Members of the Arabidopsis HRT/RPP8 family of resistance genes confer resistance to both viral and oomycete pathogens

When and how to kill a plant cell: infection strategies of plant pathogenic fungi

Fungi cause severe diseases on a broad range of crop and ornamental plants, leading to significant economical losses. Plant pathogenic fungi exhibit a huge variability in their mode of infection, differentiation and function of infection structures and nutritional strategy. In this review, advances in understanding mechanisms of biotrophy, necrotrophy and hemibiotrophic lifestyles are described. Special emphasis is given to the biotrophy-necrotrophy switch of hemibiotrophic pathogens, and to biosynthesis, chemical diversity and mode of action of various fungal toxins produced during the infection process.

Genetic basis for the hierarchical interaction between Tobamovirus spp. and L resistance gene alleles from different pepper species

The pepper L gene conditions the plant's resistance to Tobamovirus spp. Alleles L(1), L(2), L(3), and L(4) confer a broadening spectra of resistance to different virus pathotypes. In this study, we report the genetic basis for the hierarchical interaction between L genes and Tobamovirus pathotypes. We cloned L(3) using map-based methods, and L(1), L(1a), L(1c), L(2), L(2b), and L(4) using a homology-based method. L gene alleles encode coiled-coil, nucleotide-binding, leucine-rich repeat (LRR)-type resistance proteins with the ability to induce resistance response to the viral coat protein (CP) avirulence effectors by themselves. Their different recognition spectra in original pepper species were reproduced in an Agrobacterium tumefaciens-mediated transient expression system in Nicotiana benthamiana. Chimera analysis with L(1), which showed the narrowest recognition spectrum, indicates that the broader recognition spectra conferred by L(2), L(2b), L(3), and L(4) require different subregions of the LRR domain. We identified a critical amino acid residue for the determination of recognition spectra but other regions also influenced the L genes' resistance spectra. The results suggest that the hierarchical interactions between L genes and Tobamovirus spp. are determined by the interaction of multiple subregions of the LRR domain of L proteins with different viral CP themselves or some protein complexes including them.

Blue light photoreceptors are required for the stability and function of a resistance protein mediating viral defense in Arabidopsis

This light-perciving ability of plants requires the activities of proteins termed photoreceptors. In addition to various growth and developmental processes, light also plays a role in plant defense against pathogens and is required for activation of several defense genes and regulation of the cell death response. However, the molecular or biochemical basis of light modulated regulation of defense signaling is largely unclear. We demonstrate a direct role for blue-light photoreceptors in resistance (R) protein-mediated plant defense against Turnip Crinkle Virus (TCV) in Arabidopsis. The blue-light photoreceptors, cryptochrome (CRY) 2 and phototropin (PHOT) 2, are specifically required for maintaining the stability of the R protein HRT, and thereby resistance to TCV. Exogenous application of the phytohormone salicylic acid elevates HRT levels in phot2 but not in cry2 background. These data indicate that CRY2 and PHOT2 function distinctly in maintaining post-transcriptional stability of HRT. HRT-mediated resistance is also dependent on CRY1 and PHOT1 proteins, but these do not contribute to the stability of HRT. HRT interacts with the CRY2/PHOT2-interacting protein COP1, a E3 ubiquitin ligase. Exogenous application of a proteasome inhibitor prevents blue-light-dependent degradation of HRT, suggesting that HRT is degraded via the 26S proteasome. These and the fact that PHOT2 interacts directly with the R protein RPS2 suggest that blue-light photoreceptors might be involved in regulation and/or signaling mediated by several R proteins.

The Arabidopsis downy mildew resistance gene RPP8 is induced by pathogens and salicylic acid and is regulated by W box cis elements

Plants disease resistance (R) genes encode specialized receptors that are quantitative, rate-limiting defense regulators. R genes must be expressed at optimum levels to function properly. If expression is too low, downstream defense responses are not activated efficiently. Conversely, overexpression of R genes can trigger autoactivation of defenses with deleterious consequences for the plant. Little is known about R gene regulation, particularly under defense-inducing conditions. We examined regulation of the Arabidopsis thaliana gene RPP8 (resistance to Hyaloperonospora arabidopsidis, isolate Emco5). RPP8 was induced in response to challenge with H. arabidopsidis or application of salicylic acid, as shown with RPP8-Luciferase transgenic plants and quantitative reverse-transcription polymerase chain reaction of endogenous alleles. The RPP1 and RPP4 genes were also induced by H. arabidopsidis and salicylic acid, suggesting that some RPP genes are subject to feedback amplification. The RPP8 promoter contains three W box cis elements. Site-directed mutagenesis of all three W boxes greatly diminished RPP8 basal expression, inducibility, and resistance in transgenic plants. Motif searches indicated that the W box is the only known cis element that is statistically overrepresented in Arabidopsis nucleotide-binding leucine-rich repeat promoters. These results indicate that WRKY transcription factors can regulate expression of surveillance genes at the top of the defense-signaling cascade.

Cryptochrome 2 and phototropin 2 regulate resistance protein-mediated viral defense by negatively regulating an E3 ubiquitin ligase

Light harvested by plants is essential for the survival of most life forms. This light perception ability requires the activities of proteins termed photoreceptors. We report a function for photoreceptors in mediating resistance (R) protein-derived plant defense. The blue-light photoreceptors, cryptochrome (CRY) 2 and phototropin (PHOT) 2, are required for the stability of the R protein HRT, and thereby resistance to Turnip Crinkle virus (TCV). Exposure to darkness or blue-light induces degradation of CRY2, and in turn HRT, resulting in susceptibility. Overexpression of HRT can compensate for the absence of PHOT2 but not CRY2. HRT does not directly associate with either CRY2 or PHOT2 but does bind the CRY2-/PHOT2-interacting E3 ubiquitin ligase, COP1. Application of the proteasome inhibitor, MG132, prevents blue-light-dependent degradation of HRT, consequently these plants show resistance to TCV under blue-light. We propose that CRY2/PHOT2 negatively regulate the proteasome-mediated degradation of HRT, likely via COP1, and blue-light relieves this repression resulting in HRT degradation.

Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping

The model plant Arabidopsis thaliana exhibits extensive natural variation in resistance to parasites. Immunity is often conferred by resistance (R) genes that permit recognition of specific races of a disease. The number of such R genes and their distribution are poorly understood. In this study, we investigated the basis for resistance to the downy mildew agent Hyaloperonospora arabidopsidis ex parasitica (Hpa) in a global sample of A. thaliana. We implemented a combined genome-wide mapping of resistance using populations of recombinant inbred lines and a collection of wild A. thaliana accessions. We tested the interaction between 96 host genotypes collected worldwide and five strains of Hpa. Then, a fraction of the species-wide resistance was genetically dissected using six recently constructed populations of recombinant inbred lines. We found that resistance is usually governed by single dominant R genes that are concentrated in four genomic regions only. We show that association genetics of resistance to diseases such as downy mildew enables increased mapping resolution from quantitative trait loci interval to candidate gene level. Association patterns in quantitative trait loci intervals indicate that the pool of A. thaliana resistance sources against the tested Hpa isolates may be predominantly confined to six RPP (Resistance to Hpa) loci isolated in previous studies. Our results suggest that combining association and linkage mapping could accelerate resistance gene discovery in plants.

Genetic and physical fine mapping of Scmv2, a potyvirus resistance gene in maize

Sugarcane mosaic virus (SCMV) is an important virus pathogen both in European and Chinese maize production, causing serious losses in grain and forage yield in susceptible cultivars. Two major resistance loci confer resistance to SCMV, one located on chromosome 3 (Scmv2) and one on chromosome 6 (Scmv1). We developed a large isogenic mapping population segregating in the Scmv2, but not the Scmv1 region, to minimize genetic variation potentially affecting expression of SCMV resistance. We fine mapped Scmv2 to a region of 0.28 cM, covering a physical distance of 1.3426 Mb, and developed six new polymorphic SSR markers based on publicly available BAC sequences within this region. At present, we still have three recombinants left between Scmv2 and the nearest polymorphic marker on either side of the Scmv2 locus. The region showed synteny to a 1.6 Mb long sequence on chromosome 12 in rice. Analysis of the public B73 BAC library as well as the syntenic rice region did not reveal any similarity to known resistance genes. However, four new candidate genes with a possible involvement in movement of virus were detected.

The coevolution of plants and viruses: resistance and pathogenicity

Virus infection may damage the plant, and plant defenses are effective against viruses; thus, it is currently assumed that plants and viruses coevolve. However, and despite huge advances in understanding the mechanisms of pathogenicity and virulence in viruses and the mechanisms of virus resistance in plants, evidence in support of this hypothesis is surprisingly scant, and refers almost only to the virus partner. Most evidence for coevolution derives from the study of highly virulent viruses in agricultural systems, in which humans manipulate host genetic structure, what determines genetic changes in the virus population. Studies have focused on virus responses to qualitative resistance, either dominant or recessive but, even within this restricted scenario, population genetic analyses of pathogenicity and resistance factors are still scarce. Analyses of quantitative resistance or tolerance, which could be relevant for plant-virus coevolution, lag far behind. A major limitation is the lack of information on systems in which the host might evolve in response to virus infection, that is, wild hosts in natural ecosystems. It is presently unknown if, or under which circumstances, viruses do exert a selection pressure on wild plants, if qualitative resistance is a major defense strategy to viruses in nature, or even if characterized genes determining qualitative resistance to viruses did indeed evolve in response to virus infection. Here, we review evidence supporting plant-virus coevolution and point to areas in need of attention to understand the role of viruses in plant ecosystem dynamics, and the factors that determine virus emergence in crops.

Tomato plants transformed with the inhibitor-of-virus-replication gene are partially resistant to Botrytis cinerea

Tomato plants transformed with a cDNA clone encoding the inhibitor-of-virus-replication (IVR) gene were partially resistant to Botrytis cinerea. This resistance was observed as a significant reduction in the size of lesions induced by the fungus in transgenic plants compared with the lesions on the nontransgenic control plants. This resistance was weakened when plants were kept at an elevated temperature, 32 degrees C, before inoculation with B. cinerea compared with plants kept at 17 to 22 degrees C prior to inoculation. Resistance correlated with the presence of IVR transcripts, as detected by reverse transcription-polymerase chain reaction. This is one of the few cases in which a gene associated with resistance to a virus also seems to be involved in resistance to a fungal disease.

WRR4, a broad-spectrum TIR-NB-LRR gene from Arabidopsis thaliana that confers white rust resistance in transgenic oilseed Brassica crops

White blister rust caused by Albugo candida (Pers.) Kuntze is a common and often devastating disease of oilseed and vegetable brassica crops worldwide. Physiological races of the parasite have been described, including races 2, 7 and 9 from Brassica juncea, B. rapa and B. oleracea, respectively, and race 4 from Capsella bursa-pastoris (the type host). A gene named WRR4 has been characterized recently from polygenic resistance in the wild brassica relative Arabidopsis thaliana (accession Columbia) that confers broad-spectrum white rust resistance (WRR) to all four of the above Al. candida races. This gene encodes a TIR-NB-LRR (Toll-like/interleukin-1 receptor-nucleotide binding-leucine-rich repeat) protein which, as with other known functional members in this subclass of intracellular receptor-like proteins, requires the expression of the lipase-like defence regulator, enhanced disease susceptibility 1 (EDS1). Thus, we used RNA interference-mediated suppression of EDS1 in a white rust-resistant breeding line of B. napus (transformed with a construct designed from the A. thaliana EDS1 gene) to determine whether defence signalling via EDS1 is functionally intact in this oilseed brassica. The eds1-suppressed lines were fully susceptible following inoculation with either race 2 or 7 isolates of Al. candida. We then transformed white rust-susceptible cultivars of B. juncea (susceptible to race 2) and B. napus (susceptible to race 7) with the WRR4 gene from A. thaliana. The WRR4-transformed lines were resistant to the corresponding Al. candida race for each host species. The combined data indicate that WRR4 could potentially provide a novel source of white rust resistance in oilseed and vegetable brassica crops.

Endosome-associated CRT1 functions early in resistance gene-mediated defense signaling in Arabidopsis and tobacco

Resistance gene-mediated immunity confers protection against pathogen infection in a wide range of plants. A genetic screen for Arabidopsis thaliana mutants compromised for recognition of turnip crinkle virus previously identified CRT1, a member of the GHKL ATPase/kinase superfamily. Here, we demonstrate that CRT1 interacts with various resistance proteins from different structural classes, and this interaction is disrupted when these resistance proteins are activated. The Arabidopsis mutant crt1-2 crh1-1, which lacks CRT1 and its closest homolog, displayed compromised resistance to avirulent Pseudomonas syringae and Hyaloperonospora arabidopsidis. Additionally, resistance-associated hypersensitive cell death was suppressed in Nicotiana benthamiana silenced for expression of CRT1 homolog(s). Thus, CRT1 appears to be a general factor for resistance gene-mediated immunity. Since elevation of cytosolic calcium triggered by avirulent P. syringae was compromised in crt1-2 crh1-1 plants, but cell death triggered by Nt MEK2(DD) was unaffected in CRT1-silenced N. benthamiana, CRT1 likely functions at an early step in this pathway. Genome-wide transcriptome analysis led to identification of CRT1-Associated genes, many of which are associated with transport processes, responses to (a)biotic stress, and the endomembrane system. Confocal microscopy and subcellular fractionation revealed that CRT1 localizes to endosome-like vesicles, suggesting a key process in resistance protein activation/signaling occurs in this subcellular compartment.

Mechanisms of recognition in dominant R gene mediated resistance

One branch of plant innate immunity is mediated through what is traditionally known as race-specific or gene-for-gene resistance wherein the outcome of an attempted infection is determined by the genotypes of both the host and the pathogen. Dominant plant disease resistance (R) genes confer resistance to a variety of biotrophic pathogens, including viruses, encoding corresponding dominant avirulence (Avr) genes. R genes are among the most highly variable plant genes known, both within and between populations. Plant genomes encode hundreds of R genes that code for NB-LRR proteins, so named because they posses nucleotide-binding (NB) and leucine-rich repeat (LRR) domains. Many matching pairs of NB-LRR and Avr proteins have been identified as well as cellular proteins that mediate R/Avr interactions, and the molecular analysis of these interactions have led to the formulation of models of how products of R genes recognize pathogens. Data from multiple NB-LRR systems indicate that the LRR domains of NB-LRR proteins determine recognition specificity. However, recent evidence suggests that NB-LRR proteins have co-opted cellular recognition co-factors that mediate interactions between Avr proteins and the N-terminal domains of NB-LRR proteins.

Altering expression of benzoic acid/salicylic acid carboxyl methyltransferase 1 compromises systemic acquired resistance and PAMP-triggered immunity in arabidopsis

Methyl salicylate (MeSA), which is synthesized in plants from salicylic acid (SA) by methyltransferases, has roles in defense against microbial and insect pests. Most of the MeSA that accumulates after pathogen attack is synthesized by benzoic acid/SA carboxyl methyltransferase 1 (AtBSMT1). To investigate the role of AtBSMT1 in plant defense, transgenic Arabidopsis with altered AtBSMT1 function or expression were assessed for their ability to resist pathogen infection. A knockout mutant (Atbsmt1) failed to accumulate MeSA following pathogen infection; these plants also failed to accumulate SA or its glucoside in the uninoculated leaves and did not develop systemic acquired resistance (SAR). However, the Atbsmt1 mutant exhibited normal levels of effector-triggered immunity and pathogen-associated molecular pattern (PAMP)-triggered immunity to Pseudomonas syringae and Hyaloperonospora arabidopsidis. Analyses of transgenic Arabidopsis plants overexpressing AtBSMT1 revealed that they accumulate elevated levels of MeSA in pathogen-infected leaves but fail to develop SAR. Since the levels of SA and its glucoside were reduced in uninoculated systemic leaves of these plants whereas MeSA levels were elevated, AtBSMT1-mediated conversion of SA to MeSA probably compromised SAR development by suppressing SA accumulation in uninoculated leaves. PAMP-triggered immunity also was compromised in the AtBSMT1 overexpressing plants, although effector-triggered immunity was not.

Hyaloperonospora Arabidopsidis as a pathogen model

Hyaloperonospora arabidopsidis, a downy mildew pathogen of the model plant Arabidopsis, has been very useful in the understanding of the relationship between oomycetes and their host plants. This naturally coevolving pathosystem contains an amazing level of genetic diversity in host resistance and pathogen avirulence proteins. Oomycete effectors identified to date contain a targeting motif, RXLR, enabling effector entry into the host cell. The availability of the H. arabidopsidis genome sequence has enabled bioinformatic analyses to identify at least 130 RXLR effectors, potentially used to quell the host's defense mechanism and manipulate other host cellular processes. Currently, these effectors are being used to reveal their targets in the host cell. Eventually this will result in an understanding of the mechanisms used by a pathogen to sustain a biotrophic relationship with a plant.

Maintenance of genetic variation in plants and pathogens involves complex networks of gene-for-gene interactions

The RPP13 [recognition of Hyaloperonospora arabidopsidis (previously known as Peronospora parasitica)] resistance (R) gene in Arabidopsis thaliana exhibits the highest reported level of sequence diversity among known R genes. Consistent with a co-evolutionary model, the matching effector protein ATR13 (A. thaliana-recognized) from H. arabidopsidis reveals extreme levels of allelic diversity. We isolated 23 new RPP13 sequences from a UK metapopulation, giving a total of 47 when combined with previous studies. We used these in functional studies of the A. thaliana accessions for their resistance response to 16 isolates of H. arabidopsidis. We characterized the molecular basis of recognition by the expression of the corresponding ATR13 genes from these 16 isolates in these host accessions. This allowed the determination of which alleles of RPP13 were responsible for pathogen recognition and whether recognition was dependent on the RPP13/ATR13 combination. Linking our functional studies with phylogenetic analysis, we determined that: (i) the recognition of ATR13 is mediated by alleles in just a single RPP13 clade; (ii) RPP13 alleles in other clades have evolved the ability to detect other pathogen ATR protein(s); and (iii) at least one gene, unlinked to RPP13 in A. thaliana, detects a different subgroup of ATR13 alleles.

Virus resistance induced by NB-LRR proteins involves Argonaute4-dependent translational control

Active resistance to viruses is afforded by plant disease resistance (R) genes, which encode proteins with nucleotide-binding (NB) and leucine-rich repeat (LRR) domains. Upon recognition of pathogen-derived elicitors, these NB-LRR proteins are thought to initiate a number of signaling pathways that lead to pathogen restriction. However, little is known about the molecular mechanisms that ultimately curtail virus accumulation. Here, we show that the co-expression of a plant NB-LRR protein with its cognate elicitor results in an antiviral response that inhibits the translation of virus-encoded proteins in Nicotiana benthamiana. This antiviral response is dependent on viral cis elements, and, upon activation of the NB-LRR protein, viral transcripts accumulate but do not associate with ribosomes. The induced inhibition of viral transcript translation and NB-LRR-mediated virus resistance were compromised by the downregulation of Argonaute4-like genes. Argonaute proteins have been implicated in small RNA-mediated RNA degradation, and in degradation-independent translational control. Our results suggest that the engagement of Argonaute proteins in the specific translational control of viral transcripts is a key factor in virus resistance mediated by NB-LRR proteins.

The fractionated orthology of Bs2 and Rx/Gpa2 supports shared synteny of disease resistance in the Solanaceae

Comparative genomics provides a powerful tool for the identification of genes that encode traits shared between crop plants and model organisms. Pathogen resistance conferred by plant R genes of the nucleotide-binding-leucine-rich-repeat (NB-LRR) class is one such trait with great agricultural importance that occupies a critical position in understanding fundamental processes of pathogen detection and coevolution. The proposed rapid rearrangement of R genes in genome evolution would make comparative approaches tenuous. Here, we test the hypothesis that orthology is predictive of R-gene genomic location in the Solanaceae using the pepper R gene Bs2. Homologs of Bs2 were compared in terms of sequence and gene and protein architecture. Comparative mapping demonstrated that Bs2 shared macrosynteny with R genes that best fit criteria determined to be its orthologs. Analysis of the genomic sequence encompassing solanaceous R genes revealed the magnitude of transposon insertions and local duplications that resulted in the expansion of the Bs2 intron to 27 kb and the frequently detected duplications of the 5'-end of R genes. However, these duplications did not impact protein expression or function in transient assays. Taken together, our results support a conservation of synteny for NB-LRR genes and further show that their distribution in the genome has been consistent with global rearrangements.

Visual markers for detecting gene conversion directly in the gametes of Arabidopsis thaliana

Measuring meiotic gene conversion is important both because of its role in the fundamental mechanisms of meiotic recombination and because of its influence on linkage relationships and allelic diversity in the genome. Historically, gene conversion has been most thoroughly examined in fungal organisms through the use of tetrad analysis. Here we describe a method for using tetrad analysis in the model plant Arabidopsis thaliana to detect and quantify gene conversion events - a resource unavailable in most other higher eukaryotic model systems.

High level expression of a virus resistance gene, RCY1, confers extreme resistance to Cucumber mosaic virus in Arabidopsis thaliana

A coiled coil-nucleotide binding site-leucine rich repeat-type resistance gene, RCY1, confers resistance to a yellow strain of Cucumber mosaic virus, CMV(Y), in Arabidopsis thaliana ecotype C24. Resistance to CMV(Y) in C24 is accompanied by a hypersensitive response (HR) that is characterized by the development of necrotic local lesions at the primary infection sites. To further study the HR and resistance to CMV(Y) in ecotype Col-0, which is susceptible to CMV(Y), Col-0 were transformed with RCY1. Systemic spread of CMV(Y) was completely suppressed in RCY1-transformed Col-0 (Col::pRCY1 lines 2 to 6), whereas virulent strain CMV(B2) spread and multiplied systemically in these transgenic lines similar to that in wild-type Col-0. Interestingly, the resistant phenotype of Col::pRCY1 varied among the lines. In lines 3 and 6, in which levels of RCY1 transcript were similar to that in wild-type C24, the HR and resistance to CMV(Y) was induced. Line 4, which expresses moderately elevated levels of RCY1 transcript, exhibited moderately enhanced resistance compared with that in C24 or line 3. In contrast, lines 2 and 5, which highly overexpress the RCY1 gene, did not exhibit either visible lesions or a micro-HR on the inoculated leaves. Moreover, virus coat protein was not detected in either inoculated or noninoculated upper leaves of these two lines, suggesting that extreme resistance (ER) to CMV(Y) was induced by high levels of expression of RCY1. Furthermore, in transgenic lines expressing hemagglutinin (HA) epitope-tagged RCY1 (Col::pRCY1-HA), high levels of accumulation of RCY1-HA protein were also correlated with the ER phenotype. Global gene expression analysis in line 2, which highly overexpresses RCY1, indicated that expression of several defense-related genes were constitutively elevated compared with wild-type Col-0. Despite this, line 2 did not have enhanced resistance to other avirulent and virulent pathogens. Take together, constitutive accumulation of high levels of RCY1 protein appears to regulate the strength of RCY1-conferred resistance in a gene-for-gene manner and implies that ER and HR-associated resistance differ only in the strength of resistance.

Characterization of resistance mechanism in transgenic Nicotiana benthamiana containing Turnip crinkle virus coat protein

Two transgenic lines, of Nicotiana benthamiana expressing Turnip crinkle virus (TCV)-coat protein (CP) gene with contrasting phenotype, the highest (#3) and the lowest (#18) CP expressers, were selected and challenged with the homologous TCV. The former, the highest expresser, showed nearly five times more CP expression than the latter. Progenies of #3 and #18 lines showed 30 and 100% infection rates, respectively. The infected progenies of #3 line showed mild and delayed symptom with TCV. This is a coat protein-mediated resistance (CP-MR), and its resistance level is directly proportional to CP transgene expression. However, CP-MR of the transgenic plants was specific only for TCV but not for heterologous viruses. Newly growing leaves of those infected progenies of #3 line did not show any visible symptoms at 4-week post-inoculation (wpi) with TCV, suggesting a reversal from infection. This was confirmed by RT-PCR analysis with the disappearance of the target at 4 wpi. This is a case of RNA-mediated resistance, and a threshold level of transgene expression may be needed to achieve the silent state. To confirm the RNA silencing, we infiltrated Agrobacterium carrying TCV-CP into leaves of progenies of #3 and performed RT-PCR analysis. The results indicate that TCV-CP's suppressor activity against RNA silencing itself can be silenced by the homologous expression of TCV-CP in the transgenic plants. The transgenic plants containing TCV-CP seem to be a model system to study viral protection mediated by a combination of protein and RNA silencing.

HRT-mediated hypersensitive response and resistance to Turnip crinkle virus in Arabidopsis does not require the function of TIP, the presumed guardee protein

The Arabidopsis resistance protein HRT recognizes the Turnip crinkle virus (TCV) coat protein (CP) to induce a hypersensitive response (HR) in the resistant ecotype Di-17. The CP also interacts with a nuclear-targeted NAC family of host transcription factors, designated TIP (TCV-interacting protein). Because binding of CP to TIP prevents nuclear localization of TIP, it has been proposed that TIP serves as a guardee for HRT. Here, we have tested the requirement for TIP in HRT-mediated HR and resistance by analyzing plants carrying knockout mutation in the TIP gene. Our results show that loss of TIP does not alter HR or resistance to TCV. Furthermore, the mutation in TIP neither impaired the salicylic acid-mediated induction of HRT expression nor the enhanced resistance conferred by overexpression of HRT. Strikingly, the mutation in TIP resulted in increased replication of TCV and Cucumber mosaic virus, suggesting that TIP may play a role in basal resistance but is not required for HRT-mediated signaling.

Genetic and histological studies on the delayed systemic movement of Tobacco Mosaic Virus in Arabidopsis thaliana

BACKGROUND

Viral infections and their spread throughout a plant require numerous interactions between the host and the virus. While new functions of viral proteins involved in these processes have been revealed, current knowledge of host factors involved in the spread of a viral infection is still insufficient. In Arabidopsis thaliana, different ecotypes present varying susceptibilities to Tobacco mosaic virus strain U1 (TMV-U1). The rate of TMV-U1 systemic movement is delayed in ecotype Col-0 when compared with other 13 ecotypes.We followed viral movement through vascular tissue in Col-0 plants by electronic microscopy studies. In addition, the delay in systemic movement of TMV-U1 was genetically studied.

RESULTS

TMV-U1 reaches apical leaves only after 18 days post rosette inoculation (dpi) in Col-0, whereas it is detected at 9 dpi in the Uk-4 ecotype. Genetic crosses between Col-0 and Uk-4 ecotypes, followed by analysis of viral movement in F1 and F2 populations, revealed that this delayed movement correlates with a recessive, monogenic and nuclear locus. The use of selected polymorphic markers showed that this locus, denoted DSTM1 (Delayed Systemic Tobamovirus Movement 1), is positioned on the large arm of chromosome II. Electron microscopy studies following the virion's route in stems of Col-0 infected plants showed the presence of curved structures, instead of the typical rigid rods of TMV-U1. This was not observed in the case of TMV-U1 infection in Uk-4, where the observed virions have the typical rigid rod morphology.

CONCLUSION

The presence of defectively assembled virions observed by electron microscopy in vascular tissue of Col-0 infected plants correlates with a recessive delayed systemic movement trait of TMV-U1 in this ecotype.

The involvement of the Arabidopsis CRT1 ATPase family in disease resistance protein-mediated signaling

Resistance (R) gene-mediated immunity provides plants with rapid and strain-specific protection against pathogen infection. Our recent study using the genetically tractable Arabidopsis and turnip crinkle virus (TCV) pathosystem revealed a novel component, named CRT1 (compromised for recognition of the TCV CP), that is involved in general R gene-mediated signaling, including that mediated by HRT, an R gene against TCV. The Arabidopsis CRT1 gene family contains six additional members, of which two share high homology to CRT1 (75 and 81% a.a. identity); either CRT1 or its closest homolog restore the cell death phenotype suppressed by crt1. Analysis of single knock-out mutants for CRT1 and its closest homologs suggest that each may have unique and redundant functions. Here, we provide insight into the screening conditions that enabled identification of a mutant gene despite the presence of functionally redundant family members. We also discuss a potential mechanism that may regulate the interaction between CRT1 and R proteins.

Overexpression of the Arabidopsis thaliana EDS5 gene enhances resistance to viruses

The Arabidopsis thaliana ENHANCED DISEASE SUSCEPTIBILITY 5 gene (EDS5) is required for salicylic acid (SA) synthesis in pathogen-challenged plants. SA and EDS5 have an important role in the Arabidopsis RCY1 gene-conferred resistance against the yellow strain of Cucumber mosaic virus [CMV(Y)], a Bromoviridae, and HRT-conferred resistance against the Tombusviridae, Turnip crinkle virus (TCV). EDS5 expression and SA accumulation are induced in response to CMV(Y) inoculation in the RCY1-bearing ecotype C24. To further discern the involvement of EDS5 in Arabidopsis defence against viruses, we overexpressed the EDS5 transcript from the constitutively expressed Cauliflower mosaic virus 35S gene promoter in ecotype C24. In comparison to the non-transgenic control, the basal level of salicylic acid (SA) was twofold higher in the 35S:EDS5 plant. Furthermore, viral spread and the size of the hypersensitive response associated necrotic local lesions (NLL) were more highly restricted in CMV(Y)-inoculated 35S:EDS5 than in the non-transgenic plant. The heightened restriction of CMV(Y) spread was paralleled by more rapid induction of the pathogenesis-related gene, PR-1, in the CMV(Y)-inoculated 35S:EDS5 plant. The 35S:EDS5 plant also had heightened resistance to the virulent CMV strain, CMV(B2), and TCV. These results suggest that, in addition to R gene-mediated gene-for-gene resistance, EDS5 is also important for basal resistance to viruses. However, while expression of the Pseudomonas putida nahG gene, which encodes the SA-degrading salicylate hydroxylase, completely suppressed 35S:EDS5-conferred resistance against CMV(Y) and TCV, it only partially compromised resistance against CMV(B2), indicating that SA-dependent and -independent mechanisms are associated with 35S:EDS5-conferred resistance against viruses.

Frequent sequence exchanges between homologs of RPP8 in Arabidopsis are not necessarily associated with genomic proximity

Disease resistance (R) genes are often clustered in plant genomes and may exhibit heterogeneous rates of evolution. Some (type I R genes) have evolved rapidly through frequent sequence exchanges, while others (type II R genes) have evolved independently and tend to be conserved in different genotypes or related species. The RPP8 resistance gene in Arabidopsis thaliana is located at a complex locus that also harbors the sequence-related resistance genes HRT and RCY1 in different ecotypes. We sequenced 98 homologs of RPP8 from A. thaliana, Arabidopsis arenosa and Arabidopsis lyrata. Three lineages of type II and one lineage of type I RPP8 homologs were identified. Two of the three lineages of type II genes are each represented by a single-copy locus on either chromosomes I or V. Chromosome V contains two small clusters of RPP8 paralogs. One cluster contains both type I and type II genes and the other comprises only type I genes. These multi-copy loci have expanded and contracted through unequal crossovers, which have generated chimeric genes as well as variations in copy number. Sequence exchanges, most likely gene conversions, were detected between RPP8 homologs that are spatially separated by 2.2 Mb and 12 cM. The sequence exchanges between type I homologs within a locus have been more frequent than sequence exchanges between homologs from two different loci, indicating the influence of chromosomal position on the evolution of these R genes. However, physical distance was not the only factor determining the frequency of sequence exchange, because some closely linked paralogs exhibited little sequence exchange. At least two distinct lineages of type II RPP8 homologs were identified in different species, with obvious allelic/orthologous relationships within each lineage. Therefore, the differentiation of type I and type II RPP8 homologs seems to have occurred before speciation of A. thaliana, A. arenosa and A. lyrata.

R protein activation: another player revealed

Resistance proteins play an integral role in plant innate immunity by perceiving pathogens and triggering defense responses. In this issue of Cell Host & Microbe, Kang et al. uncover CRT1, an ATPase essential for resistance to turnip crinkle virus in Arabidopsis mediated by the Resistance (R) protein HRT. CRT1 interacts with an array of R proteins in vivo, suggesting that it plays a role in R protein activation.

CRT1, an Arabidopsis ATPase that interacts with diverse resistance proteins and modulates disease resistance to turnip crinkle virus

Plant immunity frequently involves the recognition of pathogen-encoded avirulence (avr) factors by their corresponding plant resistance (R) proteins. This triggers the hypersensitive response (HR) where necrotic lesions formed at the site(s) of infection help restrict pathogen spread. HRT is an Arabidopsis R protein required for resistance to turnip crinkle virus (TCV). In a genetic screen for mutants compromised in the recognition of TCV's avr factor, we identified crt1 (compromised recognition of TCV), a mutant that prematurely terminates an ATPase protein. Following TCV infection, crt1 developed a spreading HR and failed to control viral replication and spread. crt1 also suppressed HR-like cell death induced by ssi4, a constitutively active R protein, and by Pseudomonas syringae carrying avrRpt2. Furthermore, CRT1 interacts with HRT, SSI4, and two other R proteins, RPS2 and Rx. These data identify CRT1 as an important mediator of defense signaling triggered by distinct classes of R proteins.

Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula

The nucleotide-binding site (NBS)-Leucine-rich repeat (LRR) gene family accounts for the largest number of known disease resistance genes, and is one of the largest gene families in plant genomes. We have identified 333 nonredundant NBS-LRRs in the current Medicago truncatula draft genome (Mt1.0), likely representing 400 to 500 NBS-LRRs in the full genome, or roughly 3 times the number present in Arabidopsis (Arabidopsis thaliana). Although many characteristics of the gene family are similar to those described on other plant genomes, several evolutionary features are particularly pronounced in M. truncatula, including a high degree of clustering, evidence of significant numbers of ectopic translocations from clusters to other parts of the genome, a small number of more evolutionarily stable NBS-LRRs, and numerous truncations and fusions leading to novel domain compositions. The gene family clearly has had a large impact on the structure of the genome, both through ectopic translocations (potentially, a means of seeding new NBS-LRR clusters), and through two extraordinarily large superclusters. Chromosome 6 encodes approximately 34% of all TIR-NBS-LRRs, while chromosome 3 encodes approximately 40% of all coiled-coil-NBS-LRRs. Almost all atypical domain combinations are in the TIR-NBS-LRR subfamily, with many occurring within one genomic cluster. This analysis shows the gene family not only is important functionally and agronomically, but also plays a structural role in the genome.

Characterization of natural and induced variation in the LOV1 gene, a CC-NB-LRR gene conferring victorin sensitivity and disease susceptibility in Arabidopsis

The fungus Cochliobolus victoriae, the causal agent of Victoria blight, produces a compound called victorin that is required for pathogenicity of the fungus. Victorin alone reproduces disease symptoms on sensitive plants. Victorin sensitivity and susceptibility to C. victoriae were originally described on oats but have since been identified on Arabidopsis thaliana. Victorin sensitivity and disease susceptibility in Arabidopsis are conferred by LOV1, a coiled-coil-nucleotide-binding-leucine-rich repeat (CC-NB-LRR) protein. We sequenced the LOV1 gene from 59 victorin-insensitive mutants and found that the spectrum of mutations causing LOV1 loss of function was similar to that found to cause loss of function of RPM1, a CC-NB-LRR resistance protein. Also, many of the mutated residues in LOV1 are in conserved motifs required for resistance protein function. These data indicate that LOV1 may have a mechanism of action similar to resistance proteins. Victorin sensitivity was found to be the prevalent phenotype in a survey of 30 Arabidopsis ecotypes, and we found very little genetic variation among LOV1 alleles. As selection would not be expected to preserve a functional LOV1 gene to confer victorin sensitivity and disease susceptibility, we propose that LOV1 may function as a resistance gene to a naturally-occurring pathogen of Arabidopsis.

A RanGAP protein physically interacts with the NB-LRR protein Rx, and is required for Rx-mediated viral resistance

Race-specific disease resistance in plants is mediated by the products of host disease resistance (R) genes. Plant genomes possess hundreds of R gene homologs encoding nucleotide-binding and leucine-rich repeat (NB-LRR) proteins. NB-LRR proteins induce a disease resistance response following recognition of pathogen-encoded avirulence (Avr) proteins. However, little is known about the general mechanisms by which NB-LRR proteins recognize Avr proteins or how they subsequently induce defense responses. The Rx NB-LRR protein of potato confers resistance to potato virus X (PVX). Using a co-purification strategy, we have identified a Ran GTPase-activating protein (RanGAP2) as an Rx-interacting protein. We show by co-immunoprecipitation that this interaction is mediated in planta through the putative signaling domain at the Rx amino terminus. Overexpression of RanGAP2 results in activation of certain Rx derivatives. Likewise, knocking down RanGAP2 expression in Nicotiana benthamiana by virus-induced gene silencing compromises Rx-mediated resistance to PVX. Thus, we have demonstrated a novel role for a RanGAP in the function of a plant disease resistance response.

Silencing of the major family of NBS-LRR-encoding genes in lettuce results in the loss of multiple resistance specificities

The RGC2 gene cluster in lettuce (Lactuca sativa) is one of the largest known families of genes encoding nucleotide binding site-leucine-rich repeat (NBS-LRR) proteins. One of its members, RGC2B, encodes Dm3 which determines resistance to downy mildew caused by the oomycete Bremia lactucae carrying the cognate avirulence gene, Avr3. We developed an efficient strategy for analysis of this large family of low expressed genes using post-transcriptional gene silencing (PTGS). We transformed lettuce cv. Diana (carrying Dm3) using chimeric gene constructs designed to simultaneously silence RGC2B and the GUS reporter gene via the production of interfering hairpin RNA (ihpRNA). Transient assays of GUS expression in leaves accurately predicted silencing of both genes and were subsequently used to assay silencing in transgenic T(1) plants and their offspring. Levels of mRNA were reduced not only for RGC2B but also for all seven diverse RGC2 family members tested. We then used the same strategy to show that the resistance specificity encoded by the genetically defined Dm18 locus in lettuce cv. Mariska is the result of two resistance specificities, only one of which was silenced by ihpRNA derived from RGC2B. Analysis of progeny from crosses between transgenic, silenced tester stocks and lettuce accessions carrying other resistance genes previously mapped to the RGC2 locus indicated that two additional resistance specificities to B. lactucae, Dm14 and Dm16, as well as resistance to lettuce root aphid (Pemphigus bursarius L.), Ra, are encoded by RGC2 family members.

Mapping of genome-wide resistance gene analogs (RGAs) in maize (Zea mays L.)

Isolation and mapping of genome-wide resistance (R) gene analogs (RGAs) is of importance in identifying candidate(s) for a particular resistance gene/QTL. Here we reported our result in mapping totally 228 genome-wide RGAs in maize. By developing RGA-tagged markers and subsequent genotyping a population consisting of 294 recombinant inbred lines (RILs), 67 RGAs were genetically mapped on maize genome. Meanwhile, in silico mapping was conducted to anchor 113 RGAs by comparing all 228 RGAs to those anchored EST and BAC/BAC-end sequences via tblastx search (E-value < 10(-20)). All RGAs from different mapping efforts were integrated into the existing SSR linkage map. After accounting for redundancy, the resultant RGA linkage map was composed of 153 RGAs that were mapped onto 172 loci on maize genome, and the mapped RGAs accounted for approximate three quarters of the genome-wide RGAs in maize. The extensive co-localizations were observed between mapped RGAs and resistance gene/QTL loci, implying the usefulness of this RGA linkage map in R gene cloning via candidate gene approach.

Plastidial fatty acid levels regulate resistance gene-dependent defense signaling in Arabidopsis

In Arabidopsis, resistance to Turnip Crinkle Virus (TCV) depends on the resistance (R) gene, HRT, and the recessive locus rrt. Resistance also depends on salicylic acid (SA), EDS1, and PAD4. Exogenous application of SA confers resistance in RRT-containing plants by increasing HRT transcript levels in a PAD4-dependent manner. Here we report that reduction of oleic acid (18:1) can also induce HRT gene expression and confer resistance to TCV. However, the 18:1-regulated pathway is independent of SA, rrt, EDS1, and PAD4. Reducing the levels of 18:1, via a mutation in the SSI2-encoded stearoyl-acyl carrier protein-desaturase, or by exogenous application of glycerol, increased transcript levels of HRT as well as several other R genes. Second-site mutations in the ACT1-encoded glycerol-3-phosphate acyltransferase or GLY1-encoded glycerol-3-phosphate dehydrogenase restored 18:1 levels in HRT ssi2 plants and reestablished a dependence on rrt. Resistance to TCV and HRT gene expression in HRT act1 plants was inducible by SA but not by glycerol, whereas that in HRT pad4 plants was inducible by glycerol but not by SA. The low 18:1-mediated induction of R gene expression was also dependent on ACT1 but independent of EDS1, PAD4, and RAR1. Intriguingly, TCV inoculation did not activate this 18:1-regulated pathway in HRT plants, but instead resulted in the induction of several genes that encode 18:1-synthesizing isozymes. These results suggest that the 18:1-regulated pathway may be specifically targeted during pathogen infection and that altering 18:1 levels may serve as a unique strategy for promoting disease resistance.

[Host factors and their relevance to virus infection in plants]

Virus infection is established when viral proteins can interact with host factors to execute replication and/or cell-to-cell movement. Even after the virus infection has started, host resistance reactions, if trigged, would suppress further virus propagation. We would like to introduce what we understand about host factors as determinants of infection establishment and as key resistance molecules. Genome-wide information of Arabidopsis is providing us much information about such host factors involved in virus infection.

Identification and characterization of NBS-LRR class resistance gene analogs in faba bean (Vicia faba L.) and chickpea (Cicer arietinum L.)

A PCR approach with degenerate primers designed from conserved NBS-LRR (nucleotide binding site-leucine-rich repeat) regions of known disease-resistance (R) genes was used to amplify and clone homologous sequences from 5 faba bean (Vicia faba) lines and 2 chickpea (Cicer arietinum) accessions. Sixty-nine sequenced clones showed homologies to various R genes deposited in the GenBank database. The presence of internal kinase-2 and kinase-3a motifs in all the sequences isolated confirm that these clones correspond to NBS-containing genes. Using an amino-acid sequence identity of 70% as a threshold value, the clones were grouped into 10 classes of resistance-gene analogs (RGA01 to RGA10). The number of clones per class varied from 1 to 30. RGA classes 1, 6, 8, and 9 were comprised solely of clones isolated from faba bean, whereas classes 2, 3, 4, 5, and 7 included only chickpea clones. RGA10, showing a within-class identity of 99%, was the only class consisting of both faba bean and chickpea clones. A phylogenetic tree, based on the deduced amino-acid sequences of 12 representative clones from the 10 RGA classes and the NBS domains of 6 known R genes (I2 and Prf from tomato, RPP13 from Arabidopsis, Gro1-4 from potato, N from tobacco, L6 from flax), clearly indicated the separation between TIR (Toll/interleukin-1 receptor homology: Gro1-4, L6, N, RGA05 to RGA10)- and non-TIR (I2, Prf, RPP13, RGA01 to RGA04)-type NBS-LRR sequences. The development of suitable polymorphic markers based on cloned RGA sequences to be used in genetic mapping will facilitate the assessment of their potential linkage relationships with disease-resistance genes in faba bean and chickpea. This work is the first to report on faba bean RGAs.

Sources of natural resistance to plant viruses: status and prospects

SUMMARY Globally, virus diseases are common in agricultural crops and have a major agronomic impact. They are countered through the deployment of genetic resistance against the virus, or through the use of a range of farming practices based upon the propagation of virus-free plant material and the exclusion of the virus vectors from the growing crop. We review here the current status of our knowledge of natural virus resistance genes, and consider the future prospects for the deployment of these genes against virus infection.

Unique pattern of R-gene variation within populations in Arabidopsis

An understanding of the variation pattern in disease resistance (R) genes is essential for its use in breeding programs aimed at neutralizing the threat of pathogens. Although the variation between populations is well known, there is little research about R-gene variation patterns within populations. Here, we investigate the polymorphism at three R-gene loci of 39 individual plants from nine populations of Arabidopsis thaliana. Our data suggest that alleles of each locus from individuals within a local population were either nearly identical, or highly diverse as ones between populations. The vast majority (92.5%) of within-population variation was shared globally, with high levels of allelic diversity (up to 11.7%) and abundant diverse-alleles. This unique pattern of within-population variation at R-loci suggests that individual plants within a population had the great potential to maintain a high level of globally-shared polymorphisms, and that the diversifying selection was the major force maintaining such polymorphisms. Consequently, the shared-polymorphism became recyclable for new R-genes, as the corresponding avirulence re-emerges in pathogen populations.

Elicitors, effectors, and R genes: the new paradigm and a lifetime supply of questions

The plant basal immune system can detect broadly present microbe-associated molecular patterns (MAMPs, also called PAMPs) and induce defenses, but adapted microbes express a suite of effector proteins that often act to suppress these defenses. Plants have evolved other receptors (R proteins) that detect these pathogen effectors and activate strong defenses. Pathogens can subsequently alter or delete their recognized effectors to avoid defense elicitation, at risk of a fitness cost associated with loss of those effectors. Significant research progress is revealing, among other things, mechanisms of MAMP perception, the host defense processes and specific host proteins that pathogen effectors target, the mechanisms of R protein activation, and the ways in which pathogen effector suites and R genes evolve. These findings carry practical ramifications for resistance durability and for future resistance engineering. The present review uses numerous questions to help clarify what we know and to identify areas that are ripe for further investigation.

Single amino acid alterations in Arabidopsis thaliana RCY1 compromise resistance to Cucumber mosaic virus, but differentially suppress hypersensitive response-like cell death

Resistance to an yellow strain of Cucumber mosaic virus [CMV(Y)] in Arabidopsis thaliana ecotype C24 is conferred by the CC-NBS-LRR type R gene, RCY1. RCY1-conferred resistance is accompanied by a hypersensitive response (HR), which is characterized by the development of necrotic local lesion (NLL) at the site of infection that restricts viral spread. To further characterize the role of RCY1 in NLL formation we have identified six recessive CMV(Y)-susceptible rcy1 mutants, four of which contain single amino acid substitutions in RCY1: rcy1-2 contains a D to N substitution in the CC domain, rcy1-3 and rcy1-4 contain R to K and E to K substitutions, respectively, in the LRR domain, and rcy1-6 contains a W to C substitution in the NBS domain. The rcy1-5 and rcy1-7 contain nonsense mutations in the LRR and NBS domains, respectively. Although the virus systemically spread in all six rcy1 mutants, HR-associated cell death was differentially induced in these mutants. In comparison to the wild type C24 plant, HR was not observed in the CMV(Y)-inoculated leaves of the rcy1-3, rcy1-5, rcy1-6 and rcy1-7 mutants. In contrast, delayed NLL development was observed in the virus inoculated leaves of the rcy1-2 and rcy1-4 mutants. In addition, necrosis accompanied by elevated accumulation of PR gene transcript also appeared in the non-inoculated leaves of the rcy1-2 and rcy1-4 mutants. Trans-complementation was observed between the rcy1-2 and rcy1-4 alleles; in F1 plants derived from a cross between rcy1-2 and rcy1-4, HR associated cell death was accelerated and systemic spread of the virus was partially suppressed than in the homozygous rcy1-2 and rcy1-4 plants. Our results suggest that the CC, NBS and LRR domains of RCY1 are required for restriction of virus spread but differentially impact the induction of HR-like cell death. Furthermore, these results also predict inter-molecular interaction involving RCY1 in Arabidopsis resistance to CMV(Y).

Plant signal transduction and defense against viral pathogens

Viral infection of plants is a complex process whereby the virus parasitizes the host and utilizes its cellular machinery to multiply and spread. In turn, plants have evolved signaling mechanisms that ultimately limit the ingress and spread of viral pathogens, resulting in resistance. By dissecting the interaction between host and virus, knowledge of signaling pathways that are deployed for resistance against these pathogens has been gained. Advances in this area have shown that resistance signaling against viruses does not follow a prototypic pathway but rather different host factors may play a role in resistance to different viral pathogens. Some components of viral resistance signaling pathways also appear to be conserved with those functioning in signaling pathways operational against other nonviral pathogens, however, these pathways may or may not overlap. This review aims to document the advances that have improved our understanding of plant resistance to viruses.

Contrasting patterns of evolution between allelic groups at a single locus in Arabidopsis

Heterogeneities in evolutionary pattern among different loci are commonly observed. To see whether the heterogeneity can also be observed among allelic groups in a single locus, we investigated the coding sequence and the flanking regions of Rpp13, a disease resistance gene in up to 60 accession lines from worldwide populations in Arabidopsis thaliana. An extraordinarily high level of polymorphism (pi=0.098) and four distinct clades were found in the leucine-rich repeat (LRR) region in this gene. No obvious geographic relationship with the clades was observed, and such clades were not observed in the other regions in and around this gene. The average genetic diversity among the clades ranged from 10 to 14.6% in the LRR. The levels of polymorphism within each clade varied largely, and significant heterogeneity in evolutionary rates among clades was detected. A statistically significant departure from neutrality was also detected by Fu & Li's tests. These results suggest that both directional and diversifying selection are working on this locus, and that natural selection can cause heterogeneity in evolutionary rate, even among allele groups in a locus.

A viral resistance gene from common bean functions across plant families and is up-regulated in a non-virus-specific manner

Genes involved in a viral resistance response in common bean (Phaseolus vulgaris cv. Othello) were identified by inoculating a geminivirus reporter (Bean dwarf mosaic virus expressing the green fluorescent protein), extracting RNA from tissue undergoing the defense response, and amplifying sequences with degenerate R gene primers. One such gene (a TIR-NBS-LRR gene, RT4-4) was selected for functional analysis in which transgenic Nicotiana benthamiana were generated and screened for resistance to a range of viruses. This analysis revealed that RT4-4 did not confer resistance to the reporter geminivirus; however, it did activate a resistance-related response (systemic necrosis) to seven strains of Cucumber mosaic virus (CMV) from pepper or tomato, but not to a CMV strain from common bean. Of these eight CMV strains, only the strain from common bean systemically infected common bean cv. Othello. Additional evidence that RT4-4 is a CMV R gene came from the detection of resistance response markers in CMV-challenged leaves of RT4-4 transgenic plants, and the identification of the CMV 2a gene product as the elicitor of the necrosis response. These findings indicate that RT4-4 functions across two plant families and is up-regulated in a non-virus-specific manner. This experimental approach holds promise for providing insights into the mechanisms by which plants activate resistance responses against pathogens.

Distinct domains in the ARC region of the potato resistance protein Rx mediate LRR binding and inhibition of activation

Plant nucleotide binding and leucine-rich repeat (NB-LRR) proteins contain a region of homology known as the ARC domain located between the NB and LRR domains. Structural modeling suggests that the ARC region can be subdivided into ARC1 and ARC2 domains. We have used the potato (Solanum tuberosum) Rx protein, which confers resistance to Potato virus X (PVX), to investigate the function of the ARC region. We demonstrate that the ARC1 domain is required for binding of the Rx N terminus to the LRR domain. Domain-swap experiments with Rx and a homologous disease resistance gene, Gpa2, showed that PVX recognition localized to the C-terminal half of the LRR domain. However, inappropriate pairings of LRR and ARC2 domains resulted in autoactive molecules. Thus, the ARC2 domain is required to condition an autoinhibited state in the absence of elicitor as well as for the subsequent elicitor-induced activation. Our data suggest that the ARC region, through its interaction with the LRR, translates elicitor-induced modulations of the C terminus into a signal initiation event. Furthermore, we demonstrate that physical disruption of the LRR-ARC interaction is not required for signal initiation. We propose instead that this activity can lead to multiple rounds of elicitor recognition, providing a means of signal amplification.

Distinct domains in the ARC region of the potato resistance protein Rx mediate LRR binding and inhibition of activation

Plant nucleotide binding and leucine-rich repeat (NB-LRR) proteins contain a region of homology known as the ARC domain located between the NB and LRR domains. Structural modeling suggests that the ARC region can be subdivided into ARC1 and ARC2 domains. We have used the potato (Solanum tuberosum) Rx protein, which confers resistance to Potato virus X (PVX), to investigate the function of the ARC region. We demonstrate that the ARC1 domain is required for binding of the Rx N terminus to the LRR domain. Domain-swap experiments with Rx and a homologous disease resistance gene, Gpa2, showed that PVX recognition localized to the C-terminal half of the LRR domain. However, inappropriate pairings of LRR and ARC2 domains resulted in autoactive molecules. Thus, the ARC2 domain is required to condition an autoinhibited state in the absence of elicitor as well as for the subsequent elicitor-induced activation. Our data suggest that the ARC region, through its interaction with the LRR, translates elicitor-induced modulations of the C terminus into a signal initiation event. Furthermore, we demonstrate that physical disruption of the LRR-ARC interaction is not required for signal initiation. We propose instead that this activity can lead to multiple rounds of elicitor recognition, providing a means of signal amplification.

The disease resistance gene Dm3 is infrequent in natural populations of Lactuca serriola due to deletions and frequent gene conversions at the RGC2 locus

Resistance genes can exhibit heterogeneous patterns of variation. However, there are few data on their frequency and variation in natural populations. We analysed the frequency and variation of the resistance gene Dm3, which confers resistance to Bremia lactucae (downy mildew) in 1033 accessions of Lactuca serriola (prickly lettuce) from 49 natural populations. Inoculations with an isolate of Bremia lactucae carrying avirulence gene Avr3 indicated that the frequency of Dm3 in natural populations of L. serriola was very low. Molecular analysis demonstrated that Dm3 was present in only one of the 1033 wild accessions analysed. The sequence of the 5' region of Dm3 was either highly conserved among accessions, or absent. In contrast, frequent chimeras were detected in the 3' leucine-rich repeat-encoding region. Therefore low frequency of the Dm3 specificity in natural populations was due to either the recent evolution of Dm3 specificity, or deletions of the whole gene as well as variation in 3' region caused by frequent gene conversions. This is the most extensive analysis of the prevalence of a known disease resistance gene to date, and indicates that the total number of resistance genes in a species may be very high. This has implications for the scales of germplasm conservation and exploitation of sources of resistance.

Genome-wide isolation of resistance gene analogs in maize (Zea mays L.)

Conserved domains or motifs shared by most known resistance (R) genes have been extensively exploited to identify unknown R-gene analogs (RGAs). In an attempt to isolate all potential RGAs from the maize genome, we adopted the following three methods: modified amplified fragment length polymorphism (AFLP), modified rapid amplification of cDNA ends (RACE), and data mining. The first two methods involved PCR-based isolations of RGAs with degenerate primers designed based on the conserved NBS domain; while the third method involved mining of RGAs from the maize EST database using full-length R-gene sequences. A total of 23 and 12 RGAs were obtained from the modified AFLP and RACE methods, respectively; while, as many as 109 unigenes and 77 singletons with high homology to known R-genes were recovered via data-mining. Moreover, R-gene-like ESTs (or RGAs) identified from the data-mining method could cover all RACE-derived RGAs and nearly half AFLP-derived RGAs. Totally, the three methods resulted in 199 non-redundant RGAs. Of them, at least 186 were derived from putative expressed R-genes. RGA-tagged markers were developed for 55 unique RGAs, including 16 STS and 39 CAPS markers.

Multiple resistance traits control Plum pox virus infection in Arabidopsis thaliana

Twelve Arabidopsis accessions were challenged with Plum pox potyvirus (PPV) isolates representative of the four PPV strains. Each accession supported local and systemic infection by at least some of the PPV isolates, but high variability was observed in the behavior of the five PPV isolates or the 12 Arabidopsis accessions. Resistance to local infection or long-distance movement occurred in about 40% of all the accession-isolate combinations analyzed. Except for Nd-1, all accessions showed resistance to local infection by PPV-SoC; in the Landsberg erecta (Ler) accession, this resistance was compromised by sgt1 and rar1 mutations, suggesting that it could be controlled by an R gene-mediated resistance pathway. While most of the susceptible accessions were symptomless, PPV induced severe symptoms on inflorescences in C24, Ler, and Bay-0 as early as 15 days after inoculation. Genetic analyses indicated that these interaction phenotypes are controlled by different genetic systems. The restriction of long-distance movement of PPV-El Amar and of another member of genus Potyvirus, Lettuce mosaic virus, in Col-0 requires the RTM genes, indicating for the first time that the RTM system may provide a broad range, potyvirus-specific protection against systemic infection. The restriction to PPV-PS long-distance movement in Cvi-1 is controlled by a single recessive gene, designated rpv1, which was mapped to chromosome 1. The nuclear inclusion polymerase b-capsid protein region of the viral genome appears to be responsible for the ability of PPV-R to overcome rpv1-mediated resistance.