infected N. benthamiana plants in the infiltrated leaf (d) and in the systemic upper leaves (e). (f) Northern blot analysis to measure TMV-GFP RNA accumulation in the upper leaves of TRV infected N. benthamiana (lanel) and MS4-5 (lane 2) plants. TMV-GFP RNA accumulation in the upper leaves of TRV-N infected MS4-5 plants (lane 3). TMV-GFP RNA accumulation was measured 10 days after infection. In each lane, 5 μg of total RNA was loaded. The blot was probed with the MP gene of TMV. The picture of the ethidium bromide stained gel shown below the blot indicates equal loading of RNA.

[0018] FIG. 4. TMV-GFP response to TRV-VIGS of N. (a) Plants were first infiltrated with pTRV1 and pTRV2-N. After 8 days, the upper leaf was infiltrated with TMV-GFP to monitor resistance and susceptible responses. (b) Suppression phenotype of N in MS4-5 plants in the infiltrated leaf. (c) Suppression phenotype in MS4-5 plants in the upper un-infiltrated leaves.

[0019] FIG. 5. VIGS effect on N, Rar1, EDS1 and NPR1 transcription in MS4-5 plants. Ethidium bromide-stained agarose gels showing RT-PCR products. The first strand cDNA was generated from total RNA isolated from silenced and non-silenced plants using oligo (dT) primer and reverse trascriptase. This first strand cDNA was used in a PCR reaction using gene specific primers. A, E, G, I: typical PCR products of N, Rar1, EDS1, and NPR1 derived from TRV infected non-silenced plants. B, F, H, and J: typical PCR products of N, Rar1, EDS1, and NPR1 derived from TRV-N, TRV-Rar1, TRV-EDS1 and TRV-NPR1 infected silenced plants. C and D (internal control): typical PCR products for EF1a derived from TRV alone infected (C) and TRV-VIGS vector infected (D) plants. Arrow indicates 600 bp size fragment in marker (M) lane. Lanes 1-7 corresponds to products from PCR cycle number 20, 25, 30, 35, 40, 45, and 50. Lane 8 represents the control in which the RT reaction mix, without reverse transcriptase, was used as a template.

[0020] FIG. 6. Amino acid sequence comparison of the predicted tobacco Rar1 (tRar1) protein with the barley Rar1 (bRar1) (Shirasu et al., 1999). CLUSTALW produced alignment file was formatted using BOXSHADE program (http://www.ch.embnet.org/software/BOX_form.html). Identical amino acids are shaded in black and conservative substitutions are shaded in gray. Two conserved CHORD domains (CHORD-I and II) and one conserved CCCH domain are shown. Asterisks (*) indicate invariant conserved cystein and histidine residues within the CHORD and CCCH domains.

[0021] FIG. 7. Amino acid comparison of the predicted tobacco EDS1 (tEDS1) protein with Arabidopsis EDS1 (AtEDS1) (Falk et al., 1999). CLUSTALW produced alignment file was formatted using BOXSHADE program (http://www.ch.embnet.org/software/BOX_form.html). Identical amino acids are shaded in black and conservative substitutions are shaded in gray. Asterisks (*) indicate the conserved putative lipase catalytic triad consisting of serine (S125), aspartate (D186) and histidine (H322). The eds1-1 mutation (E466K) position in Arabidopsis (Falk et al., 1999) is shown in bold italics and underlined.

[0022] FIG. 8. Alignment of tobacco NPR1 (tNPR1) and Arabidopsis NPR1/NIM1 (AtNPR1) (Cao et al., 1997) amino acid sequence. CLUSTALW produced alignment file was formatted using BOXSHADE program (http://www.ch.embnet.org/software/BOX_form.html). Identical amino acids are shaded in black and conservative substitutions are shaded in gray. Ankyrin repeats are underlined. Asterisks amino acids that affect the function of NPR1 in Arabidopsis. Amino acids required for nuclear localization of NPR1 in Arabidopsis are shown in italics and double underlined.

[0023] FIG. 9. TRV mediated VIGS of EDS1, Rar1 and NPR1/NIM1. TMV response in MS4-5 plants silenced for EDS1 (a), Rar1 (b), and NPR1/NIM1 (c); photographs were taken after 10 days of infection. Panel d represents the RNA gel blot analysis to measure TMV-GFP RNA accumulation in plants infected first with TRV or TRV derivatives and then followed by TMV-GFP infection. Lane 1: control N. benthamiana infected with TRV. Lane 2 - 6: MS4-5 plants infected with TRV (lane 2); TRV-N (lane 3); TRV-Rar1 (lane 4); TRV-EDS1 (lane 5); TRVNPR1/NIM1 (lane 6). Ten μg of total RNA was used in lane 6 and in all other lanes 5 μg was used. The MP gene of TMV was used as a probe. The picture of the ethidium bromide stained gel shown below the blot indicates equal loading of RNA.

[0024] FIG. 10. Recombinant TRV infects tomato. (a,b) TRV based VIGS vectors. TRV cDNA clones were placed in between duplicated CaMV 35S promoter (2 3 35S) and nopaline synthase terminator (NOSt) in a T-DNA vector. RdRp, RNA dependent RNA polymerase; 16K, 16 kDa cysteine rich protein; MP, movement protein; CP, coat protein; LB and RB, left and right borders of T-DNA; Rz, self-cleaving ribozyme; MCS, multiple cloning sites. (c) Accumulation of genomic TRV RNA1 (gRNA1) and RNA2 (gRNA2) and subgenomic RNA1a (sgRNA1a) and RNA1b (sgRNA1b) in the systemic leaves of recombinant TRV-infected tomato plants. Tomato plants were infiltrated with Agrobacterium alone (lane 1) or Agrobacterium containing pTRV1 and pTRV2 (lane 2). Ten days after infiltration, blots were prepared using 5 μg of total RNA and probed with 32P-labeled cDNA fragments corresponding to the 3′ ends of RNA1 and RNA2. The picture of the ethidium bromide stained gel shown below the blot demonstrates the equal loading of RNA.

[0025] FIG. 11. Method of inoculation of Agrobacterium-containing TRV clones onto tomato plants. Agrobacterium cultures containing pTRV1 and pTRV2 carrying tomato PDS (pTRV2-tPDS) were mixed in a 1:1 ratio and infiltrated on to 3-week-old tomato plants using 1 ml needleless syringe (a) or sprayed using an artist's airbrush (b). The silencing effect was visible 10 days after Agrobacterium infiltration or spray.

[0026] FIG. 12. Silencing of the tomato PDS gene. Infection of tomato plants with recombinant TRV alone (a) or TRV carrying the tomato PDS (TRV-tPDS) (b). Infection with TRV-tPDS silences endogenous PDS in Micro-tom tomato plants and causes inhibition of carotenoid biosynthesis resulting in photo-bleaching phenotype (b).

[0027] FIG. 13. RT-PCR analysis showing the effect of VIGS on tPDS, tCTR1, tCTR2, tRbcS and EST cLED3L14 transcription. Ethidium bromide-stained agarose gels showing RT-PCR products. The first strand cDNA was generated from total RNA isolated from silenced and non-silenced plants using an oligo (dT) primer and reverse transcriptase. This first strand cDNA was used in a PCR reaction using gene specific primers. (a) Typical PCR products for EF1a derived from TRV alone infected (left) and TRV-VIGS vector-infected (right) tomato plants. (b) Typical PCR products of Micro-tom tomato plants, either PDS silenced (right) or non-silenced, infected with TRV alone (left). (c,d) Typical PCR products for tCTR1 (c)and tCTR2 (d)derived from non-silenced TRV infected (left) and TRV-tCTR1 infected (right) VF36 tomato plants. (e, f, g) Typical PCR products for tCTR2, tRbcS and EST cLED3L14 silenced (right) or non-silenced TRV-alone infected (left) VF36 tomato plants, respectively. Lanes 1-6 correspond to products from PCR cycle number 15, 18, 21, 24, 27, and 30. Lane 7 represents the control, in which the RT reaction mix without reverse transcriptase was used as a template in the reaction. Lane M represents marker.

[0028] FIG. 14. Silencing of the tomato CTR1 and N. benthamiana CTR1 genes. (a) tCTR1 silenced (right) and non-silenced (left) phenotype in VF36 tomato plants. (b) NbCTR1 silenced (right) and non-silenced (left) phenotype in N. benthamiana plants. (c) Expression of CHIB gene in wild-type (lane 1), tCTR1-silenced (lane 2) and non-silenced (lane 3) VF36 tomato plants. Ten micrograms of total RNA isolated from these plants was blotted and probed with 32P-labeled CHIB cDNA fragment. The picture of the ethidium bromide-stained gel shown below the blot demonstrates equal loading of RNA.

[0029] FIG. 15. Map of pTRV2 GATEWAY vector and schematic representation of cloning PCR products. (a) Modified pTRV2 vector based on the GATEWAY cloning technology containing attP1 and attP2 recombination sites. (b) PCR products flanked by attB1 and attB2 sites can be directly recombined into attP1 and attP2 containing pTRV2 vector using BP CLONASE enzyme. The resulting attL1- and attL2-containing recombinant clone is shown.

[0030] FIG. 16. Schematic representation of cloning tomato ESTs into the pTRV2-attR2-attR1 vector. (a) Modified pTRV2 vector based on the GATEWAY cloning technology containing attR1 and attR2 recombination sites. (b) PCR products flanked by attB1 and attB2 sites can be directly recombined into attP1- and attP2-containing pDONR-mod using BP CLONASE enzyme. The resulting attL1- and attL2-containing pDONR-mod vector can be recombined with pTRV2 containing attR1 and attR2 using LR CLONASE enzyme. The resulting attB1- and attB2-containing recombinant clone is shown. (c) Tomato EST products generated by PCR using a common set primer with attB1 and attB2 sites shown in (b). M, marker; 1-10, different tomato EST PCR products. (d) Restriction digestion of plasmids prepared from two independent colonies recovered from E. coli transformed with each recombination reaction mixture containing pTRV2-attR2-attR1 and tomato EST PCR products. Plasmids were cut with XbaI-SacI to release the inserts. Some inserts do not match the PCR product size shown in (c) because of internal restriction sites.

[0031] FIG. 17. Silencing of the tomato RbcS using the pTRV2 GATEWAY vector. Infection of VF36 tomato plants with recombinant TRV GATEWAY alone (a) or TRV GATEWAY carrying the tomato RbcS (TRV-tRbcS) (b). Infection with TRV-tRbcS silences endogenous RbcS and causes development of pale yellow leaves (b).

[0032] FIG. 18. A sequence comparison of the amino acid sequence of the 194 kDa TRV-RNA1 replicase disclosed herein (denoted as “Y-POL”) with the sequence as presented in Ratcliff et al. 2001 (denoted as “D-POL”).

[0033] FIG. 19. A sequence comparison of the amino acid sequence of the movement protein of TRV-RNA1 disclosed herein (denoted “Y-MP”) with the sequence as presented in Ratcliff et al. 2001 (denoted as “D-MP”).

[0034] FIG. 20. A sequence comparison of the nucleic acid sequence of the TRV-RNA1 sequence disclosed herein (denoted “Y-RNA1”) with the sequence as presented in Ratcliff et al. 2001 (denoted as “D-RNA 1”).

[0035] FIG. 21. A sequence comparison of the amino acid sequence of the movement protein of TRV-RNA2 disclosed herein (denoted “Y-RNA2”) with the sequence as presented in Ratcliff et al. 2001 (denoted as “D-RNA2”).

DETAILED DESCRIPTION OF THE INVENTION

[0036] 1. Tobacco Rattle Virus Vectors

[0037] In certain aspects, the invention provides novel tobacco rattle virus (TRV) nucleic acids, and novel vectors based on TRV nucleic acids. TRV is a positive strand RNA virus with a bipartite genome, meaning that the genome is divided into two positive-sense, single-stranded RNAs, that may be separately encapsidated into viral particles. The two TRV genomic RNAs are referred to as TRV-RNA1 and TRV-RNA2. RNA1 encodes polypeptides that mediate replication and movement in the host plant, while RNA2 encodes coat protein. Certain aspects of the invention provide novel TRV-RNA1 or TRV-RNA2 sequences that provide efficient plant transformation capabilities, and TRV-based vectors (termed “TRV vectors”) containing such sequences.

[0038] A TRV-RNA1 vector, as the term is used herein, is a DNA or RNA vector that comprises a TRV-RNA1 replicon. A TRV-RNA1 replicon is a nucleic acid sequence that may be replicated by the action of a TRV replicase (an RNA polymerase) and comprises a sense or complementary sequence derived from a TRV RNA1. Generally, when introduced into a host plant cell, a TRV-RNA1 vector provides a replicase that mediates replication of the TRV RNA1 replicon, and a movement protein that mediates movement in a host plant. In certain embodiments, a TRV-RNA1 replicon comprises a replication start site, one or more TRV replicases, such as 134 kDa and 194 kDa replicases, a movement protein, and a cysteine-rich protein, such as a TRV 16 kDa cysteine-rich protein. In certain embodiments, one or more RNA1 sequences that are not needed for infection of a desired host plant are deleted in the construction of a TRV-RNA1 replicon.

[0039] In certain embodiments, the invention provides novel TRV-RNA1 sequences that may be used for plant transformation directly or may be placed in vector to make a TRV-RNA1 vector. The term “recombinant nucleic acid” includes any nucleic acid comprising at least two sequences which are not present together in nature. A recombinant nucleic acid is also any nucleic acid containing a man-made alteration, such as a nucleotide insertion, deletion or substitution relative to a naturally occurring sequence. A recombinant nucleic acid may be generated in vitro, for example by using the methods of molecular biology, or in vivo, for example by insertion of a nucleic acid at a novel chromosomal location by homologous or non-homologous recombination. An example of a novel TRV-RNA 1 sequence is shown in Example 1. This sequence differs from the RNA 1 of the TRV Ppk20 isolate at 9 bases (G1266 is changed to A, T2291 is changed to C, C3094 is changed to T, C3130 is changed to T, A3634 is changed to G, G4123 is changed to A, G4254 is changed to T, G4642 is changed to A, G5559 is changed to A). These differences at the nucleotide sequence level give rise to three amino acid changes (S355N and S697P in the replicase ORF; V781 in the 29K movement protein). Any of these nine base changes may be engineered separately or in various combinations into RNA1 sequences. Furthermore, RNA1 sequences may be truncated, rearranged, modified by insertion, deletion or point mutation, or otherwise altered, and yet it will generally be discernable what nucleotide is present at the positions corresponding to the original nucleotide positions 1266, 2291, 3094, 3130, 3634, 4123, 4254, 4642 and 5559. Such variations, and especially those variations that retain replicase and mobility functionalities are intended to be encompassed herein. A TRV-RNA1 replicon may be designed to include a heterologous sequence, such as a recombination site or a gene silencing insert, as described for RNA2 below. The TRV-RNA1 cDNA of SEQ ID NO:1 is stable at room temperature in E. coli and therefore disruption of the replicase ORF by inclusion of an intron is not required to allow manipulation and maintenance of such TRV-RNA1 vectors in E. coli host cells. However, it is possible to disrupt the TRV-RNA1 sequence with an intron, such as intron 3 of the Arabidopsis Col-0 nitrate reductase NIA1 gene (Wilkinson and Crawford, 1993; Ratcliffe et al., 2001), if desired. The intron sequence will generally be removed by the splicing machinery of a host plant cell. In certain embodiments, TRV-RNA1 vectors comprising novel TRV-RNA1 sequences provided herein show improved effectiveness for infection of host plants.

[0040] Replicase proteins from TRV and related viruses mediate the replication of RNA molecules. Accordingly, where the TRV vector is a DNA vector, it will generally be desirable to include a plant active promoter situated so as to stimulate transcription of (operably linked to) a TRV-RNA1 or TRV-RNA2 replicon. For example, a plant active promoter may be situated at the 5′-end of a TRV-RNA1 or TRV-RNA2 replicon. The term “plant active promoter” refers to a promoter that functions in a host plant that is infected with the TRV vector. In one embodiment, a plant active promoter is the Cauliflower Mosaic Virus 35S (“CaMV35S”) promoter that is expressed at a high level in many plant tissues. Other plant active promoters include the maize glutathione-S-transferase isoform II (GST-II-27) gene promoter (WO93/01294, ICI Ltd), the DEX promoter (Plant Journal (1997) 11: 605-612) and promoters that are transcribed by the TRV replicase, such as subgenomic promoters from related tobraviruses, e.g. pea early browning virus or pepper ringspot virus. In certain embodiments, a TRV-RNA1 or TRV-RNA2 is operably linked to two or more plant active promoters. In certain embodiments, it may be desirable to include an additional plant active promoter to drive additional expression of the coat protein or the heterologous nucleic acid. In certain embodiments, coat protein is expressed from a subgenomic RNA, transcription of which is stimulated by an endogenous TRV subgenomic promoter.

[0041] A TRV-RNA2 vector, as the term is used herein, is a DNA or RNA vector that comprises a TRV-RNA2 replicon. A TRV-RNA2 replicon is a nucleic acid sequence that is replicated by the action of a TRV replicase and that comprises a sense or complementary sequence derived from a TRV-RNA2. A TRV-RNA2 replicon will typically include a heterologous sequence. A heterologous sequence is a sequence that is not normally part of an RNA2 of a naturally occurring TRV. In certain embodiments, a heterologous sequence is a recombination site that is designed to facilitate the insertion of a sequence of interest. A recombination site may be, for example, a restriction enzyme (RE) cleavage site, a series of RE cleavage sites, or a recombinase recognition site. Recombination sites are further described below. In certain embodiments, a heterologous sequence is a sequence of interest, such as a gene for expression in a host plant cell or a sequence that causes gene silencing (a gene silencing insert) of one or more genes in a host plant cell. As part of the TRV-RNA2 replicon, the heterologous sequence is positioned relative to RNA2 sequences in such a manner that it is replicated by the replicase. Generally, when introduced into a host plant cell, a TRV-RNA2 vector provides expression of the heterologous sequence and may also provide expression of other RNA2 sequences, such as a viral coat protein. In certain embodiments, a TRV-RNA2 replicon comprises a replication start site, a viral coat protein, such as a TRV viral coat protein and a heterologous sequence. In certain embodiments, one or more RNA2 sequences that are not needed for infection of a desired host plant (e.g. 29.4 kDa and 32.8 kDa non-structural proteins) are deleted in the construction of a TRV-RNA2 replicon.

[0042] In certain embodiments, the invention provides novel TRV-RNA2 sequences that may be used in a TRV vector. An example of a novel TRV-RNA2 sequence is shown in Example 2. This sequence differs from TRV-RNA2 sequences of Ppk20 at numerous positions (base insertions at nucleotides 287, 380, 3490, 3662 and 3756; base changes T338C, A339T, C340A, G342C, C343G, A344C, T654C, C3509T, A3660G). Any of these changes may be engineered separately or in various combinations into RNA2 sequences. Furthermore, RNA2 sequences may be truncated, rearranged, modified by insertion, deletion or point mutation, or otherwise altered, and yet it will generally be discernable what nucleotide is present at the positions corresponding to the original nucleotide positions 287, 380, 3490, 3662, 3756, 338, 339, 340, 342, 343, 344, 654, 3509 and 3660 positions. Such variations, and especially those variations that do not disrupt replication and coat protein production are subjects of this invention. In certain embodiments, novel TRV-RNA2 nucleic acids and vectors comprising novel TRV-RNA2 sequences provided herein show improved effectiveness for infection of host plants.

[0043] The TRV coat protein may be any naturally occurring TRV coat protein or coat protein from a related virus or variant thereof (e.g. mutant, or other variant, or a substantially homologous derivative) provided that the coat protein retains the ability to encapsulate and permit movement of the TRV genome. Examples of TRV coat protein amino acid and nucleic acid sequences are shown in Example 2. As used herein, the term “substantially homologous” means that the sequence in question shares at least about 70%, or 80% identity, most preferably at least about 90%, 95%, 96%, 97%, 98% or 99% identity with the reference sequence. Identity may be at the nucleotide sequence and/or encoded amino acid sequence level. Homology may be over the full-length of the reference sequence or may be over a functional portion. Identity may be determined by the BLAST program, of Altschul et al. (1990) J. Mol. Biol. 215: 403-10, or BestFit, which is part of the Wisconsin Package, Version 8, September 1994, (Genetics Computer Group, 575 Science Drive, Madison, Wis., USA, Wisconsin 53711). Optionally, sequence comparisons are made using FASTA and FASTP (see Pearson & Lipman, 1988. Methods in Enzymology 183: 63-98). Generally, default parameters should be employed.

[0044] Within a TRV replicon, it is preferable that non-essential ORFs or other sequences are not present, provided that the cDNA can still be used to generate replicating, infectious transcripts. Preferably, where the replicon is based on TRV RNA2 of ppk20, two open reading frames (37K and 32.8K) are deleted to leave only the 5′ and 3′ untranslated regions and the viral gene encoding the coat-protein. The deleted ORFs may be replaced by a heterologous nucleotide sequence between the coat protein and the untranslated region (UTR).

[0045] In certain embodiments, a transcriptional terminator may be positioned at the 3′-end of an RNA transcript to limit readthrough of the transcript. For example, a transcriptional terminator may be positioned at the 3′-end of a TRV-RNA1 or TRV-RNA2 replicon. A commonly used plant transcriptional terminator is a nopaline synthase terminator (NOSt).

[0046] In certain embodiments, it may be desirable to generate a precise 3′ end of an RNA transcript. This can be achieved, for example, by including a ribozyme sequence at the 3′ end that will mediate autocleavage at the 3′ end of the RNA at a defined site. A ribozyme may be positioned close to what would be the natural end point of a TRV RNA1 or RNA2 sequence so that the replicon will contain few, if any, non-TRV nucleotides at the 3′ end. An example of a ribozyme is described in Turpen et al, 1993.

[0047] Recombination sites for replicons and vectors are well known in the art and include, for example, restriction sites, topoisomerase sites, recombinase sites, integrase sites and transposase sites. Restriction sites may be placed in adjacent or overlapping positions to form a “multiple cloning site” or MCS. As another example, the GATEWAY Cloning Technology (Invitrogen Corp., Carlsbad, Calif.) uses a modified version of a site-specific recombination system used by phage lambda to integrate its DNA into the E. coli chromosome. Phage lambda has specific recombination sites called attP, and E. coli has a specific recombination site called attB. Phage lambda integration is catalyzed by two enzymes: the phage lambda protein Int (Integrase) and the E. coli protein IHF (Integration Host Factor). Upon integration, the recombination between attB (25 nt) and attP (243 nt) sites generate attL (100 nt) and attR (168 nt) sites that flank the integrated phage lambda DNA. The process is reversible and excision is catalyzed by Int and IHF in combination with the phage lambda protein Xis. The attL and attR sites surrounding the inserted phage DNA recombine site-specifically during the excision event to reform the attP site in phage 1 and the attB site in the E. coli chromosome. In the GATEWAY system, a vector such as a pTRV2 vector, is engineered to have attR1 and attR2 sites flanking the position at which the desired insert (e.g. heterologous nucleic acid for gene silencing) is to be inserted. The insert is prepared so as to have attB 1 and attB2 sites, and the insert is then recombined with the attR1 and attR2 sites. Often a selectable marker, such as an antibiotic resistance cassette or a positive selection marker such as the ccdB gene is present between the attR insertion sites to allow selection of successful recombinants.

[0048] Accordingly, a heterologous nucleic acid in a TRV-RNA2 or TRV-RNA1 nucleic acid may include one or more att sites and may also include one or more selectable markers between the att sites.

[0049] Other examples of recombination sites for inclusion in replicons and vectors include the Cre-lox recombinase system such as is used in the Creatorm Gene Cloning & Expression System (BD Biosciences Clontech, Palo Alto, California) and the TOPO® cloning systems (Invitrogen Corp., Carlsbad, Calif.) that employ topoisomerase I-mediated cloning.

[0050] An example of a TRV-RNA1 replicon comprises a replication start site, a coding sequence for a 134 kDa replicase and 194 kDa replicase (often overlapping, where an optional stop codon determines which protein is produced), a coding sequence for a movement protein, a coding sequence for a 16 kDa cysteine-rich protein and a transcriptional terminator, such as a NOSt. The TRV-RNA1 sequences contain one or more of the following differences from the Ppk20 RNA1: G1266A, T2291C, C3094T, C3130T, A3634G G4123A, G4254T, G4642A, G5559A. Optionally, a self-cleaving ribozyme is positioned 5′ to the NOSt. In this example, the TRV-RNA1 replicon is operably linked to one, or optionally two plant active promoters, such as CaMV 35S promoters. The replicon may be a DNA molecule that is transcribed to produce RNA which is a substrate for the TRV replicase, or the replicon may be an RNA. If the replicon is delivered to a plant cell as part of a DNA vector, the plant active promoter will generally drive synthesis of an RNA strand that is then replicated and spread through the plant by the action of the TRV proteins. An example of a TRV-RNA1 replicon sequence is shown in SEQ ID NO:1.

[0051] In an exemplary embodiment, a TRV-RNA2 replicon comprises a replication start site, a coding sequence for a TRV coat protein, a heterologous sequence and a transcriptional terminator, such as a NOSt. The TRV-RNA2 sequences contain one or more of the following differences from the Ppk20 RNA2: base insertions at nucleotides 287, 380, 3490, 3662 and 3756; base changes T338C, A339T, C340A, G342C, C343G, A344C, T654C, C3509T, A3660G. In an “empty” vector, the heterologous sequence includes a recombination site (optionally including multiple recombination sites and selectable marker genes, as in the case of many GATEWAY-derived vectors). For a traditional cloning vector, the recombination site is an RE cleavage site, such as an EcoRI, BamHI, Smal or NotI sequence that allows cleavage with an RE and insertion of a nucleic acid sequence of interest. In a “filled” vector, a nucleic acid of interest has been inserted, and the heterologous sequence comprises the nucleic acid of interest. Depending on the recombination site, there may also be remnants of the recombination site flanking one or both sides of the nucleic acid of interest. The heterologous nucleic acid sequence may be positioned between the coat protein coding sequence and the 3′ UTR portions of the TRV-RNA2, or at essentially any location that does not interfere with other replicon functionalities. In this example, the TRV-RNA2 replicon is operably linked to one, or optionally two, plant active promoters, such as CaMV35S promoters. If the replicon is delivered to a plant cell as part of a DNA vector, the plant active promoter will generally drive synthesis of an RNA strand that is then replicated and spread through the plant by the action of the TRV proteins. An example of a TRV-RNA2 replicon sequence is shown in SEQ ID NO:5.

[0052] In certain embodiments, a TRV-RNA1 or TRV-RNA2 replicon is a component of a vector. Generally a vector is a nucleic acid construct that is designed to facilitate propagation and introduction into a host cell. In certain embodiments, the vector is a DNA vector designed for use with Agrobacterium-mediated transformation and contains T DNA sequences flanking the TRV-RNA1 or TRV-RNA2 replicon. The flanking T DNA sequences mediate insertion of the replicon into the genome of a host plant cell. Vectors for use with Agrobacterium are referred to as binary transformation vectors, and many are known in the art, such as pGreen (Ratcliff et al.) or pCASS2 (Shi et al., 1997). In certain embodiments, a vector is designed to be maintained in E. coli, and such a vector will generally include an E. coli origin of replication and a selectable marker, such as an antibiotic resistance gene. In certain embodiments, a vector may include a plant selectable marker. A vector may also be designed, for example, for introduction by particle bombardment, e.g. by using a gun equipped to deliver tungsten microparticles coated with vector or by exposing cells to silicon whiskers. See, e.g. Taylor and Fauquet, 2002, DNA and Cell Biology 21:963-77. In the case of such delivery systems, the vector may be RNA or DNA and need not contain any specific sequences to facilitate transfer to a plant chromosome.

[0053] For TRV-RNA2 vectors designed to provide expression of a protein of interest in a host plant cells, the heterologous sequence encoding the protein of interest may include or be operably linked to a plant active promoter, such as a CaMV 35S promoter or a viral promoter that is recognized by a TRV replicase, such as a promoter from a related virus (e.g. the Pea Early Browning Virus Coat Protein subgenomic promoter).

[0054] For TRV-RNA2 vectors designed as gene silencing vectors the heterologous sequence will be a “targeting sequence” which corresponds to a sequence in a target gene, either in the sense or anti-sense orientation, or a sequence which has sufficient homology to a target sequence for down-regulation of expression of the target gene to occur. Such a targeting sequence may be included in the vector anywhere in the TRV-RNA2 replicon irrespective of the location of any promoter (provided it does not interfere with the replicative functions of the TRV-RNA2 replicon). A targeting sequence may, for example, be derived from a plant nuclear gene or transgene, or a gene on an extrachromosomal element such as a plastid.

[0055] The complete sequence corresponding to the coding sequence (in reverse orientation for anti-sense) need not be used. For example fragments of sufficient length may be used. It is a routine matter for the person skilled in the art to screen fragments of various sizes and from various parts of the coding sequence to optimize the relationship between target and targeting sequence. It may be preferable that there is complete sequence identity between the targeting sequence in the vector and the target sequence in the plant, although total complementarity or similarity of sequence is not essential. One or more nucleotides may differ in the targeting sequence from the target gene. Thus, a targeting sequence employed in a construct in accordance with the present invention may be a wild-type sequence (e.g. gene) selected from those available, or a substantially homologous mutant, derivative, variant or allele, by way of insertion, addition, deletion or substitution of one or more nucleotides, of such a sequence. Such a sequence need not include an open reading frame or specify an RNA that would be translatable.

[0056] A further possibility is to target a conserved sequence of a gene, e.g. a sequence that is characteristic of one or more genes in one or more pathogens against which resistance is desired, such as a regulatory sequence.

[0057] Generally speaking, in the light of the present disclosure, those skilled in the art will be able to construct vectors according to the present invention. For further details see, for example, Molecular Cloning: a Laboratory Manual: 2nd edition, Sambrook et al, 1989, Cold Spring Harbor Laboratory Press. Many known techniques and protocols for manipulation of nucleic acid, for example in preparation of nucleic acid constructs, mutagenesis, sequencing, introduction of DNA into cells and gene expression, and analysis of proteins, are described in detail in Protocols in Molecular Biology, Second Edition, Ausubel et al. eds., John Wiley & Sons, 1992. Specific procedures and vectors previously used with wide success upon plants are described by Bevan, Nucl. Acids Res. (1984) 12, 8711-8721), and Guerineau and Mullineaux, (1993) Plant transformation and expression vectors. In: Plant Molecular Biology Labfax (Croy RRD ed) Oxford, BIOS Scientific Publishers, pp 121-148.

[0058] A TRV-RNA1 vector of the invention may be used to transform plants in combination with a TRV-RNA2 vector of the invention or with another TRV-RNA2 vector or construct that provides similar functionality. Likewise, a TRV-RNA2 vector of the invention may be used to transform plants in combination with a TRV-RNA2 vector of the invention or with another TRV-RNA2 vector or construct that provides similar functionality. Examples of other TRV-RNA1 and RNA2 vectors may be found, for example, in Ratcliff et al., 2001 and Hernandez et al., 1997.

[0059] In certain embodiments, the invention provides cells comprising a TRV-RNA1 or TRV-RNA2 vector of the invention. A cell may be a bacterial cell, such as an E. coli cell or an Agrobacterium tumefaciens cell. A cell comprising a TRV-RNA1 or TRV-RNA2 vector may also be a plant cell. In certain embodiments, the invention provides a plant cell comprising both a TRV-RNA1 vector and a TRV-RNA2 vector. In many instances, a vector is not itself retained in a cell, but the replicon portion is retained, and accordingly in certain embodiments, the invention provides a plant cell comprising a TRV-RNA1 replicon and a TRV-RNA2 replicon. Plant cells of the invention may be in culture, as in the case of cell suspensions or cells in the process of forming callus. Plant cells may also be situated in a living or dead plant or in a plant product.

[0060] In a further embodiment, the present invention provides a virus or viral particle including, preferably encapsulating, a TRV-RNA1 and/or TRV-RNA2 replicon of the invention.

[0061] 2. Transgenic Plants and Plant Products

[0062] In certain embodiments, the invention provides methods for making a transgenic plant, and the invention provides the resulting transgenic plants, descendants thereof, and plant products derived from such transgenic plants. The term “transgenic plant” is used to refer to a plant comprising, in one or more of its cells, an exogenous nucleic acid. Accordingly, the term “transgenic plant” is intended to include both transiently and stably transformed plants, as well as plants carrying integrated or non-integrated exogenous nucleic acids.

[0063] In general, a method for making a transgenic plant comprises introducing a TRV-RNA1 nucleic acid, replicon or vector, and/or a TRV-RNA2 nucleic acid, replicon or vector into one or more cells of a host plant. Because of the bipartite nature of TRV vectors, both a TRV-RNA1 and TRV-RNA2 will generally be introduced into one or more cells of a host plant, although a host plant may already contain one or the other of a TRV-RNA1 or TRV-RNA2. Introduction of TRV RNA1 and RNA2 nucleic acids may be done simultaneously or at different times. In certain embodiments, the TRV-RNA1 nucleic acid is a nucleic acid of the invention, and particularly a novel nucleic acid providing improved transformation efficiency. In certain embodiments, the TRV-RNA2 nucleic acid is a nucleic acid of the invention, and particularly a novel nucleic acid providing improved transformation efficiency. In certain embodiments, both the TRV-RNA1 and TRV-RNA2 nucleic acids are vectors of the invention. In many embodiments, the TRV-RNA1 and TRV-RNA2 replicons mediate the production of viral particles and movement of these particles to many different cell types of the host plant.

[0064] The method for introducing the vectors into the host plant may be selected depending on the type of vector. In the case of vectors for Agrobacterium-mediated delivery, the plant will be contacted with an Agrobacterium culture comprising a TRV-RNA1 vector and an Agrobacterium culture comprising a TRV-RNA2 vector. Agrobacterium may be introduced into a plant by a variety of ways, including infiltration, by contacting with a damaged plant portion (e.g. a leaf disc) or by spraying. As disclosed herein, spraying the mixed Agrobacterium cultures on the plant is particularly effective for obtaining high infection levels in tomato plants (plants of the genus Lycopersicon).

[0065] As noted above, particle bombardment systems may also be used to introduce TRV-RNA1 or TRV-RNA2 vectors into plants. In certain embodiments, infectious TRV-RNA1 replicons can be initiated by rub-inoculating the plant with purified RNA 1 (Matthews 1991).

[0066] TRV-RNA1 and TRV-RNA2 vectors of the invention may particularly be applied in plants that are naturally infected by TRV, including both monocots and dicots. These include, for example, plants of the genus Nicotiana (e.g. tabacum or benthamiana), plants of the genus Lycopersicon (e.g. esculentum) and plants of the genus Arabidopsis (e.g. thaliana). Others include (but are not limited to) Allium cepa; Amaranthus caudatus; Amaranthus retroflexus; Antirrhinum majus; snap-dragon; Arachis hypogaea; Avena sativa; Bellis perennis; Beta vulgaris; Brassica campestris; Brassica campestris ssp. napus; Brassica campestris ssp. pekinensis; Brassica juncea; Calendula officinalis; Capsella bursa-pastoris; Capsicum annuum; Catharanthus roseus; Cheiranthus cheiri; Chenopodium album; Chenopodium amaranticolor; Chenopodium foetidum; Chenopodium quinoa; Coriandrum sativum; Cucumis melo; Cucumis sativus; Glycine max; Gomphrena globosa; Gypsophila elegans; Helianthus annuus; Hyacinthus; Hyoscyamus niger; Lactuca sativa; Lathyrus odoratus; Linum usitatissimum; Lobelia erinus; Lupinus mutabilis; Lycopersicon pimpinellifolium; Melilotus albus; Momordica balsamina; Myosotis sylvatica; Narcissus pseudonarcissus; Nicandra physalodes; Nicotiana clevelandii; Nicotiana glutinosa; Nicotiana rustica; Nicotiana sylvestris; Nicotiana edwardsonii; Ocimum basilicum; Petunia hybrida; Phaseolus vulgaris; Phytolacca americana; Pisum sativum; Raphanus sativus; Ricinus communis; Salvia splendens; Senecio vulgaris; Solanum melongena; Solanum nigrum; Solanum tuberosum; Spinacia oleracea; Stellaria media; Trifolium pratense; Trifolium repens; Tropaeolum majus; Tulipa; Vicia faba; Vicia villosa; Viola arvensis. Other plants that may be infected include Zea maize, Hordeum vulgare, Triticum aestivum and Oryza sativa.

[0067] In those cases in which a stably transformed plant is generated, the plant may be bred so as to produce offspring that are homozygous or heterozygous for the inserted DNA. Many plants may be selfed, but plants may also be outcrossed to generate offspring with different genetic backgrounds. Therefore, in certain embodiments, the invention provides methods for making transgenic plants that involve first making a transformant that contains one or both of a TRV-RNA1 replicon and a TRV-RNA2 replicon, and then breeding or otherwise propagating the transformed plant to obtain transgenic offspring.

[0068] In certain embodiments, the invention also provides plant products obtained from transgenic plants of the invention. The term “plant product” is intended to include anything that may be obtained from a particular plant, including, for example, fruits, seeds, pollen, ovules, plant embryos, oils, juices, waxes, proteins, lipids, fatty acids, vitamins, plant tissues in whole or in part, (e.g. roots, leaves, stems, flowers, bark), cells, cell suspensions, tubers and stolons.

[0069] 3. Certain Methods Employing TRV Nucleic Acids

[0070] In certain aspects, the invention provides methods for causing decreased expression of one or more target genes by introducing into one or more cells of a plant, plant tissue or cell culture, a TRV-RNA2 replicon or vector comprising a heterologous nucleic acid for silencing a target gene or genes. Optionally, a TRV-RNA1 replicon or vector, such as a TRV-RNA1 replicon or vector disclosed herein, may also be introduced. Optionally, a TRV-RNA1 replicon or vector containing a gene silencing insert may be introduced.

[0071] In certain embodiments, the target gene or genes are pre-selected, and the heterologous nucleic acid is designed to specifically achieve partial or complete silencing of the target gene or genes. The target gene may have an unknown function or unknown loss of function phenotype, in which case a gene silencing method of the invention may be employed to analyze the phenotype by generating a partial or complete loss of function phenotype in a host plant, plant part, or in cells in culture or in a tissue sample. Generally analysis of a phenotype will include a comparison with a plant wherein the target gene is expressed normally. In certain embodiments, the target gene is obtained from a library, such as a cDNA library, or other complex pool of nucleic acids. For example, heterologous nucleic acids of suitable size for gene silencing may be obtained at random from a cDNA library and inserted into a TRV-RNA2 vector for introduction into a host plant. Each host plant that is transformed with a different TRV-RNA2 silencing construct is analyzed for one or more phenotypic characteristics, and constructs that cause a phenotype of interest may be sequenced to determine the identity of the silenced gene. As will be apparent to one of ordinary skill in the art, such methods are amenable to high throughput analysis.

[0072] In certain embodiments, the TRV-RNA2 (or TRV-RNA1) vector comprises a system of recombination sites that renders the vector particularly amenable to high throughput cloning of heterologous nucleic acids designed for suppression of gene expression. An example of such a vector is the pTRV2-attR1-attR2 vector described in Example 4, below.

[0073] In certain embodiments, the invention not only provides transient transformation assay methods to study gene function. In certain embodiments, a vector is a T7 based vector, and the vector is used in vitro to drive expression of in vitro TRV-RNA1 or RNA2 transcripts that may then be used to infect plants. Optionally one or more of the transcripts contains a gene silencing insert for use in altering expression of a host plant gene.

[0074] In certain embodiments, a plant with a stable TRV-RNA1 transformation is provided. The stably transformed plant can then be infiltrated with a TRV-RNA2 nucleic acid, containing, for example, a gene silencing insert to obtain efficient silencing. Such a system is amenable to rapid analysis of gene function. One can grow TRV-RNA2 constructs with many different inserts (e.g. inserts from a cDNA library) on plates and use a simple transient transformation method (such as a tooth pick to prick the leaves) to introduce the constructs into the TRV-RNA1 transgenic plant to induce silencing. The phenotype resulting from silencing may be observed in the local area at which the RNA2 construct was introduced.

[0075] In certain embodiments, once a candidate gene has been identified by, for example, a gene silencing approach, transgenic plants or cells may be generated using a different (non-TRV) approach, for example by introducing a dsDNA antisense construct wherein the antisense nucleic acid is expressed from a strong promoter such as a CaMV35S promoter, or, if desired, from a tissue specific or conditional promoter.

[0076] Target genes of particular interest include those that are involved in pathogen resistance or susceptibility, such as genes involved in resistance to viral infections.

[0077] In certain embodiments, a heterologous nucleic acid may be expressed in a plant or plant cells using a TRV-RNA2 vector designed for expression. Optionally, a TRV-RNA1 vector, such as a TRV-RNA1 vector disclosed herein, may also be introduced.

[0078] As described in Example 3, the invention relates in part to the discovery of certain nucleic acids involved in resistance to viral infection. Such nucleic acids include tobacco Rar1, EDS1 and NPR1/NIM1 genes. Accordingly, increased expression of a Rar1, EDS1 or NPR1/NIM1 gene may be used to confer increased resistance to a viral infection, particularly a tobamovirus infection, such as a tobacco mosaic virus. Conversely, if increased susceptibility or decreased plant responsiveness is desired, Rar1, EDS1 or NPR1/NIM1 gene expression may be decreased. Examples of Rar1 amino acid sequences from tobacco and barley are shown in FIG. 6. amples of EDS1 amino acid sequences from tobacco and Arabidopsis are shown in FIG. 7 Examples of NPR1/NIM1 amino acid sequences from tobacco and Arabidopsis are shown in FIG. 8.

EXAMPLES

[0079] The invention will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present application, and are not intended to limit the scope of the invention.

Example 1

Certain TRV-RNA1 Sequences

[0080] The following is an example of a TRV-RNA1 sequence containing nucleotides at particular positions (bolded in the sequence below) and providing improved plant transformation. The polymerase (134 kDa and 194 kDa together) open reading frame is underlined. The movement protein open reading frame is underlined in bold. The 16 kDa protein is double underlined.

(SEQ ID NO:1)
ATAAAACATTTCAATCCTTTGAACGCGGTAGAACGTGCTAATTGGATTTTGGTGAGAACG 60
CGGTAGAACGTACTTATCACCTACAGTTTTATTTTGTTTTTCTTTTTGGTTTAATCTATC 120
CAGCTTAGTACCGAGTGGGGGAAAGTGACTGGTGTGCCTAAAACCTTTTCTTTGATACTT 180
TGTAAAAATACATACAGATACAATGGCGAACGGTAACTTCAAGTTGTCTCAATTGCTCAA 240
TGTGGACGAGATGTCTGCTGAGCAGAGGAGTCATTTCTTTGACTTGATGCTGACTAAACC 300
TGATTGTGAGATCGGGCAAATGATGCAAAGAGTTGTTGTTGATAAAGTCGATGACATGAT 360
TAGAGAAAGAAAGACTAAAGATCCAGTGATTGTTCATGAAGTTCTTTCTCAGAAGGAACA 420
GAACAAGTTGATGGAAATTTATCCTGAATTCAATATCGTGTTTAAAGACGACAAAAACAT 480
GGTTCATGGGTTTGCGGCTGCTGAGCGAAAACTACAAGCTTTATTGCTTTTAGATAGAGT 540
TCCTGCTCTGCAAGAGGTGGATGACATCGGTGGTCAATGGTCGTTTTGGGTAACTAGAGG 600
TGAGAAAAGGATTCATTCCTGTTGTCCAAATCTAGATATTCGGGATGATCAGAGAGAAAT 660
TTCTCGACAGATATTTCTTACTGCTATTGGTGATCAAGCTAGAAGTGGTAAGAGACAGAT 720
GTCGGAGAATGAGCTGTGGATGTATGACCAATTTCGTGAAAATATTGCTGCGCCTAACGC 780
GGTTAGGTGCAATAATACATATCAGGGTTGTACATGTAGGGGTTTTTCTGATGGTAAGAA 840
GAAAGGCGCGCAGTATGCGATAGCTCTTCACAGCCTGTATGACTTCAAGTTGAAAGACTT 900
GATGGCTACTATGGTTGAGAAGAAAACTAAAGTGGTTCATGCTGCTATGCTTTTTGCTCC 960
TGAAAGTATGTTAGTGGACGAAGGTCCATTACCTTCTGTTGACGGTTACTACATGAAGAA 1020
GAACGGGAAGATCTATTTCGGTTTTGAGAAAGATCCTTCCTTTTCTTACATTCATGACTG 1080
GGAAGAGTACAAGAAGTATCTACTGGGGAAGCCAGTGAGTTACCAAGGGAATGTGTTCTA 1140
CTTCGAACCGTGGCAGGTGAGAGGAGACACAATGCTTTTTTCGATCTACAGGATAGCTGG 1200
AGTTCCGAGGAGGTCTCTATCATCGCAAGAGTACTACCGAAGAATATATATCAGTAGATG 1260
GGAAAACATGGTTGTTGTCCCAATTTTCGATCTGGTCGAATCAACGCGAGAGTTGGTCAA 1320
GAAAGACCTGTTTGTAGAGAAACAATTCATGGACAAGTGTTTGGATTACATAGCTAGGTT 1380
ATCTGACCAGCAGCTGACCATAAGCAATGTTAAATCATACTTGAGTTCAAATAATTGGGT 1440
CTTATTCATAAACGGGGCGGCCGTGAAGAACAAGCAAAGTGTAGATTCTCGAGATTTACA 1500
GTTGTTGGCTCAAACTTTGCTAGTGAAGGAACAAGTGGCGAGACCTGTCATGAGGGAGTT 1560
GCGTGAAGCAATTCTGACTGAGACGAAACCTATCACGTCATTGACTGATGTGCTGGGTTT 1620
AATATCAAGAAAACTGTGGAAGCAGTTTGCTAACAAGATCGCAGTCGGCGGATTCGTTGG 1680
CATGGTTGGTACTCTAATTGGATTCTATCCAAAGAAGGTACTAACCTGGGCGAAGGACAC 1740
ACCAAATGGTCCAGAACTATGTTACGAGAACTCGCACAAAACCAAGGTGATAGTATTTCT 1800
GAGTGTTGTGTATGCCATTGGAGGAATCACGCTTATGCGTCGAGACATCCGAGATGGACT 1860
GGTGAAAAAACTATGTGATATGTTTGATATCAAACGGGGGGCCCATGTCTTAGACGTTGA 1920
GAATCCGTGCCGCTATTATGAAATCAACGATTTCTTTAGCAGTCTGTATTCGGCATCTGA 1980
GTCCGGTGAGACCGTTTTACCAGATTTATCCGAGGTAAAAGCCAAGTCTGATAAGCTATT 2040
GCAGCAGAAGAAAGAAATCGCTGACGAGTTTCTAAGTGCAAAATTCTCTAACTATTCTGG 2100
CAGTTCGGTGAGAACTTCTCCACCATCGGTGGTCGGTTCATCTCGAAGCGGACTGGGTCT 2160
GTTGTTGGAAGACAGTAACGTGCTGACCCAAGCTAGAGTTGGAGTTTCAAGAAAGGTAGA 2220
CGATGAGGAGATCATGGAGCAGTTTCTGAGTGGTCTTATTGACACTGAAGCAGAAATTGA 2280
CGAGGTTGTTCCAGCCTTTTCAGCTGAATGTGAAAGAGGGGAAACAAGCGGTACAAAGGT 2340
GTTGTGTAAACCTTTAACGCCACCAGGATTTGAGAACGTGTTGCCAGCTGTCAAACCTTT 2400
GGTCAGCAAAGGAAAAACGGTCAAACGTGTCGATTACTTCCAAGTGATGGGAGGTGAGAG 2460
ATTACCAAAAAGGCCGGTTGTCAGTGGAGACGATTCTGTGGACGCTAGAAGAGAGTTTCT 2520
GTACTACTTAGATGCGGAGAGAGTCGCTCAAAATGATGAAATTATGTCTCTGTATCGTGA 2580
CTATTCGAGAGGAGTTATTCGAACTGGAGGTCAGAATTACCCGCACGGACTGGGAGTGTG 2640
GGATGTGGAGATGAAGAACTGGTGCATACGTCCAGTGGTCACTGAACATGCTTATGTGTT 2700
CCAACCAGACAAACGTATGGATGATTGGTCGGGATACTTAGAAGTGGCTGTTTGGGAACG 2760
AGGTATGTTGGTCAACGACTTCGCGGTCGAAAGGATGAGTGATTATGTCATAGTTTGCGA 2820
TCAGACGTATCTTTGCAATAACAGGTTGATCTTGGACAATTTAAGTGCCCTGGATCTAGG 2880
ACCAGTTAACTGTTCTTTTGAATTAGTTGACGGTGTACCTGGTTGTGGTAAGTCGACAAT 2940
GATTGTCAACTCAGCTAATCCTTGTGTCGATGTGGTTCTCTCTACTGGGAGAGCAGCAAC 3000
CGACGACTTGATCGAGAGATTCGCGAGCAAAGGTTTTCCATGCAAATTGAAAAGGAGAGT 3060
GAAGACGGTTGATTCTTTTTTGATGCATTGTGTTGATGGTTCTTTAACCGGAGACGTGTT 3120
GCATTTCGATGAAGCTCTCATGGCCCATGCTGGTATGGTGTACTTTTGCGCTCAGATAGC 3180
TGGTGCTAAACGATGTATCTGTCAAGGAGATCAGAATCAAATTTCTTTCAAGCCTAGGGT 3240
ATCTCAAGTTGATTTGAGGTTTTCTAGTCTGGTCGGAAAGTTTGACATTGTTACAGAAAA 3300
AAGAGAAACTTACAGAAGTCCAGCAGATGTGGCTGCCGTATTGAACAAGTACTATACTGG 3360
AGATGTCAGAACACATAACGCGACTGCTAATTCGATGACGGTGAGGAAGATTGTGTCTAA 3420
AGAACAGGTTTCTTTGAAGCCTGGTGCTCAGTACATAACTTTCCTTCAGTCTGAGAAGAA 3480
GGAGTTGGTAAATTTGTTGGCATTGAGGAAAGTGGCAGCTAAAGTGAGTACAGTACACGA 3540
GTCGCAAGGAGAGACATTCAAAGATGTAGTCCTAGTCAGGACGAAACCTACGGATGACTC 3600
AATCGCTAGAGGTCGGGAGTACTTAATCGTGGCGTTGTCGCGTCACACACAATCACTTGT 3660
GTATGAAACTGTGAAAGAGGACGATGTAAGCAAAGAGATCAGGGAAAGTGCCGCGCTTAC 3720
GAAGGCGGCTTTGGCAAGATTTTTTGTTACTGAGACCGTCTTATGACGGTTTCGGTCTAG 3780
GTTTGATGTCTTTAGACATCATGAAGGGCCTTGCGCCGTTCCAGATTCAGGTACGATTAC 3840
GGACTTGGAGATGTGGTACGACGCTTTGTTTCCGGGAAATTCGTTAAGAGACTCAAGCCT 3900
AGACGGGTATTTGGTGGCAACGACTGATTCCAATTTGCGATTAGACAATGTTACGATCAA 3960
AAGTGGAAACTGGAAAGACAAGTTTGCTGAAAAAGAAACGTTTCTGAAACCGGTTATTCG 4020
TACTGCTATGCCTGACAAAAGGAAGACTACTCAGTTGGAGAGTTTGTTAGCATTGCAGAA 4080
AAGGAACCAAGCGGCACCCGATCTACAAGAAAATGTGCACGCAACAGTTCTAATCGAAGA 4140
GACGATGAAGAAGTTGAAATCTGTTGTCTACGATGTGGGAAAAATTCGGGCTGATCCTAT 4200
TGTCAATAGAGCTCAAATGGAGAGATGGTGGAGAAATCAAAGCACAGCGGTACAGGCTAA 4260
GGTAGTAGCAGATGTGAGAGAGTTACATGAAATAGACTATTCGTCTTACATGTATATGAT 4320
CAAATCTGACGTGAAACCTAAGACTGATTTAACACCGCAATTTGAATACTCAGCTCTACA 4380
GACTGTTGTGTATCACGAGAAGTTGATCAACTCGTTGTTCGGTCCAATTTTCAAAGAAAT 4440
TAATGAACGCAAGTTGGATGCTATGCAACCACATTTTGTGTTCAACACGAGAATGACATC 4500
GAGTGATTTAAACGATCGAGTGAAGTTCTTAAATACGGAAGCGGCTTACGACTTTGTTGA 4560
GATAGACATGTCTAAATTCGACAAGTCGGCAAATCGCTTCCATTTACAACTGCAGCTGGA 4620
GATTTACAGGTTATTTGGGCTAGATGAGTGGGCGGCCTTCCTTTGGGAGGTGTCGCACAC 4680
TCAAACTACTGTGAGAGATATTCAAAATGGTATGATGGCGCATATTTGGTACCAACAAAA 4720
GAGTGGAGATGCTGATACTTATAATGCAAATTCAGATAGAACACTGTGTGCACTCTTGTC 4800
TGAATTACCATTGGAGAAAGCAGTCATGGTTACATATGGAGGAGATGACTCACTGATTGC 4860
GTTTCCTAGAGGAACGCAGTTTGTTGATCCGTGTCCAAAGTTGGCTACTAAGTGGAATTT 4920
CGAGTGCAAGATTTTTAAGTACGATGTCCCAATGTTTTGTGGGAAGTTCTTGCTTAAGAC 4980
GTCATCGTGTTACGAGTTCGTGCCAGATCCGGTAAAAGTTCTGACGAAGTTGGGGAAAAA 5040
GAGTATAAAGGATGTGCAACATTTAGCCGAGATCTACATCTCGCTGAATGATTCCAATAG 5100
AGCTCTTGGGAACTACATGGTGGTATCCAAACTGTCCGAGTCTGTTTCAGACCGGTATTT 5160
GTACAAAGGTGATTCTGTTCATGCGCTTTGTGCGCTATGGAAGCATATTAAGAGTTTTAC 5220
AGCTCTGTGTACATTATTCCGAGACGAAAACGATAAGGAATTGAACCCGGCTAAGGTTGA 5280
TTGGAAGAAGGCACAGAGAGCTGTGTCAAACTTTTACGACTGGTAATATGGAAGACAAGT 5340
CATTGGTCACCTTGAAGAAGAAGACTTTCGAAGTCTCAAAATTCTCAAATCTAGGGGCCA 5400
TTGAATTGTTTGTGGACGGTAGGAGGAAGAGACCGAAGTATTTTCACAGAAGAAGAGAAA 5460
CTGTCCTAAATCATGTTGGTGGGAAGAAGAGTGAACACAAGTTAGACGTTTTTGACCAAA 5520
GGGATTACAAAATGATTAAATCTTACGCGTTTCTAAAGATAGTAGGTGTACAACTAGTTG 5580
TAACATCACATCTACCTGCAGATACGCCTGGGTTCATTCAAATCGATCTGTTGGATTCGA 5640
GACTTACTGAGAAAAGAAAGAGAGGAAAGACTATTCAGAGATTCAAAGCTCGAGCTTGCG 5700
ATAACTGTTCAGTTGCGCAGTACAAGGTTGAATACAGTATTTCCACACAGGAGAACGTAC 5760
TTGATGTCTGGAAGGTGGGTTGTATTTCTGAGGGCGTTCCGGTCTGTGACGGTACATACC 5820
CTTTCAGTATCGAAGTGTCGCTAATATGGGTTGCTACTGATTCGACTAGGCGCCTCAATG 5880
TGGAAGAACTGAACAGTTCGGATTACATTGAAGGCGATTTTACCGATCAAGAGGTTTTCG 5940
GTGAGTTCATGTCTTTGAAACAAGTGGAGATGAAGACCATTCACGCGAAGTACGATGGTC 6000
CTTACAGACCAGCTACTACTAGACCTAAGTCATTATTGTCAAGTGAAGATGTTAAGAGAG 6060
CGTCTAATAAGAAAAACTCGTCTTAATGCATAAAGAAATTTATTGTCAATATGACGTGTG 6120
TACTCAAGGGTTGTGTGAATGAAGTCACTGTTCTTGGTCACGAGACGTGTAGTATCGGTC 6180
ATGCTAACAAATTGCGAAAGCAAGTTGCTGACATGGTTGGTGTCACACGTAGGTGTGCGG 6240
AAAATAATTGTGGATGGTTTGTCTGTGTTGTTATCAATGATTTTACTTTTGATGTGTATA 6300
ATTGTTGTGGCCGTAGTCACCTTGAAAAGTGTCGTAAACGTGTTGAAACAAGAAATCGAG 6360
AAATTTGGAAACAAATTCGACGAAATCAAGCTGAAAACATGTCTGCGACAGCTAAAAAGT 6420
CTCATAATTCGAAGACCTCTAAGAAGAAATTCAAAGAGGACAGAGAATTTGGGACACCAA 6480
AAAGATTTTTAAGAGATGATGTTCCTTTCGGGATTGATCGTTTGTTTGCTTTTTGA TTTT 6540
ATTTTATATTGTTATCTGTTTCTGTGTATAGACTGTTTGAGATTGGCGCTTGGCCGACTC 6600
ATTGTCTTACCATAGGGGAACGGACTTTGTTTGTGTTGTTATTTTATTTGTATTTTATTA 6660
AAATTCTCAATGATCTGAAAAGGCCTCGAGGCTAAGAGATTATTGGGGGGTGAGTAAGTA 6720
CTTTTAAAGTGATGATGGTTACAAAGGCAAAAGGGGTAAAACCCCTCGCCTACGTAAGCG 6780
TTATTACGCCC                      6791

[0081] The amino acid sequence for the 194 kDa polymerase (POL) sequence encoded by the TRV-RNA1 of SEQ ID NO:1 is shown below (SEQ ID NO:2). The “Z” indicates the position of codon that forms a stop position for the 134 kDa polymerase, and is read through in the 194 kDa protein. Amino acids corresponding to the above bolded nucleotides are bolded and underlined.

MANGNFKLSQLLNVDEMSAEQRSHFFDLMLTKPDCEIGQMMQRVVVDKVDDMIRERKTKD (SEQ ID NO:2)
PVIVHEVLSQKEQNKLMEIYPEFNIVFKDDKNMVHGFAAAERKLQALLLLDRVPALQEVD
DIGGQWSFWVTRGEKRIHSCCPNLDIRDDQREISRQIFLTAIGDQARSGKRQMSENELWM
YDQFRENIAAPNAVRCNNTYQGCTCRGFSDGKKKGAQYAIALHSLYDFKLKDLMATMVEK
KTKVVHAAMLFAPESMLVDEGPLPSVDGYYMKKNGKIYFGFEKDPSFSYIHDWEEYKKYL
LGKPVSYQGNVFYFEPWQVRGDTMLFSIYRIAGVPRRSLSSQEYYRRIYISRWEN_MVVVP
IFDLVESTRELVKKDLFVEKQFMDKCLDYIARLSDQQLTISNVKSYLSSNNWVLFINGAA
VKNKQSVDSRDLQLLAQTLLVKEQVARPVMRELREAILTETKPITSLTDVLGLISRKLWK
QFANKIAVGGFVGMVGTLIGFYPKKVLTWAKDTPNGPELCYENSHKTKVIVFLSVVYAIG
GITLMRRDIRDGLVKKLCDMFDIKRGAHVLDVENPCRYYEINDFFSSLYSASESGETVLP
DLSEVKAKSDKLLQQKKEIADEFLSAKFSNYSGSSVRTSPPSVVGSSRSGLGLLLEDSNV
LTQARVGVSRKVDDEEIMEQFLSGLIDTEAEIDEVVP_AFSAECERGETSGTKVLCKPLTP
PGFENVLPAVKPLVSKGKTVKRVDYFQVMGGERLPKRPVVSGDDSVDARREFLYYLDAER
VAQNDEIMSLYRDYSRGVIRTGGQNYPHGLGVWDVEMKNWCIRPVVTEHAYVFQPDKRMD
DWSGYLEVAVWERGMLVNDFAVERMSDYVIVCDQTYLCNNRLILDNLSALDLGPVNCSFE
LVDGVPGCGKSTMIVNSANPCVDVVLSTGRAATDDLIERFASKGFPCKLKRRVKTVDSFL
MHCVDGSLTGDVLHFDEALMAHAGMVYFCAQIAGAKRCICQGDQNQISFKPRVSQVDLRF
SSLVGKFDIVTEKRETYRSPADVAAVLNKYYTGDVRTHNATANSMTVRKIVSKEQVSLKP
GAQYITFLQSEKKELVNLLALRKVAAKVSTVHESQGETFKDVVLVRTKPTDDSIARGREY
LIVALSRHTQSLVYETVKEDDVSKEIRESAALTKAALARFFVTETVLZRFRSRFDVFRHH
EGPCAVPDSGTITDLEMWYDALFPGNSLRDSSLDGYLVATTDCNLRLDNVTIKSGNWKDK
FAEKETFLKPVIRTAMPDKRKTTQLESLLALQKRNQAAPDLQENVHATVLIEETMKKLKS
VVYDVGKIRADPIVNRAQMERWWRNQSTAVQAKVVADVRELHEIDYSSYMYMIKSDVKPK
TDLTPQFEYSALQTVVYHEKLINSLFGPIFKEINERKLDAMQPHFVFNTRMTSSDLNDRV
KFLNTEAAYDFVEIDMSKFDKSANRFHLQLQLEIYRLFGLDEWAAFLWEVSHTQTTVRDI
QNGMMAHIWYQQKSGDADTYNANSDRTLCALLSELPLEKAVMVTYGGDDSLIAFPRGTQF
VDPCPKLATKWNFECKIFKYDVPMFCGKFLLKTSSCYEFVPDPVKVLTKLGKKSIKDVQH
LAEIYISLNDSNRALGNYMVVSKLSESVSDRYLYKGDSVHALCALWKHIKSFTALCTLFR
DENDKELNPAKVDWKKAQRAVSNFYDW

[0082] The amino acid sequence for the movement protein (MP) encoded by the TRV-RNA1 of SEQ ID NO:1 is shown below (SEQ ID NO:3). Amino acids corresponding to the above bolded nucleotides are bolded and underlined.

MEDKSLVTLKKKTFEVSKFSNLGAIELFVDGRRKRPKYFHRRRETVLNHVGGKKSEHKLD (SEQ ID NO:3)
VFDQRDYKMIKSYAFLKIVGVQLVVTSHLPADTPGFIQIDLLDSRLTEKRKRGKTIQRFK
ARACDNCSVAQYKVEYSISTQENVLDVWKVGCISEGVPVCDGTYPFSIEVSLIWVATDST
RRLNVEELNSSDYIEGDFTDQEVFGEFMSLKQVEMKTIEAKYDGPYRPATTRPKSLLSSE
DVKRASNKKNSS

[0083] The amino acid sequence for the 16 kDa protein encoded by the TRV-RNA1 of SEQ ID NO: 1 is shown below (SEQ ID NO:4).

(SEQ ID NO:4)
MTCVLKGCVNEVTVLGHETCSIGHANKLRKQVADMVGVTRRCAENNCGWFVCVVINDFTFDVYNCCGRSHLE
KCRKRVETRNREIWKQIRRNQAENMSATAKKSHNSKTSKKKFKEDREFGTPKRFLRDDVPFGIDRLFAF

Example 2

Certain TRV-RNA2 Sequences

[0084] The following is a TRV-RNA2 sequence containing nucleotides at particular positions (bolded in the sequence below) and providing improved plant transformation. The coat protein open reading frame is underlined.

ATAAAACATTGCACCTATGGTGTTGCCCTGGCTGGGGTATGTCAGTGATCGCAGTAGAAT	60	(SEQ ID NO:5)
GTACTAATTGACAAGTTGGAGAATACGGTAGAACGTCCTTATCCAACACAGCCTTTATCC	120
CTCTCCCTGACGAGGTTTTTGTCAGTGTAATATTTCTTTTTGAACTATCCAGCTTAGTAC	180
CGTACGGGAAAGTGACTGGTGTGCTTATCTTTGAAATGTTACTTTGGGTTTCGGTTCTTT	240
AGGTTAGTAAGAAAGCACTTGTCTTCTCATACAAAGGAAAACCTGAGACGTATCGCTTAC	300
GAAAGTAGCAATGAAAGAAAGGTGGTGGTTTTAATCGCTACCGCAAAAACGATGGGGTCG	360
TTTTAATTAACTTCTCCTACGCAAGCGTCTAAACGGACGTTGGGGTTTTGCTAGTTTCTT	420
TAGAGAAAACTAGCTAAGTCTTTAATGTTATCATTAGAGATGGCATAAATATAATACTTG	480
TGTCTGCTGATAAGATCATTTTAATTTGGACGATTAGACTTGTTGAACTACAGGTTACTG	540
AATCACTTGCGCTAATCAACATGGGAGATATGTACGATGAATCATTTGACAAGTCGGGCG	600
GTCCTGCTGACTTGATGGACGATTCTTGGGTGGAATCAGTTTCGTGGAAAGATCTGTTGA	660
AGAAGTTACACAGCATAAAATTTGCACTACAGTCTGGTAGAGATGAGATCACTGGGTTAC	720
TAGCGGCACTGAATAGACAGTGTCCTTATTCACCATATGAGCAGTTTCCAGATAAGAAGG	780
TGTATTTCCTTTTAGACTCACGGGCTAACAGTGCTCTTGGTGTGATTCAGAACGCTTCAG	840
CGTTCAAGAGACGAGCTGATGAGAAGAATGCAGTGGCGGGTGTTACAAATATTCCTGCGA	900
ATCCAAACACAACGGTTACGACGAACCAAGGGAGTACTACTACTACCAAGGCGAACACTG	960
GCTCGACTTTGGAAGAAGACTTGTACACTTATTACAAATTCGATGATGCCTCTACAGCTT	1020
TCCACAAATCTCTAACTTCGTTAGAGAACATGGAGTTGAAGAGTTATTACCGAAGGAACT	1080
TTGAGAAAGTATTCGGGATTAAGTTTGGTGGAGCAGCTGCTAGTTCATCTGCACCGCCTC	1140
CAGCGAGTGGAGGTCCGATACGTCCTAATCCCTAGGGATTTAAGGACGTGAACTCTGTTG	1200
AGATCTCTGTGAAATTCAGAGGGTGGGTGATACCATATTCACTGATGCCATTAGCGACAT	1260
CTAAATAGGGCTAATTGTGACTAATTTGAGGGAATTTCCTTTACCATTGACGTCAGTGTC	1320
GTTGGTAGCATTTGAGTTTCGCAATGCACGAATTACTTAGGAAGTGGCTTGACGACACTA	1380
ATGTGTTATTGTTAGATAATGGTTTGGTGGTCAAGGTACGTAGTAGAGTCCCACATATTC	1440
GCACGTATGAAGTAATTGGAAAGTTGTCAGTTTTTGATAATTCACTGGGAGATGATACGC	1500
TGTTTGAGGGAAAAGTAGAGAACGTATTTGTTTTTATGTTCAGGCGGTTCTTGTGTGTCA	1560
ACAAAGATGGACATTGTTACTCAAGGAAGCACGATGAGCTTTATTATTACGGACGAGTGG	1620
ACTTAGATTCTGTGAGTAAATGTCCCGAAGACATTAAACTACGGTTCTTTAAGTAGATCC	1680
GTGTCTGAAGTTTTAGGTTCAATTTAAACCTACGAGATTGACATTCTCGACTGATCTTGA	1740
TTGATCGGTAAGTCTTTTGTAATTTAATTTTCTTTTTGATTTTATTTTAAATTGTTATCT	1800
GTTTCTGTGTATAGACTGTTTGAGATCGGCGTTTGGCCGACTCATTGTCTTACCATAGGG	1860
GAACGGACTTTGTTTGTGTTGTTATTTTATTTGTATTTTATTAAAATTCTCAACGATCTG	1920
AAAAAGCCTCGCGGCTAAGAGATTGTTGGGGGGTGAGTAAGTACTTTTAAAGTGATGATG	1980
GTTACAAAGGCAAAAGGGGTAAAACCCCTCGCCTACGTAAGCGTTATTACGCCC	2034

[0085] The amino acid sequence for the coat protein encoded by the TRV-RNA2 of SEQ ID NO:2 is shown below (SEQ ID NO:6).

(SEQ ID NO:6)
MGDMYDESFDKSGGPADLMDDSWVESVSWKDLLKKLHSIKFALQSGRDEITGLLAALNRQCPYSPYEQFPDK
KVYFLLDSRANSALGVIQNASAFKRRADEKNAVAGVTNIPANPNTTVTTNQGSTTTTKANTGSTLEEDLYTY
YKFDDASTAFHKSLTSLENMELKSYYRRNFEKVFGIKFGGAAASSSAPPPASGGPIRPNP

Example 3

Gene Silencing Using a Novel Tobacco Rattle Virus System

[0086] This example describes the construction of a tobacco rattle virus (TRV) vector and its used for gene silencing in plants. Virus induce gene silencing (VIGS) is initiated when a recombinant virus carrying a sequence from a host gene infects the plant. The endogenous gene transcripts homologous to the insert in the VIGS vector are degraded by a post-transcriptional gene silencing mechanism (PTGS) (Baulcombe, 1999).

[0087] Development of a TRV Based VIGS System

[0088] TRV is a bipartite positive sense RNA virus (MacFarlane, 1999). RNA1 encodes 134 and 194 kDa replicase proteins from the genomic RNA, a 29-kDa movement protein and 16-kDa cysteine-rich protein from subgenomic RNAs (FIG. 1a). RNA2 encodes the coat protein from the genomic RNA and two non-structural proteins from the subgenomic RNAs (FIG 1a). TRV RNA1 can replicate and move systemically without RNA2. To develop TRV as a VIGS vector, applicants constructed T-DNA vectors containing cDNA clones of RNA1 and RNA2 of Ppk20 strain (FIG. 1b). The cDNAs corresponding to RNA1 and RNA2 were inserted immediately following the duplicated CaMV 35S promoter transcriptional start site so that no non-TRV nucleotides are present at the 5′ end after transcription. In addition, a self-cleaving ribozyme sequence (Turpen et al., 1993) was included at the 3′ end so that only three non-viral nucleotides are predicted to be present after transcription. In the TRV RNA2 cDNA construct, the non-structural genes were replaced with a multiple cloning site (MCS) useful for cloning the target gene sequences for VIGS (FIG. 1b). The biological activity of the TRV clones was confirmed by mixing Agrobacterium cultures containing RNA1 and RNA2 T-DNA constructs and infiltrating the mixture into the leaves of N. benthamiana. An initial test with two independent RNA1 and RNA2 cDNA clones proved to be less infectious than the wild type virus (data not shown); possibly due to sequence changes introduced during RT-PCR. Therefore, sequences that were consistent among each of three independent RNA1 and RNA2 clones, though different from the GenBank sequence, were considered as correct sequences. Based on this information, applicants reconstructed the RNA1 and RNA2 cDNA clones. The infectivity of this new TRV clone was comparable to that of wild type Ppk20 virus (data not shown). The T-DNA constructs corresponding to RNA1 and RNA2 are referred to herein as pTRV1 and pTRV2, respectively.

[0089] The TRV based VIGS vectors described in this example include a variety of improvements and desirable properties. For example, the vectors include a double 35S promoter; the RNA1 cDNA is stable at room temperature in the pBIN19 vector in E. coli and therefore disruption of the polymerase ORF by inclusion of an intron is not required; transcription initiation is predicted in vivo at the first nucleotide of TRV cDNA; and inclusion of a ribozyme at the 3′ end ensures generation of a precise 3′ end of the RNA.

[0090] Applicants assessed the gene silencing efficiency of the TRV-VIGS clones by suppressing the expression of the phytoene desaturase (PDS) gene in N. benthamiana. A mixture of Agrobacterium culture containing the pTRV2-PDS and pTRV1 was infiltrated on to the 4-leaf stage N. benthamiana plants (for details see Experimental procedures). The silencing effect was monitored in the upper leaves of the plant 5-7 days post Agro-inoculation. Silencing of PDS leads to the inhibition of carotenoid synthesis, causing the plants to exhibit a photo-bleached phenotype (FIG. 1c; Kumagai et al., 1995). The PDS suppression phenotype was visible 5 days post Agro infiltration in the upper leaves of the plant and persisted indefinitely. This result indicated that the TRV-VIGS system could be successfully used to induce silencing of other desirable endogenous plant genes. Moreover, PDS suppression effect was visible uniformly throughout the entire leaf (FIG. 1c). Uniform suppression of target gene is helpful for the study of disease resistance using VIGS because often these experiments involve secondary infection with another pathogen.

[0091] Generation of N-containing Transgenic N. benthamiana to Study TMV Resistance

[0092] The N gene response to TMV infection is routinely studied using N. tabacum cv. Xanthi nc or N. tabacum cv. Samsun NN or transgenic N. tabacum cv. SR1 containing the N transgene (Holmes, 1934; Whitham et al., 1994). In tobacco, recombinant TMV-GFP virus fails to move systemically. However, TMV-GFP virus moves systemically in N. benthamiana. Therefore, applicants generated transgenic N. benthamiana lines containing the N gene construct pSPDK694. This construct contains the N promoter+cDNA-NS+Intron III containing the alternative exon+N genomic-3′end. This is the minimum N sequence required to confer resistance to TMV (Dinesh-Kumar and Baker, 2000). Applicants transformed N. benthamiana plants with pSPDK694 and generated 10 independent primary transgenic lines. Six independent transgenic lines showed HR upon infection with TMV-U1 strain with no symptoms elsewhere in the plant. Applicants isolated homozygous line, MS4-5, containing a single copy of T-DNA and was used for the experiments described in this paper. The transgenic MS4-5 line exhibits HR lesions on the inoculated leaf 48-72 h after infection with TMV (FIG. 2a). The HR lesion phenotype observed in MS4-5 plants is similar to that observed in the wild type N-containing tobacco plants (Whitham et al., 1994). In contrast, the non-transformed N. benthamiana plants fail to induce HR in response to TMV (FIG. 2b). In the VIGS assay described below, applicants use TMV-GFP virus to monitor TMV movement under UV illumination. Therefore, applicants tested the effect of TMV-GFP virus infection on MS4-5 and N. benthamiana plants. In MS4-5 plants, GFP fluorescence was observed 24 h after infection on inoculated leaves (FIG. 2c); but the upper uninoculated leaves of the infected plant did not show systemic spread of TMV-GFP even 10 days after infection (FIG. 2d). In N. benthamiana control plants, GFP fluorescence was visible in the inoculated leaf after 24 h (FIG. 2e). The infection foci as indicated by the area of GFP fluorescence spot were much bigger as compared to that of MS4-5 plants (compare FIG. 2e versus FIG. 2c). After 10 days, TMV-GFP was observed in the upper leaves of the control plants (FIG. 2f). These results suggest that transgenic N containing MS4-5 plants exhibit HR upon TMV infection and that the virus is restricted to the infection site. To confirm the phenotypic data, RNA gel blots were prepared using RNA extracted from mock and TMV infected plants and hybridized with a probe derived from the movement protein (MP) gene of TMV. In mock inoculated N. benthamiana (FIG. 2g; lane 1) and MS4-5 plants (FIG. 2g; lane 4), no hybridization signal was observed. As expected, in susceptible wild-type N. benthamiana plants, TMV-RNA accumulated to a high level in inoculated leaves (FIG. 2g; lane 2) as well as in the systemic upper leaves (FIG. 2g; lane 3). In MS4-5 transgenic plants, a low level of TMV-RNA was detected in the inoculated leaf (FIG. 2g; lane 5) and no viral RNA was detected in the upper un-inoculated leaves (FIG. 2g; lane 6). These results confirm that the MS4-5 line restricts TMV to the inoculated leaf.

[0093] In NN tobacco plants, HR and SAR to TMV are associated with the induction of PR proteins (Hooft van Huijsduijnen et al., 1986; Ward et al., 1991).Applicants investigated the induction of PR1a message in TMV inoculated leaves of wild type N. benthamiana and transgenic MS4-5 lines using RNA gel blots.NoPR1a message was detected in either mock-infected MS4-5 plants (FIG. 2h; lane 2) or in TMV infected N. benthamiana plants (FIG. 2h; lane 1). On the other hand, PR1a expression was induced in TMV infected NcontainingMS4-5 transgenic plants (FIG. 2h;lane3). These results suggest that transgenic MS4-5 lines induce PR1a message just as wild-type N-containing tobacco plants do.

[0094] Taken together, the phenotypic and molecular analyses of the MS4-5 line demonstrate that the tobacco N gene can confer resistance to TMV in heterologous N. benthamiana plants and can be used to study N-mediated signaling in TMV resistance.

[0095] Suppression of N Function Using TRV Based VIGS

[0096] Applicants tested the ability of the TRV-VIGS system to induce silencing of the N gene to determine whether the system could be used for TMV resistance pathway gene function studies. Applicants hypothesized that the suppression of N using TRV-VIGS should result in loss-of-resistance to TMV. First, applicants needed to observe whether TRV infection alone has an effect on N-mediated resistance to TMV. A mixture of Agrobacterium containing pTRV 1 and pTRV2 was infiltrated into MS4-5 and wild type N. benthamiana plants (FIG. 3a). Eight days post infiltration, the upper leaves of these plants were infiltrated with Agrobacterium containing the TMV-GFP construct to monitor resistant and susceptible phenotypes. In MS4-5 plants, an HR phenotype was observed within 72 h and the GFP fluorescence signal was restricted to the infiltrated area (FIG. 3b), and after 6 days, the signal was reduced significantly (data not shown). Systemic leaves of these plants showed no sign of TMV-GFP fluorescence even after 10 days (FIG. 3c). Wild type N. benthamiana plants showed no HR at the site of infiltration (FIG. 3d) and TMV-GFP was able to spread throughout the plant in 10 days (FIG. 3e) with no reduction in the TMV-GFP signal in the infiltrated leaf. Applicants confirmed that the TMV-GFP is restricted to the Agro-inoculation site in MS4-5 plants by Northern blot analysis (FIG. 3f) using the MP gene of TMV as a probe. In TRV infected wild-type N. benthamiana plants, TMV-GFP RNA was present in the upper un-infiltrated leaves (FIG. 3f; lane 1). There was no TMV-GFP RNA in the upper un-infiltrated leaves of TRV infected MS4-5 plants (FIG. 3f, lane 2). These results, together with the above-described phenotypic data, indicate that TRV infection alone has no effect on TMV resistance or susceptibility and could be used to study genes involved in N-mediated resistance to TMV using the TRV-based VIGS system.

[0097] To suppress N function using TRV-VIGS, applicants cloned a 1129-bp fragment of the N cDNA corresponding to nt 86-1215 (Whitham et al., 1994) into pTRV2. A mixture of Agrobacterium cultures containing pTRV1 and pTRV2-N was infiltrated onto MS4-5 plants (FIG. 4a). Eight days post-infiltration, the upper leaves were infiltrated with Agrobacterium containing a TMV-GFP plasmid. These plants were then observed for at least 20 days for movement of TMV-GFP from the infiltrated site. The TRV-N infected MS4-5 plants failed to show characteristic HR phenotype in the infiltrated leaf (FIG. 4b) and the TMVGFP was able to spread to the upper leaves (FIG. 4c). Movement of TMV-GFP into the upper parts of the MS4-5 plants was detectable 6 days after TMV-GFP infiltration. Presence of TMV-GFP RNA in systemic leaves was confined by RNA blots hybridized to a probe derived from the MP gene of TMV (FIG. 3f, lane 3). These results indicate that the N transgene function is suppressed in MS4-5 plants by TRV-VIGS.

[0098] Applicants performed semi-quantitative RT-PCR, using total RNA extracted from MS4-5 plants infected with TRV-N or TRV alone, to confirm the VIGS of the N gene at the molecular level. In TRV-N infected plants, the N message was reduced by more than 88% compared to the TRV infected control (FIG. 5a versus FIG. 5b). In both tissue RNA samples, EF1a RNA levels were similar (FIG. 5c versus FIG. 5d) and served as an internal control for RNA quality and RT-PCR amplification. These results show that the TRV based VIGS system efficiently suppresses targeted host genes and can be used as a rapid means for assaying the role of candidate genes in N-mediated resistance to TMV. Therefore, applicants set out to suppress tobacco Rar1, EDS1 and NPR1/NIM1 homologues in MS4-5 plants to investigate their role in N-mediated signaling.

[0099] Cloning of Tobacco Homologues of Rar1, EDS1, and NPR1/NIM1

[0100] In order to study the role of Rar1, EDS1 and NPR1/NIM1 in N-mediated resistance to TMV, applicants cloned tobacco homologues of these genes. Applicants used the amino acid sequence of barley Rar1 to search the Institute of Genomic Research (TIGR) tomato database using TBLASTN. Tomato EST clone TC96555 showed significant homology to barley Rar1. Based on this information, applicants designed primers described in the Experimental procedures section and performed RT-PCR to clone full-length Rar1 from N. tabacum. The nucleotide sequence of tobacco Rar1 has been deposited in GenBank (AF480487). Amino acid sequence analysis of tobacco Rar1 using a BLAST search shows 63% identity and 73% similarity to barley Rar1 (FIG. 6). Similar to barley Rar1, tobacco Rar1 contains two CHORD domains and one plant-specific CCCH domain (Shirasu et al., 1999). In addition, the tobacco Rar1 contains conserved strings of invariant cysteine and histidine residues within the CHORD domains (FIG. 6). The amino acid sequences outside the CHORD and CCCH domains are significantly different between tobacco Rar1 and barley Rar1 (FIG. 6).

[0101] To clone the tobacco EDS1 homologue, EST clones TC91460 and TC95587, which showed significant homology to Arabidopsis EDS1, were identified. Applicants cloned full length tobacco EDS1 using RT-PCR as described in the Experimental procedures section. The tobacco EDS1 sequence is deposited in GenBank (AF480489). Amino acid sequence analysis of tobacco EDS1 shows 43% identity and 58% similarity to Arabidopsis EDS1 (FIG. 7). Like Arabidopsis EDS1, tobacco EDS1 contains three lipase catalytic residues, S125, D186, H322 (Falk et al., 1999). In addition, the consensus sequence around the predicted catalytic S125 is highly conserved between tobacco EDS1 and Arabidopsis EDS1. Sequence of the eds1-1 allele in Arabidopsis indicated a change in the E466K (Falk et al., 1999), an amino acid that is conserved in tobacco EDS1.

[0102] A TIGR tomato database search using Arabidopsis NPR1/NIM1 identified EST clones TC95582, TC91366 and AW399343, which showed significant homology to the Arabidopsis NPR1. A full-length tobacco homologue of NPR1 was cloned using RT-PCR as described in the Experimental procedures section. The nucleotide sequence of full-length tobacco NPR1 has been deposited in GenBank (AF480488). Amino acid sequence analysis of tobacco NPR1 shows 52% identity and 72% similarity to Arabidopsis NPR1 (FIG. 8). Amino acid changes that lead to loss-of-function of NPR1 in Arabidopsis (Cao et al., 1997) are conserved in the tobacco NPR1 sequence (FIG. 8). In addition 4 out of 5 amino acids required for nuclear localization of Arabidopsis NPR1 (Kinkema et al., 2000) are also conserved in tobacco NPR1 (FIG. 8).

[0103] Role of Tobacco Rar1, EDS1 and NPR1/NIM1 in the Nmediated Resistance to TMV

[0104] In order to determine if Rar1, EDS1 and NPR1/NIM1 play important roles in N-mediated resistance, applicants cloned fragments of these genes into pTRV2 as described in the materials and methods section. A mixture of Agrobacterium cultures containing pTRV1 with pTRV2; pTRV2-Rar1; pTRV2-EDS1; or pTRV2-NPR1/NIM1 were each infiltrated on to 4-leaf stage MS4-5 plants. Eight days after infiltration, Agrobacterium containing the TMVGFP construct was infiltrated on to upper leaf of each of the plants. These plants were visualized under UV light 10 days later for movement of TMV-GFP. In the Rar1, EDS1 and NPR1/NIM1 suppressed plants, TMV-GFP spread into the upper leaves (FIGS. 9a-c) as visualized by the presence of GFP in the systemic leaves. More GFP fluorescence was consistently observed in the EDS1 and Rar1 than the NPR1/NIM1 silenced plants (compare FIGS. 9a-b versus FIG. 9c). Taken together, the phenotypic data suggest that suppression of Rar1-, EDS1- and NPR1/NIM1-like genes compromise N function and lead to loss-of-resistance to TMV.

[0105] To see whether the TMV-GFP is present in the upper uninfiltrated leaves of EDS1, Rar1 and NPR1/NIM1 silenced plants, applicants analysed them for the presence of TMV-GFP RNA. RNA gel blots were prepared from the upper uninfiltrated leaves and probed with the TMV MP gene. As expected, more TMV-GFP RNA was observed in EDS1 (FIG. 9d; lane 4) and Rar1 (FIG. 9d; lane 5) silenced plants than the NPR1 (FIG. 9d; lane 6) silenced plants. The amount of TMV-GFP RNA present in EDS 1 and Rar1 silenced plants was less than the amount present in susceptible N. benthamiana plants (compare FIG. 9d; lane 1 versus 4 and 5) and more than TRV-N suppressed plants (compare FIG. 9d; lane 3 versus 4 and 5). These results corroborate the phenotypic data that the suppression of Rar1-, EDS1- and NPR1/NIM1-like genes lead to loss-of-resistance to TMV.

[0106] To confirm the VIGS of Rar1, EDS1 and NPR1/NIM1 genes at the molecular level, applicants performed semiquantitative RT-PCR using total RNA extracted from MS4-5 plants infected with TRV, TRV-Rar1, TRV-EDS1 and TRV-NPR1/NIM1. In TRV-Rar1 infected plants, the Rar1 message was reduced by more than 95% compared to the TRV-infected control (FIG. 5e versus FIG. 5f). In TRV-EDS1 and TRVNPR1/NIM1 infected plants, the EDS1 (FIG. 5g versus H) and NPR1/NIM1 (FIG. 5i versus FIG. 5j) messages were reduced by more than 88% and 78%, respectively, compared to the TRV-infected control (FIG. 5a versus FIG. 5b). In all these cases, EF1 a RNA levels were similar (data not shown) and served as an internal control for RNA quality and RT-PCR amplification.

[0107] Conclusions

[0108] This example demonstrates that the TRV based systems disclosed herein can be used for VIGS and as an efficient reverse genetics tool to study gene function. Transgenic MS4-5 plants exhibit resistance to TMV by induction of HR lesions and containment of TMV to the infection site similar to wild type N-containing tobacco plants (Whitham et al., 1994) and transgenic N-containing tomato plants (Whitham et al., 1996). Tobacco and N. benthamiana belong to the same genus and therefore may contain conserved signal transduction components required for N-mediated resistance to TMV in both species. This is consistent with the observation reported by (Tai et al., 1999) that R genes may function in restricted heterologous species belonging to the same genus or family of plants. In fact, many R genes like pepper BS2, potato Rx1, and tomato Pto and Cf9 function in the heterologous Nicotiana host (Bendahmane et al., 1999; Hammond-Kosack et al., 1998; Rommens et al., 1995; Thilmony et al., 1995). Unlike tobacco, N. benthamiana plants show less auto-fluorescence under UV illumination and support movement of the TMV-GFP recombinant virus. Therefore, the MS4-5 N-containing N. benthamiana transgenic line will be useful in studies aimed towards understanding cellular and physiological events associated with N-mediated HR using TMV-GFP recombinant virus in the future.

[0109] Requirement of tobacco Rar1-, EDS1-, and NPR1/NIM1-like genes for the function of the N gene described in this report provide the first evidence for the role of these genes in a viral resistance pathway. From this work and that of others, EDS1 constitutes the converging point of signaling pathways mediated by the functional TIR-NBS-LRR class of R genes. In addition to EDS1, NDR1 is involved in converging race-specific resistance pathways in Arabidopsis (Aarts et al., 1998). However, this convergence involves distinct subclasses of NBS-LRR R genes. NDR1 is required for the function of the CC-NBS-LRR class of R genes. Requirement of Rar1 for virus resistance (this report) and some powdery mildew resistance genes in barley (Schulze-Lefert and Vogel, 2000) provide another example of converging points in the disease resistance signaling pathways. Moreover, Rar1 represents the first example of a signalling component shared by CC-NBS-LRR (Mla12) and TIR-NBS-LRR (N) type of race-specific R genes. Our observations suggest that the tobacco NPR1/NIM1-like gene is required for TMV resistance. However, NPR1/NIM1 is not required for function of the HRT-mediated resistance to the virus TCV in Arabidopsis (Kachroo et al., 2000). The Arabidopsis NPR1/NIM1 has been shown to interact with members of the basic leucine zipper (bZIP) family of transcription factors like TGA2, TGA3 and TGA6 (NIF1) (Despres et al., 2000; Zhang et al., 1999; Zhou et al.,2000). To date, the biological significance of these NPR1/NIM1-TGA interactions is not known. Our VIGS phenotypic data suggests that suppression of individual TGA factors has no effect on N-mediated resistance to TMV (Y.L., M.S., S.P.D-K, unpublished observations). However, suppression of multiple TGA factors simultaneously by mixed infections results in loss-of-resistance to TMV. Further molecular and biochemical analyses of this phenotypic data are necessary to understand the exact role of NPR1-TGA factors in N-mediated resistance to TMV.

[0110] Applicants have tested the role of 18 additional candidate genes like SIPK, SIPKK, WIPK, NtMEK1 and NtMEK2, COI1, WRKY factors, etc. Our phenotypic analysis suggests that 10 of these genes may play a role in N-mediated resistance to TMV (Y.L., M.S., and S.P.D-K, unpublished observations). Further functional analysis of these genes at the molecular and biochemical level should help to better understand N mediated signal transduction pathway leading to TMV resistance.

[0111] VIGS is known to suppress sequences of highly homologous genes. Therefore, one should be cautious in interpreting VIGS results. In Arabidopsis, EDS1, NPR1 and Rar1 are single copy genes. N. benthamiana genomic DNA blot analysis suggests that there are two copies of EDS1, NPR1 and Rar1 in this plant. This is consistent with the aneuploidy nature of N. benthamiana (1n number=19 chromosome) compared to the diploid members of Nicotiana (1n number=12 chromosome) (Smith, 1979). Therefore, data presented in this report indicates that the Rar1-, EDS1- and NPR1/NIM1-like genes of tobacco are required for function of the N gene.

[0112] In RNAi, the RNA degradation is triggered by double stranded RNA (dsRNA) and occurs in a 2-step process. In the first step, double stranded RNA (dsRNA) is processed into shorter, 21-25 nucleotide long sense and antisense units. These small RNAs, called short interfering RNA or siRNA, in the second step act as guide sequences to identify homologous transcripts and target them for destruction (Nishikura, 2001). Recent evidence suggests that there are secondary siRNAs appear to derive from the action of RNA-dependent RNA polymerase (RdRp) (Sijen et al., 2001). The RdRp plays a role in cyclic amplification of initial siRNAs into secondary siRNAs. These secondary siRNAs exhibited a distinct polarity, 5′ to 3′ on the antisense strand. Therefore, in the future to overcome the silencing of other highly homologous genes, one could target the 5′ untranslated region of the gene for silencing.

[0113] The availability of the Arabidopsis genome sequence (AGI, 2001) and a large number of plant-expressed sequence tags (ESTs) (The Institute of Genomic Research) provide a wealth of information about the plant genome. Therefore, the VIGS assay described here will offer a means to test the function of homologous gene sequences in N. benthamiana. Data presented in Example 4 demonstrates that the TRV based VIGS system described here induces efficient gene silencing in other plants as well, including Arabidopsis and tomato plants. Therefore, TRV-VIGS will offer an efficient reverse genetics tool to test gene function in different plant systems of choice. Even though the VIGS approach is a rapid method to ascertain function by gene inactivation, one of the main disadvantages is that the phenotype observed is not transmittable to the next generation because of this, it is not possible to perform genetic crosses, suppressor or enhancer screens and other long-term genetic manipulations. However, transgenic expression of a replicating PVX (termed PVX amplicon) containing the plant exon sequence consistently induces the silencing of the corresponding endogenous gene in subsequent generations (Angell and Baulcombe, 1997). Therefore, the generation of a TRV-based amplicon containing transgenic lines of Rar1, EDS1 and NPR1 will provide an invaluable resource for further genetic analyses. So far, Dangl (1999) reports that classical forward genetics screens to identify components of a given resistance response have yielded only a few genes because of redundancy or lethality (Dangl, 1999). The VIGS approach described here may help to overcome this problem because the VIGS ‘phenotype’ is conditional, loss of mutations due to organismal lethality should not occur. In the future, large-scale screens using a normalized cDNA library in the TRV-based VIGS system, in conjunction with microarray analysis and two-hybrid experiments should facilitate identification of additional components of the defense pathways in plants.

[0114] Experimental Procedures

[0115] Plasmid Construction

[0116] pTRV1 (RNA1).

[0117] The first strand cDNA of TRV-RNA1 was derived from total RNA extracted from TRV-Ppk20 infected N. benthamiana leaves using primer OYL64 (5′-

GGCCCGGGCCCGTTTCGTCCTTTAGGGACTCGTCAGTGTACTGATATAAG
TACAGACGGGCGTAATAACGCTTACGTAGGCGAGGGGTTTTACC-3′)

[0118] (SEQ ID NO:7) and superscript reverse transcriptase (Gibco/BRL). The primer OYL64 contains an XmaI restriction site (bold), a ribozyrne sequence (underlined), and a sequence complementary to TRVRNA1 bases 6755-6791 (italicized). This first strand cDNA was used as template with upstream primer OYL61 (5′-ATAAAACATTTCAATCCTTTGAACGCGGTAGAACG -3′) (SEQ ID NO:8) corresponding to TRV- RNA1 bases 1-35 and the downstream primer OYL64 to PCR amplify the full-length cDNA of TRV-RNA1. The PCR amplified product was digested by XmaI and cloned into StuI-XmaI-cut pYL44, which is a derivative of pBIN19 binary T-DNA vector (Frisch et al., 1995) carrying the duplicated cauliflower mosaic virus (CaMV) 35S promoter from pCASS2 (Shi et al., 1997) and nopaline synthase (NOS) terminator. The entire sequence of cDNA corresponding to TRV Ppk20 strain RNA1 is deposited in GenBank (AF406990).

[0119] pTRV2 (RNA2).

[0120] Two cDNA fragments corresponding to bases 1-1646 and 3470-3855 of TRV Ppk20 RNA2 (GenBank Z36974) were amplified by RT-PCR and cloned into StuI-SacI restricted pCASS2 (Shi et al., 1997) to obtain pYL36. During RT-PCR, multiple restriction enzyme sites were included between two fragments at base 1646 for cloning foreign DNA sequences, and a self-cleaving ribozyme sequence was also engineered at the 3′-end of viral RNA2 cDNA. Plasmid pTRV2 was generated by subcloning the HindIII-EcoICR1 restricted fragment of pYL36 into HindIII-HpaI restricted pCAMBIA0390 T-DNA vector. The complete sequence of pTRV2 is deposited in GenBank (AF406991).

[0121] pTRV2-derivatives.

[0122] The cDNA fragments corresponding to PDS, NPR1/NIM1, Rar1, EDS1 and N were PCR amplified and cloned into pTRV2. A 369-bp fragment of tobacco PDS that corresponds to nt 878-1246 of tomato PDS (GenBank #M88683) was amplified using a forward primer (5′-CTG ACG AGC TTT CGA TGC AGT GCA T-3′) (SEQ ID NO: 9) and a reverse primer (5′-ATA TAT GGA CAT TTA TCA CAG GAA C-3′) (SEQ ID NO: 10). A 1129-bp fragment corresponding to nt 86-1215 of N cDNA (Whitham et al., 1994) was amplified using a forward primer (5′-ATG GAG CTA TGA TGT TTT CTT AAG TTT TAG-3′) (SEQ ID NO:11) and a reverse primer (5′-GAA GGC CTT TAG CAT AAT TTA CTA CCT C-3′) (SEQ ID NO:12). A 468-bp fragment corresponding to nt 186-654 of tobacco Rar1 was amplified using primers: 5′-AGG AAA GCA CAC AAC AGA AAA ACC-3′ (SEQ ID NO:13) and 5′-GTG CCA TCC TTT GGT GCA TGG AGG-3′) (SEQ ID NO:14). A 548-bp fragment corresponding to nt 1290-1837 of tobacco EDS1 was amplified using a forward primer (5′-GAG TAT CAG ACC AAG TGT GAT ATC CG-3′) (SEQ ID NO:15) and a reverse primer (5′-GCT GAG GTG GGA GTG TTT TCC ACC-3′) (SEQ ID NO:16). A 753-bp fragment corresponding to nt 1014-1767 of tobacco NPR1 was amplified using primers: 5′-GAA AGA GCC TAA AAT TGT AGT GTC-3′ (SEQ ID NO:17) and 5′-CTA TTT CCT AAA AGG GAG CTT ATT-3′ (SEQ ID NO:18). The identity of these constructs was confirmed by DNA sequencing.

[0123] pSPDK661 (TMV-GFP): The TMV cDNA fragment from 30B TMVGFP (Shivprasad et al., 1998) was cloned into pBIN19 derivative pYL44. A ribozyme sequence (Turpen et al., 1993) based on the satellite virusoid of subterranean clover mottle virus was engineered at the 3′ end of the TMV cDNA.

[0124] pSPDK694 (N gene). The XhoI fragment from pSPDK450 (Dinesh-Kumar and Baker, 2000) was cloned into SalI -cut pCAMBIA2300.

[0125] Cloning Rar1-, EDS 1- and NPR1/NIM1-like genes from

[0126] Tobacco

[0127] The 5′ and 3′ ends of tobacco Rar1, EDS1 and NPR1/NIM1 genes were cloned using SMRT RACE cDNA amplification kit (CLONTECH, Calif., USA). Rar1 5′ RACE product was generated using a nested universal primer (NUP) from the kit as a forward primer and a Rar1 gene specific primer (5′-CCT TTC ATC CGG TCA TGG AAG ATA GCG-3′) (SEQ ID NO:19) as a reverse primer. Rar1 3′ RACE product was generated using a gene specific forward primer (5′-AGG AAA GCA CAC AAC AGA AAA ACC-3′) (SEQ ID NO:20) and a universal reverse primer (UPM) from the kit. EDS1 5′-and 3′ RACE products were generated using NUP and an EDS1 gene specific primer (5′-GTT TCT TAG TTC CTC CAC TTC TGC-3′) (SEQ ID NO:21) and EDS1 gene specific primer (5′-GAG TAT CAG ACC AAG TGT GAT ATC CG-3′) (SEQ ID NO:22) and UPM, respectively. NPR1/NIM1 5′ RACE product was generated by using NUP and NPR1/NIM1 specific primer (5′-CAA CGT GGA AAG AAG CGT TTT CCA AG-3′) (SEQ ID NO:23). NPR1/NIM1 3′ RACE product was generated using NPR1/NIM1 specific primer (5′-TCT TGC TAT GGC AGG CGA TGA TTT G-3′) (SEQ ID NO:24) and UPM. In all cases, the RACE products were cloned into TOPO cloning vector (INVITROGEN, Carlsbad, Calif., USA). At least 5 independent 5′ and 3′ RACE clones were sequenced. RACE 5′ and 3′ overlapping sequences were assembled using the DNA STAR SEQMAN program to obtain full length sequences of Rar1, EDS1 and NPR1/NIM1.

[0128] Plant Transformation

[0129] N. benthamiana plants were transformed with pSPDK694 using Agrobacterium-mediated leaf disc transformation (Horsch et al., 1985) and kanamycin (150 μg 1−1) selection. Presence of the transgene was confirmed by PCR using N specific primers.

[0130] VIGS Assay and GFP Imaging

[0131] N. benthamiana plants were grown in pots at 25° C. in a growth chamber under 16 h light/8 h dark cycle. For VIGS assay, pTRV1 or pTRV2 and its derivatives were introduced into Agrobacterium strain GV2260 by electroporation (BIO-RAD, Calif., USA). Agrobacterium cultures at O.D.600=0.8 containing TRV or TRVderivative plasmids were mixed in 1:1 ratio and infiltrated onto the lower leaf of 4-leaf stage plants using a 1-ml needleless syringe. Experiments in which the suppression effect of N, EDS1, Rar1 and NPR1/NIM1 on TMV resistance is investigated, these plants received a secondary infiltration with Agrobacterium cultures at O.D.600=0.5 containing TMV-GFP construct 8 days after TRV infiltration. At this time, TRV-PDS infected plants exhibit silenced phenotype for PDS. Each silencing experiment was repeated at least 5 times and each experiment included at least four independent plants. In experiments where TMV-GFP virus was used, the inoculum was prepared from systemic infected leaves of N. benthamiana plants infiltrated with Agrobacterium containing TMV-GFP plasmid pSPDK661. GFP imaging was done using UV illumination and photographs were taken using OLYMPUS CAMEDIA E10 digital camera.

[0132] RNA Isolation, Northern Blot and RT-PCR Analysis

[0133] Total RNA was extracted from silenced and non-silenced N. benthamiana plants using RNAwiz solution (Ambion, Tex., USA) and treated with RNase-free DNase (Gene Hunter, Tex., USA). First strand cDNA was synthesized using 10 μg of total RNA, oligo d(T)primer and superscript reverse transcriptase (Gibco/BRL, Md., USA). Semi-quantitative RT-PCR was performed as described in (Burton et al., 2000). For RT-PCR, primers that anneal outside the region targeted for silencing were used to ensure that the endogenous gene is tested. The intensities of PCR generated fragments were analysed and quantified using Gel Doc 2000 and Quantity One Version 4.2.1 (BIO-RAD, Calif., USA). RNA blots were prepared using 5 or 10 μg of total RNA following the method described in (Ausubel et al., 1998). To determine TMV or TMV-GFP transcript levels, RNA blots were hybridized with a probe derived from the MP gene of TMV. To determine PR1a message level, a fragment of PR1a derived from tobacco PR1a cDNA (Payne et al., 1988) was used as a probe.

[0134] DNA Gel Blot Analysis

[0135] The DNA gel blot analysis was performed as described in Dellaporta and Moreno (1994). DNA from N. benthamiana was purified using Qiagen plant DNeasy extraction kit. Ten micrograms of genomic DNA was digested with restriction enzymes, fractionated on 0.8% agarose gel, and blotted onto a Zetaprobe membrane (BIO-RAD). The [a-32P]dCTP-labelled probe corresponding to the fragments of EDS1, NPR1 and Rar1 genes used in silencing were made by the random priming method (Pharmacia Corporation, Peapack, N.J., USA).

Example 4

TRV Systems in Tomato

[0136] A tobacco rattle virus (TRV)-based VIGS vector for efficient silencing of genes in tomato is described in this example. A modified vector based on the GATEWAY vector system is also described. The modified vector permits efficient cloning of tomato ESTs in a high throughput manner for silencing.

[0137] Recombinant TRV Infects Tomato

[0138] The TRV vector system described in Example 3 was tested for its ability to cause systemic infection in tomato. A mixture of Agrobacterium cultures containing TRV-RNA1 (pTRV1) and TRV-RNA2 (pTRV2) T-DNA constructs (FIGS. 10a,b) was infiltrated onto the lower leaves of 3-week-old Lycopersicon esculentum cultivar VF36 (referred to as VF36) or L. esculentum cultivar Micro-tom (referred to as Micro-tom) plants (Scott and Harbaugh, 1989). Ten days post-Agro-infiltration, total RNA was prepared from the upper un-infiltrated leaves. RNA blots were hybridized with probes derived from the 3′ ends of RNA1 and RNA2. Genomic RNA1 and 2, and sub-genomic RNA1a and 1b were detected only in those plants infiltrated with Agrobacterium-containing TRV clones (FIG. 10c; lane 1) and were absent in the control Agro-infiltrated plants (FIG. 10c; lane 2). These results clearly showed that recombinant TRV can efficiently replicate and spread systemically in tomato plants.

[0139] Silencing of the Tomato PDS Gene Using TRV-VIGS Vector

[0140] Next, applicants tested whether the TRV clones could induce gene silencing in tomato plants. In order to do so, applicants examined the ability of the TRV-VIGS vector to suppress the expression of the endogenous phytoene desaturase gene (PDS) in Micro-tom tomato. A mixture of Agrobacterium cultures containing pTRV2, carrying tomato PDS (pTRV2-tPDS), and pTRV1, was infiltrated onto the lower leaves of 3-week-old tomato plants (FIG. 11a). PDS silencing in N. benthamiana inhibits carotenoid biosynthesis, causing the plants to exhibit a photo-bleached phenotype (Kumagi et al., 1995). Tomato plants infected with pTRV-tPDS developed a photo-bleached phenotype in the upper leaves 10 days post-Agro-infiltration and remained white for at least 1 month (FIG. 12). The Agrobacterium infiltration method of infecting pTRV-tPDS resulted in the PDS silencing phenotype in only five out of 10 tomato plants (50% efficiency). In contrast, when this technique was applied in N. benthamiana, all plants infected with pTRV-NbPDS exhibited PDS silencing. To improve the silencing efficiency, applicants tested a spray technique for the delivery of TRV into tomato plants (FIG. 11b). The Agrobacterium mixture was sprayed onto 3-week-old tomato plants using an artist's airbrush (see the Experimental procedures section). This method resulted in substantial improvement in the silencing efficiency. Of the 10 plants sprayed with pTRV-tPDS, nine (90%) exhibited the PDS suppression phenotype. These results suggest that spraying Agrobacterium is more effective than infiltration in the induction of silencing in tomato plants. Perhaps the Agrobacterium infiltration method is not very efficient due to the compact architecture of the young tomato leaves. Additionally, wounding caused by the spray technique may mobilize T-DNA transfer more effectively into the tomato cells. Semi-quantitative RT-PCR was performed to confirm PDS silencing. The primers that anneal to the PDS gene outside the region targeted for silencing were used. In pTRV-tPDS infected plants, the PDS message was reduced by more than 78% compared with the TRV infected controls (FIG. 13b). The level of EF1a RNA was similar in TRV-tPDS and TRV alone infected tissue and served as an internal control for RNA quality and RT-PCR amplification (FIG. 13a). The level of suppression of PDS in tomato by the TRV-VIGS vector is comparable with PDS silencing in N. benthamiana.

[0141] The fact that TRV effectively caused the VIGS of PDS in tomato suggests that other nuclear genes could be targeted for silencing in a similar manner. Silencing of the CTR1 homolog in tomato and N. benthamiana leads to a constitutive ethylene response phenotype. The phytohormone ethylene participates in a variety of physiological processes in plants including germination, cell elongation, flower and leaf senescence, sex determination, fruit ripening and abscission, wounding and pathogen infection (Abeles et al., 1992; Johnson and Ecker, 1998). In Arabidopsis, the CTR1 (constitutive triple response 1) gene encodes a Raf-like mitogen-activated protein kinase kinase kinase (MAPKKK) that functions downstream of an ethylene receptor and negatively regulates the ethylene response (Kieber et al., 1993). The ctr1 loss-of-function mutation confers a phenotype in which plants are severely dwarfed and constitutively express ethylene inducible genes (Kieber et al., 1993). In tomato, there are two CTR1-like genes, tCTR1 (Wang and Li, 1997; Zegzouti et al., 1999) and tCTR2 (AJ005077). tCTR1 is 58% identical and 65% similar to Arabidopsis CTR1 at the amino acid level. tCTR2 is 60% identical and 76% similar to tCTR1 in the C-terminus kinase domain but only 38% identical and 55% similar in the N-terminus non-kinase domain. The tCTR2 kinase domain bears a high degree of homology to Arabidopsis EDR1 (85% identical) at the amino acid level. The Arabidopsis EDR1 gene encodes a putative MAPKKK and the mutant, edr1, has an elevated resistance to Pseudomonas syringae and Erysiphe cichoracearum (Frye et al., 2001). The biological functions of tCTR1 and tCTR2 in tomato have not been examined.

[0142] To examine whether tCTR1 and tCTR2 are true homologs of the Arabidopsis CTR1 gene, applicants silenced these genes in tomato and in N. benthamiana using the TRVVIGS assay. Suppression of tCTR1 in VF36 tomato plants resulted in a constitutive ethylene response phenotype similar to that observed in Arabidopsis. They were severely dwarfed compared with the non-silenced plants (FIG. 14a). On the other hand, the suppression of tCTR2 had no effect on plant growth or development (data not shown). Since tomato and tobacco share very high sequence similarity, applicants investigated whether CTR1 homologs of tobacco can induce a similar phenotype in N. benthamiana. As expected, suppression of NbCTR1 leads to a severe dwarf phenotype similar to that observed in tomato (FIG. 14b) and NbCTR2 suppression had no effect. To confirm the tCTR1 suppression at the molecular level, applicants performed semiquantitative RT-PCR. In TRV-tCTR1 infected plants, the tCTR1 message was reduced by more than 81% compared to the controls infected with TRV alone (FIG. 13c). In both tissue RNA samples, EF1a expression levels were similar (data not shown) and served as an internal control.

[0143] Because the region targeted for silencing tCTR1 has 70% similarity to tCTR2 at the nucleotide level, applicants tested whether TRV-tCTR1 could also suppress tCTR2. Semi-quantitative RT-PCR analysis-using primers that anneal to tCTR2, showed that the tCTR2 message level is not affected in the TRV-tCTR1 silenced plants (FIG. 13d). To rule out the possibility that the absence of a developmental phenotype in TRV-tCTR2 suppressed plants is due to lack of suppression of endogenous tCTR2, applicants performed semiquantitative RT-PCR analysis. In tCTR2 silenced plants there was an 85% reduction of tCTR2 mRNA compared with the TRV infected control plants (FIG. 13e). These results suggest that tCTR2 is effectively silenced by VIGS although there is no visible phenotype.

[0144] The mutation in CTR1 in Arabidopsis causes constitutive expression of CHITINASE B (CHIB), an ethylene inducible gene (Kieber et al., 1993). Applicants examined the level of CHIB RNA expression in tCTR1 suppressed tomato plants using RNA blots hybridized with the CHIB gene. CHIB was not detected in wild-type plants (FIG. 14c, lane 1) and very low expression was observed in non-silenced TRV infected plants (FIG. 14c, lane 3). However, in the tCTR1 silenced plants, the CHIB gene was highly expressed (FIG. 14c, lane 2). These results suggest that suppression of tCTR1 in tomato leads to constitutive expression of ethylene-regulated genes. Taken together, these results show that the TRV based VIGS vector can efficiently phenocopy the effects of mutations in different nuclear genes in tomato.

[0145] Modification of the TRV2 Vector for High Throughput Cloning.

[0146] In the TIGR (The Institute of Genomic Research) database there are over 100 000 tomato ESTs corresponding to 29 000 unique sequence clones (Uni ESTs). Many of these ESTs show homology to genes in Arabidopsis. The TRV-VIGS approach described in this example offers great promise for studying tomato Uni-EST function. However, insertion of tomato ESTs into pTRV2 using a traditional cloning method is labor-intensive and time-consuming. Therefore, applicants modified the pTRV2 clone using the GATEWAY system (Invitrogen, Calif., USA). The GATEWAY technology allows fast and easy cloning that is restriction enzyme- and ligation-free. Consequently, the Uni ESTs can be cloned en masse into this pTRV2 vector.

[0147] The construct, pTRV2-attP1-attP2, was generated to facilitate en masse cloning of tomato ESTs (FIG. 15a). The PCR products flanked by attB1 and attB2 sequences directionally recombine in vitro at attP1 and attP2 sites contained in the plasmid when incubated with the BP CLONASE enzyme (FIG. 15b). When this reaction mixture is transformed into an E. coli strain such as DH10B, only recombinants can grow because the ccdB gene, contained in the plasmid, is lethal. The resulting recombinant plasmid will contain flanking attL1 and attL2 sequences (FIG. 15b). Applicants cloned the N. benthamiana PDS gene into the pTRV2-attP1-attP2 vector to test the efficiency of cloning and silencing. Efficiency of cloning a PCR product flanked by attB1 and attB2 into this vector is about 95%. However, when applicants tested this vector for the efficiency of silencing PDS gene in N. benthamiana, a very low level of patchy suppression was observed. RT-PCR confirmed that the clone was infectious, but the PCR fragment obtained from amplification of RNA extracted from infected plants was smaller than expected. Since, both attL1 and attL2 sequences are direct repeats of 100 bp, applicants reasoned that PDS flanked by these repeat sequences may have been deleted upon infection of plants with the vector, and failure to suppress PDS would result.

[0148] In order to overcome this deletion problem, applicants generated the vector pTRV2-attR2-attR1 (FIG. 16a). In the first step, the PCR products flanked by attB1 and attB2 sequences directionally recombine in vitro at attP1 and attP2 sites on the pDONR-mod plasmid when incubated with the BP CLONASE enzyme (FIG. 16b). In the second step, the intermediate attL1-attL2-containing pDONR-mod vector directionally recombines with attR2 and attR1 sites in the pTRV2 vector, when incubated with the LR CLONASE enzyme. (FIG. 7b). Therefore, the resulting plasmid has only a 23-bp flanking sequence of attB1 and attB2. Moreover, these sequences are not direct repeats. The efficiency of cloning a target sequence for silencing into this vector is about 90%.

[0149] To determine whether the pTRV2-attR2-attR1 vector efficiently mediates gene silencing similar to original pTRV2 vector, applicants cloned PDS and the small sub-unit of the ribulose bisphosphate carboxylase (tRbcS). Compared with PDS, the RbcS is encoded by a multigene family and is expressed in abundance. The efficiency of silencing PDS was similar to that of the original pTRV2 vector. The tRbcS silenced plants developed pale yellow leaves 12 days post-Agro-infiltration compared to the TRV alone infected control plants (FIG. 17). This phenotype is similar to that reported by Ratcliff et al. (2001) in N. benthamiana. Furthermore, semiquantitative RT-PCR analysis suggests that the endogenous tRbcS mRNA is reduced by 76% compared with the TRV infected control plants (FIG. 13f).

[0150] In order to demonstrate that tomato ESTs can be easily cloned into the pTRV2-attR2-attR1 destination vector, applicants cloned 10 tomato ESTs that bear homology to a serine/threonine kinase (The Institute of Genomic Research). Primer sequences were designed that annealed to vector sequences flanking the tomato ESTs. The attB1 sequence was included in the forward primer and the attB2 sequence was included in reverse primer (FIG. 16b). These primer sets were then used to amplify ESTs by PCR (FIG. 16c). The PCR products with terminal attB1 and attB2 sequences were incubated with the pDONR-mod vector containing the attP1 and attP2 recombination site and the BP CLONASE enzyme. The pTRV2-attR2-attR1 destination vector containing the attR1 and attR2 recombination site and the LR CLONASE enzyme were added. This mixture was transformed into DH10B chemical competent cells and selected on kanamycin-containing LB plates. This single-tube protocol for cloning attB-PCR products directly into pTRV2-attR2-attR1 resulted in a 95-100% success rate. Inserts containing clones were verified by restriction enzyme digestion (FIG. 16d) and by sequencing the vector-insert junctions. These results suggest that tomato ESTs can be cloned into the pTRV2-attR2-attR1 vector for silencing en masse.

[0151] In order to demonstrate that the above described TRV-EST clones can be used for silencing corresponding endogenous genes, applicants silenced EST cLED3L14 (TIGR) (corresponding PCR product and the clone is shown in FIGS. 16c,d; lane 2). This EST shows highest homology to potato protein kinase StCPK1 (Lakatos et al., 1998). Suppression of the endogenous gene corresponding to this EST showed no visible phenotype (data not shown) even though the mRNA is reduced by 82% compared with the TRV-alone control (FIG. 4g). These results indicate that the tomato EST clones in TRV-attR2-attR1 vector can be used successfully to silence corresponding endogenous genes in tomato.

[0152] Conclusions

[0153] Gene silencing methods that do not rely on transformation offer a tremendous advantage for gene function analysis. In this report applicants show that recombinant TRV infects tomato plants and can be used to silence genes efficiently. The results suggest that a spray technique to deliver Agrobacterium to tomato plant cells is better for obtaining high efficiency silencing compared with the routinely used Agrobacterium infiltration method. Using this TRV-based VIGS system, applicants demonstrate that tCTR1 is a true homolog of the Arabidopsis CTR1 gene. Suppression of tCTR1 in tomato and N. benthamiana induces a constitutive ethylene response phenotype, while suppression of tCTR2 does not. Even though TCTR1 and tCTR2 share up to 60% sequence similarity at the nucleotide level, suppression of tCTR1 using the VIGS vector had no effect on tCTR2 gene expression. Finally, applicants have modified the TRV2 vector using the GATEWAY recombination system in order to clone tomato ESTs en masse with one set of primers. This provides a rapid way to test tomato EST function. Using this vector, applicants show that tRbcS and an endogenous gene corresponding to tomato EST cLED3L14 can be successfully silenced. Therefore, the modified TRV2 vector will facilitate production of normalized cDNA libraries or the cloning of large sets of genes for large-scale functional genomics in the future.

[0154] Experimental Procedures

[0155] Plasmid construction:

[0156] pTRV1 and pTRV2 VIGS vectors are described in Example 3.

[0157] pTRV2-tPDS: a 409-bp fragment of PDS cDNA fragment corresponding to bases 858-1266 of tomato PDS gene was PCR amplified from tomato VF36 cDNA using Taq DNA polymerase and the primers 5′-CGG TCT AGA GGC ACT CAA CTT TAT AAA CC-3′ (SEQ ID NO:25) and 5′-CGG GGA TCC CTT CAG TTT TCT GTC AAA CC-3′ (SEQ ID NO:26). The resulting PCR product was cloned into XbaI-BamHI-cut pTRV2.

[0158] pTRV2-tCTR1: a 690-bp fragment of tCTR1 cDNA fragment corresponding to bases 1906-2595 of tomato CTR1 (Wang and Li, 1997) was PCR amplified from tomato VF36 cDNA using Taq DNA polymerase and the primers 5′-CGG GAA TTC GTT GCA ATT ATC AAG CGG TTG CG-3′ (SEQ ID NO:27) and 5′- CGG CTC GAG TCA TGA GAG CAA CTG CAT GTC TG T-3′ (SEQ ID NO:28). The resulting PCR product was cloned into EcoRI-XhoI-cut pTRV2.

[0159] pTRV2-tCTR2: a 537-bp fragment of CTR2 cDNA fragment corresponding to bases 2506-3042 of tomato CTR2 (GenBank #AJ005077) was PCR amplified from tomato VF36 cDNA using Taq DNA polymerase and the primers 5′-CGG GAA TTC GCC CTT GAT GTG GCA AAG GGC AT-3′ (SEQ ID NO:29) and 5′-CGG CTC GAG GTA GAA TTT ACT GAG ATT TCC TG-3′ (SEQ ID NO:30). The resulting PCR product was cloned into EcoRI-XhoI-cut pTRV2.

[0160] pTRV2-NbCTR1: a 690-bp of CTRI cDNA fragment was PCR amplified from N. benthamiana cDNA using Taq DNA polymerase and the primers used to amplify tCTR1. The resulting PCR product was cloned into EcoRI-XhoI-cut pTRV2.

[0161] pTRV2-NbCTR2: a 537-bp of CTR2 cDNA fragment was PCR amplified from N. benthamiana cDNA using Taq DNA polymerase and the primers used to amplify tCTR2. The resulting PCR product was cloned into EcoRI-XhoI-cut pTRV2.

[0162] pTRV2-attP1-attP2: The DNA fragment containing attP1-ccdBCmR.- attP2 amplified from pDONR201 (Invitrogen, Carlsbad, Calif., USA) using primers 5′-CGG GAA TTC TAG AGG CGC GCC AAA TAA TGA TTT TAT TTT GAC TGA TAG TGA C-3′ (SEQ ID NO:31) and 5′-C GGC TCG AGA GCT CAA ATA ATG ATT TTA TTT TGA CTG ATA GTG AC-3′ (SEQ ID NO:32). This PCR product was cloned into EcoRI-XhoI-cut pTRV2 (Liu et al., 2002).

[0163] pDONR-mod: This vector was generated by deleting the fragment containing the kanamycin gene between PvuI and NruI of pDONR201 (Invitrogen) and religating the vector.

[0164] pTRV2-attR2-attR1: HindIII-DraIII(T4 DNA polymerase treated) fragment of pYL156 (Liu et al., 2002) containing 2×CaMV promoter and TRV-RNA2 cDNA with the NOS terminator was cloned into pBin19 to obtain pYL276. pTRV2-attR1-attR2 was obtained by inserting the GATEWAY conversion cassette B (Invitrogen) into pYL276 at the Stul site.

[0165] pTRV2-attL1-NbPDS-attL2 and pYL157: N. benthamiana PDS cDNA containing the attB1 and attB2 sequences was obtained by PCR amplification using the TRV-PDS clone (Liu et al., 2002) as template and primers: 5′-G GGG ACA AGT TTG TAC AAA AAA GCA GGC TCT GAC GAG CTT TCG ATG CAG-3′ (SEQ ID NO:33) and 5′-GGG GAC CAC TTT GTA CAA GAA AGC TGG GTA TAT ATG GAC ATT TAT CAC A -3′ (SEQ ID NO:34). This PDS PCR product was recombined into pTRV2- attP 1 -attP2 using the BP CLONASE enzyme reaction (Invitrogen).

[0166] pTRV2-attB2-NbPDS-attB1: N. benthamiana PDS cDNA containing the attB1 and attB2 sequences was obtained by PCR, as described above. This PDS PCR product was recombined into pDONR-mod vector containing the attP1 and attP2 recombination sites using the BP CLONASE enzyme. To this, the pTRV2-attR1-attR2 destination vector and the LR CLONASE enzyme was added. This mixture was transformed into DH10B chemical competent cells and selected on kanamycin-containing LB plates.

[0167] pTRV2-attB2-tRbcS-attB1: A 500-bp tRbcS cDNA containing the attB1 and attB2 sequences was obtained by PCR using VF36 cDNA and primers 5′-GGG GAC AAG TTT GTA CAA AAA AGC AGG CTC TGC TTC CTC TGT CAT TTC TTC AGC-3′ (SEQ ID NO:35) and 5′- GGG GAC CAC TTT GTA CAA GAA AGC TGG GTC CAC TTG ACG CAC ATT GTC GAA TCC -3′(SEQ ID NO:36). This PCR product was recombined into pTRV2-attR2-attR1 vector as described above for cloning PDS.

[0168] pTRV2-attB2-tomato ESTs-attB1: 10 tomato ESTs that bear homology to serine/threonine kinases were amplified by PCR using a forward primer containing the attB1 sequence and a reverse primer containing the attB2 sequence, which anneals to the vector pBluescript SK (−) containing tomato ESTs. The forward primer is 5′-G GGG ACA AGT TTG TAC AAA AAA GCA GGC TCC CCC GGG CTG CAG GAA TTC-3′ (SEQ ID NO:37) and the reverse primer is G GGG ACC ACT TTG TAC AAG AAA GCT GGG TGG TAC CGG GCC CCC CCT CGA G-3′ (SEQ ID NO:38). The resulting PCR products with terminal attB1 and attB2 sequences were precipitated and incubated with pDONR-mod vector containing the attP1 and attP2 recombination sites and the BP CLONASE enzyme. To this, the pTRV2-attR2-attR1 destination vector containing the attR1 and attR2 recombination sites and the LR CLONASE enzyme was added. This mixture was transformed into DH10B chemical competent cells and selected on kanamycin-containing LB plates. Clones were verified by restriction enzyme digestion and by sequencing the vector-insert junctions.

[0169] Agro-infiltration and Spray

[0170] N. benthamiana and tomato plants were grown in pots at 25° C. in a growth chamber under 16 h light/8 h dark cycle with 60% humidity. For the VIGS assay, pTRV1 or pTRV2 and its derivatives were introduced into Agrobacterium strain GV3101 by electroporation (BIO-RAD, Hercules, Calif., USA). A 5-ml culture was grown overnight at 28° C. in the appropriate antibiotic selection medium. The next day, the culture was inoculated into a 50-ml LB medium containing antibiotics, 10 mM MES and 20 mM acetosyringone. The culture was grown overnight in a 28° C. shaker. Agrobacterium cells were harvested and resuspended in infiltration media (10 mM MgCl2, 10 mM MES, 200 mM acetosyringone), adjusted to an O.D. of 2.0 and left at room temperature for 3 h. Agrobacterium was infiltrated using a needleless 1 ml syringe or sprayed using an artist's airbrush (Paasche, Harwood Heights, Ill., USA, model VL80) connected to a portable air compressor (Campbell Havsfeld, Harrison, Ohio, USA) set at 75 psi. Plants were left covered overnight.

[0171] RNA Isolation, Northern Blot and RT-PCR Analysis

[0172] Total RNA was extracted from silenced and non-silenced tomato plants using the RNAwiz solution (Ambion, Austin, Tex., USA) and treated with RNase-free DNase (Gene Hunter, Nashville, Tenn., USA). First strand cDNA was synthesized using 1 μg of total RNA, oligo d(T)primer and superscript reverse transcriptase (Invitrogen). Semi-quantitative RT-PCR was performed as described in (Burton et al., 2000; Liu et al., 2002). For RT-PCR, primers that anneal outside the region targeted for silencing were used to ensure that only the endogenous gene was being tested. The intensities of PCR-generated fragments were analyzed and quantified using Gel Doc 2000 and Quantity One Version 4.3 (BIORAD, Calif.).RNA blots were prepared using 5 or 10 μg of total RNA. To confirm TRV infection, RNA blots were hybridized with a probe derived from the 3′-end of TRV RNA1 (bases 5351-6791) and RNA2 (bases 1245-2103). To determine the CHIB message level, a fragment of CHIB was PCR amplified from tomato cDNA using primers 5′-ACT GTT TCC TTA GAG AGC AAG GTA G-3 (SEQ ID NO:39)′ and 5′-CAA CTA ATA GTC CGT TTC CAA AAG ACC-3′ (SEQ ID NO:40) and this fragment was used as a probe.

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[0228] While specific embodiments of the subject inventions have been discussed, the above specification is illustrative and not restrictive. Many variations of the inventions will become apparent to those skilled in the art upon review of this specification and the claims below. The full scope of the inventions should be determined by reference to the claims, along with their full scope of equivalents, and the specification, along with such variations.

Claims

1. A recombinant nucleic acid comprising a TRV-RNA1 nucleotide sequence of SEQ ID NO: 1, or a complement thereof.

2. The recombinant nucleic acid of claim 1, wherein the TRV-RNA1 nucleotide sequence is operably linked to a plant active promoter.

3. The recombinant nucleic acid of claim 1, wherein a transcription terminator is positioned within about 1000 bases downstream of the 3′ end of the TRV-RNA1 nucleotide sequence.

4. The recombinant nucleic acid of claim 1, wherein a self-cleaving ribozyme sequence is positioned within about 100 bases downstream of the 3′ end of the TRV-RNA1 nucleotide sequence.

5. The nucleic acid of claim 1, wherein the nucleic acid is a ribonucleic acid.

6. A vector comprising a TRV-RNA1 nucleotide sequence of SEQ ID NO: 1, or a complement thereof.

7. The vector of claim 6, wherein the recombinant nucleic acid is positioned between a T DNA left border sequence and a T DNA right border sequence.

8. The vector of claim 6, wherein the TRV-RNA1 nucleotide sequence is operably linked to a plant active promoter.

9. The vector of claim 6, wherein the vector is pTRV1.

10. A cell comprising a recombinant TRV-RNA1 nucleic acid of SEQ ID NO: 1, or a complement thereof.

11. The cell of claim 10, wherein the cell is a plant cell.

12. A cell of claim 10 comprising a vector that comprises the TRV-RNA1 nucleotide sequence of SEQ ID NO: 1, or a complement thereof.

13. The cell of claim 10, wherein the cell is a bacterial cell.

14. The cell of claim 13, wherein the bacterial cell is selected from the group consisting of Escherichia coli and Agrobacterium tumefaciens.

15. A plant comprising a recombinant TRV-RNA1 nucleic acid of SEQ ID NO: 1, or a complement thereof.

16. The plant of claim 15, wherein the plant is selected from the group consisting of: a monocot and a dicot.

17. The plant of claim 15, wherein the plant is selected from the group consisting of: a Lycopersicon species., a Nicotiana species, an Arabidopsis species, a Capsicum species and a Solanum species.

18. The plant of claim 15, wherein the plant is transiently transformed with the TRV-RNA1 nucleic acid.

19. A plant product obtained from a plant of claim 15.

20. The plant product of claim 19, wherein the plant product is selected from the group consisting of: a seed, a fruit, a leaf sample, a pollen sample, and a cell suspension.

21. A virus or viral particle comprising a recombinant TRV-RNA1 nucleic acid of SEQ ID NO: 1, or a complement thereof.

22. A recombinant nucleic acid comprising a TRV-RNA1 nucleotide sequence of SEQ ID NO: 1, or a complement thereof, and a heterologous nucleotide sequence.

23. A recombinant nucleic acid comprising a TRV-RNA2 nucleotide sequence of SEQ ID NO:5, or a complement thereof, and a heterologous nucleotide sequence.

24. The recombinant nucleic acid of claim 23, wherein the TRV-RNA2 nucleotide sequence is operably linked to a plant active promoter.

25. The recombinant nucleic acid of claim 23, wherein the heterologous nucleotide sequence includes a recombination site.

26. The recombinant nucleic acid of claim 25, wherein the heterologous nucleotide sequence includes a recombination site selected from the group consisting of: a restriction enzyme cleavage site, a multiple cloning site, an integrase recognition site, a transposase recognition site and a recombinase recognition site.

27. The recombinant nucleic acid of claim 23, wherein the heterologous nucleotide sequence is a gene silencing insert.

28. The recombinant nucleic acid of claim 23, wherein a transcription terminator is positioned within about 1000 bases downstream of the 3′ end of the TRV-RNA2 nucleotide sequence.

29. The recombinant nucleic acid of claim 23, wherein a self-cleaving ribozyme is positioned within about 100 bases downstream of the 3′ end of the TRV-RNA2 nucleotide sequence.

30. The recombinant nucleic acid of claim 23, wherein the nucleic acid is a ribonucleic acid.

31. A vector comprising a TRV-RNA2 nucleotide sequence of SEQ ID NO:5, or a complement thereof, and a heterologous nucleotide sequence.

32. The vector of claim 31, wherein the recombinant nucleic acid is positioned between a T DNA left border sequence and a T DNA right border sequence.

33. The vector of claim 31, wherein the TRV-RNA2 nucleotide sequence is operably linked to a plant active promoter.

34. The vector of claim 31, wherein the heterologous nucleotide sequence includes a recombination site.

35. The vector of claim 31, wherein the heterologous nucleotide sequence is a sequence for causing gene silencing.

36. The vector of claim 31, wherein the vector is pTRV2.

37. A cell comprising a recombinant nucleic acid comprising a TRV-RNA2 nucleotide sequence of SEQ ID NO:5, or a complement thereof, and a heterologous nucleotide sequence.

38. The cell of claim 37, comprising a vector that comprises the recombinant nucleic acid comprising a TRV-RNA2 nucleotide sequence of SEQ ID NO:5, or a complement thereof, and a heterologous nucleotide sequence.

39. The cell of claim 37, wherein the cell is selected from the group consisting of: a bacterial cell and a plant cell.

40. The cell of claim 39, wherein the cell is a bacterial cell selected from the group consisting of Escherichia coli and Agrobacterium tumefaciens.

41. A plant comprising a recombinant nucleic acid comprising a TRV-RNA2 nucleotide sequence of SEQ ID NO:5, or a complement thereof, and a heterologous nucleotide sequence.

42. The plant of claim 41, wherein the plant is selected from the group consisting of: a monocot and a dicot.

43. The plant of claim 41, wherein the plant is selected from the group consisting of: a Lycopersicon species., a Nicotiana species, an Arabidopsis species, a Capsicum species and a Solanum species.

44. A plant product obtained from a plant of claim 41.

45. The plant product of claim 44, wherein the plant product is selected from the group consisting of: a seed, a fruit, a leaf sample, a pollen sample, and a cell suspension.

46. A virus or viral particle comprising a recombinant nucleic acid comprising a TRV-RNA2 nucleotide sequence of SEQ ID NO:5, or a complement thereof, and a heterologous nucleotide sequence.

47. A plant comprising: a) a first recombinant nucleic acid comprising a TRV-RNA1 nucleotide sequence of SEQ ID NO: 1; and b) a second recombinant nucleic acid comprising a TRV-RNA2 nucleotide sequence of SEQ ID NO:5, and a heterologous nucleotide sequence.

48. A method for making a transgenic plant, the method comprising introducing into one or more cells of the plant: a) a recombinant nucleic acid comprising a TRV-RNA1 nucleotide sequence of SEQ ID NO: 1, or a complement thereof, and b) a recombinant nucleic acid comprising a TRV-RNA2 nucleotide sequence.

49. The method of claim 48, further comprising generating offspring from the plant.

50. The method of claim 48, wherein the plant is transiently transformed.

51. A transgenic plant produced by the method of claim 48.

52. A method for making a transgenic plant, the method comprising introducing into one or more cells of the plant: a) a recombinant nucleic acid comprising a TRV-RNA1 nucleotide sequence; and b) a recombinant nucleic acid comprising a TRV-RNA2 nucleotide sequence of SEQ ID NO:5, or a complement thereof, and a heterologous nucleotide sequence.

53. The method of claim 52, further comprising generating offspring from the plant.

54. The method of claim 53, wherein the plant is transiently transformed.

55. A transgenic plant produced by the method of claim 53.

56. A method for making a transgenic plant, the method comprising: introducing a recombinant nucleic acid comprising (a) a TRV-RNA2 nucleotide sequence of SEQ ID NO:5, or a complement thereof, and (b) a heterologous nucleotide sequence, into one or more cells of a plant that is stably transformed with a recombinant nucleic acid comprising a TRV-RNA1 nucleotide sequence.

57. The method of claim 56, wherein the plant is transiently transformed with the recombinant nucleic acid comprising (a) a TRV-RNA2 nucleotide sequence of SEQ ID NO:5, or a complement thereof, and (b) a heterologous nucleotide sequence.

58. The method of claim 56, wherein the plant is transformed with a vector comprising (a) the TRV-RNA2 nucleotide sequence of SEQ ID NO:5, or a complement thereof, and (b) the heterologous nucleotide sequence.

59. The method of claim 56, wherein the heterologous nucleotide sequence includes a gene silencing insert.

60. A method for decreasing the expression of a gene in one or more cells of a plant, the method comprising introducing into one or more cells of the plant a vector comprising: (a) a TRV-RNA2 nucleotide sequence of SEQ ID NO:5, or a complement thereof, and (b) a gene silencing insert, wherein expression of the gene silencing insert causes down-regulation of expression of the gene in the plant or portion of the plant.

61. A method for evaluating the function of a selected gene in a plant, the method comprising: a) introducing a vector of claim 34 into one or more cells of the plant, wherein the nucleotide sequence for causing gene silencing is designed to cause decreased expression of the selected gene, and b) observing at least one phenotype of the plant.

62. A method for introducing a TRV vector into one or more cells of a tomato plant, the method comprising: spraying the tomato plant with a liquid mixture comprising Agrobacterium cells containing the TRV vector.

63. A vector comprising a TRV-RNA1 replicon, wherein the TRV-RNA1 replicon comprises a TRV-RNA1 sequence having one or more of the following nucleotides at the specified positions, or positions corresponding thereto: A at 1266, Cat 2291, T at 3094, Tat 3130, G at 3634, A at 4123, T at 4254, A at 4642 and A at 5559.

64. A vector comprising a TRV-RNA1 replicon, wherein the TRV-RNA1 replicon comprises TRV-RNA1 sequence encoding one or more of the following polypeptides: the replicase of SEQ ID NO:2, the movement protein of SEQ ID NO:3 and the 16 kDa protein of SEQ ID NO:4.

65. A vector comprising a TRV-RNA2 replicon, wherein the TRV-RNA2 replicon comprises a TRV-RNA2 sequence having one or more of the following nucleotides at the specified positions, or positions corresponding thereto: an AG insertion at 287, a CG insertion at 380, a G insertion at 3490, a GCC insertion at 3662, a G insertion at 3756, C at 338, T at 339, A at 340, C at 342, G at 343, C at 344, C at 654, T at 3509 and G at 3660.