The coat protein is required for the elicitation of the Capsicum L2 gene-mediated resistance against the tobamoviruses

Reversion of a resistance-breaking mutation shows reversion costs and high virus diversity at necrotic local lesions

An instance of host range evolution relevant to plant virus disease control is resistance breaking. Resistance breaking can be hindered by across-host fitness trade-offs generated by negative effects of resistance-breaking mutations on the virus fitness in susceptible hosts. Different mutations in pepper mild mottle virus (PMMoV) coat protein result in the breaking in pepper plants of the resistance determined by the L³ resistance allele. Of these, mutation M138N is widespread in PMMoV populations, despite associated fitness penalties in within-host multiplication and survival. The stability of mutation M138N was analysed by serial passaging in L³ resistant plants. Appearance on passaging of necrotic local lesions (NLL), indicating an effective L³ resistance, showed reversion to nonresistance-breaking phenotypes was common. Most revertant genotypes had the mutation N138K, which affects the properties of the virus particle, introducing a penalty of reversion. Hence, the costs of reversion may determine the evolution of resistance-breaking in addition to resistance-breaking costs. The genetic diversity of the virus population in NLL was much higher than in systemically infected tissues, and included mutations reported to break L³ resistance other than M138N. Infectivity assays on pepper genotypes with different L alleles showed high phenotypic diversity in respect to L alleles in NLL, including phenotypes not reported in nature. Thus, high diversity at NLL may potentiate the appearance of genotypes that enable the colonization of new host genotypes or species. Collectively, the results of this study contribute to better understanding the evolutionary dynamics of resistance breaking and host-range expansions.

The effect of organic farming on water reusability, sustainable ecosystem, and food toxicity

Water is a fundamental necessity for people's well-being and the ecosystem's sustainability; however, its toxicity due to agrochemicals usage for food production leads to the deterioration of water quality. The poor water quality diminishes its reusability, thus limiting efficient water usage. Organic farming is one of the best ways that does not only reduce the deterioration of water quality but also decrease food toxicity. In organic farming, the crop is grown with no/less chemical usage. Besides, organic farming maintains biodiversity and reduces the anthropogenic footprint on soil, air, water, wildlife, and especially on the farming communities. Fields that are organically managed continuously for years have fewer pest populations and were attributed to increased biodiversity and abundance of multi-trophic interactions as well as to changes in plant metabolites. Fewer insect pests (pathogen vectors), in turn, would result in fewer crop diseases and increase crop production. This review highlights that organic farming may play a critical role in the reduction of pests and pathogens, which eventually would reduce the need for chemical reagents to protect crops, improving yield quality and water reusability.

From Player to Pawn: Viral Avirulence Factors Involved in Plant Immunity

In the plant immune system, according to the 'gene-for-gene' model, a resistance (R) gene product in the plant specifically surveils a corresponding effector protein functioning as an avirulence (Avr) gene product. This system differs from other plant-pathogen interaction systems, in which plant R genes recognize a single type of gene or gene family because almost all virus genes with distinct structures and functions can also interact with R genes as Avr determinants. Thus, research conducted on viral Avr-R systems can provide a novel understanding of Avr and R gene product interactions and identify mechanisms that enable rapid co-evolution of plants and phytopathogens. In this review, we intend to provide a brief overview of virus-encoded proteins and their roles in triggering plant resistance, and we also summarize current progress in understanding plant resistance against virus Avr genes. Moreover, we present applications of Avr gene-mediated phenotyping in R gene identification and screening of segregating populations during breeding processes.

Capsicum annum Hsp26.5 promotes defense responses against RNA viruses via ATAF2 but is hijacked as a chaperone for tobamovirus movement protein

The expression of Capsicum annuum HEAT SHOCK PROTEIN 26.5 (CaHsp26.5) was triggered by the inoculation of Tobacco mosaic virus pathotype P0 (TMV-P0) but its function in the defense response of plants is unknown. We used gene silencing and overexpression approaches to investigate the effect of CaHsp26.5 expression on different plant RNA viruses. Moreover, we performed protein-protein and protein-RNA interaction assays to study the mechanism of CaHsp26.5 function. CaHsp26.5 binding to a short poly-cytosine motif in the 3'-untranslated region of the genome of some viruses triggers the expression of several defense-related genes such as PATHOGENESIS-RELATED GENE 1 with the help of a transcription factor, NAC DOMAIN-CONTAINING PROTEIN 81 (ATAF2). Thus, an elevated CaHsp26.5 level was accompanied by increased plant resistance against plant viruses such as Cucumber mosaic virus strain Korea. However, the movement proteins of Pepper mild mottle virus pathotype P1,2,3 and TMV-P0 were shown to be able to interact with CaHsp26.5 to maintain the integrity of their proteins. Our work shows CaHsp26.5 as a positive player in the plant defense response against several plant RNA viruses. However, some tobamoviruses can hijack CaHsp26.5's chaperone activity for their own benefit.

CaLecRK-S.5, a pepper L-type lectin receptor kinase gene, accelerates Phytophthora elicitin-mediated defense response

Innate immunity in plants relies on the recognition of pathogen-associated molecular patterns (PAMPs) by pattern-recognition receptors (PRRs) located on the plant cell surface. CaLecRK-S.5, a pepper L-type lectin receptor kinase, has been shown to confer broad-spectrum resistance through priming activation. To further elucidate the molecular mechanism of CaLecRK-S.5, transgenic tobacco plants were generated in this study. Interestingly, hemizygous transgenic plants exhibited a high accumulation of CaLecRK-S.5, but this accumulation was completely abolished in homozygous transgenic plants by a cosuppression mechanism. Gain-of-function and loss-of-function analyses revealed that CaLecRK-S.5 plays a positive role in Phytophthora elicitin-mediated defense responses.

Random Mutagenesis of Virus Gene for the Experimental Evaluation of the Durability of NB-LRR Class Plant Virus Resistance Gene

NB-LRR class plant virus resistance gene is a one of the key players that shape the plant-virus interaction. Evolutionary arms race between plants and viruses often results in the breakdown of virus resistance in plants, which leads to a disastrous outcome in agricultural production. Although studies have analyzed the nature of plant virus resistance breakdown, it is still difficult to foresee the breakdown of a given virus resistance gene. In this chapter, we provide a protocol for evaluating the durability of plant virus resistance gene, which comprises the random mutagenesis of a virus gene, the introduction of the mutagenized gene into a virus context with highly efficient inoculation system, and the efficient screening of virus mutants that can overcome or escape a virus resistance.

Tobamoviruses as Models for the Study of Virus Evolution

The study of tobacco mosaic virus and other tobamovirus species has greatly contributed to the development of all areas of virology, including virus evolution. Research with tobamoviruses has been pioneer, or particularly significant, in all major areas of research in this field, including: the characterization of the genetic diversity of virus populations, the mechanisms and rates of generation of genetic diversity, the analysis of the genetic structure of virus populations and of the factors that shape it, the adaptation of viruses to hosts and the evolution of host range, and the evolution of virus taxa and of virus-host interactions. Many of these continue to be hot topics in evolutionary biology, or have been identified recently as such, including (i) host-range evolution, (ii) predicting the overcoming of resistance in crops, (iii) trade-offs between virus life-history traits in virus evolution, and (iv) the codivergence of viruses and hosts at different taxonomical and spatial scales. Tobamoviruses may be particularly appropriate to address these topics with plant viruses, as they provide convenient experimental systems, and as the detailed knowledge on their molecular and structural biology allows the analysis of the mechanisms behind evolutionary processes. Also, the extensive information on parameters related to infection dynamics and population structure may facilitate the development of realistic models to predict virus evolution. Certainly, tobamoviruses will continue to be favorite system for the study of virus evolution.

Pleiotropic Effects of Resistance-Breaking Mutations on Particle Stability Provide Insight into Life History Evolution of a Plant RNA Virus

In gene-for-gene host-virus interactions, virus evolution to infect and multiply in previously resistant host genotypes, i.e., resistance breaking, is a case of host range expansion, which is predicted to be associated with fitness penalties. Negative effects of resistance-breaking mutations on within-host virus multiplication have been documented for several plant viruses. However, understanding virus evolution requires analyses of potential trade-offs between different fitness components. Here we analyzed whether coat protein (CP) mutations in Pepper mild mottle virus that break L-gene resistance in pepper affect particle stability and, thus, survival in the environment. For this purpose, CP mutations determining the overcoming of L 3 and L 4 resistance alleles were introduced in biologically active cDNA clones. The kinetics of the in vitro disassembly of parental and mutant particles were compared under different conditions. Resistance-breaking mutations variously affected particle stability. Structural analyses identified the number and type of axial and side interactions of adjacent CP subunits in virions, which explained differences in particle stability and contribute to understanding of tobamovirus disassembly. Resistance-breaking mutations also affected virus multiplication and virulence in the susceptible host, as well as infectivity. The sense and magnitude of the effects of resistance-breaking mutations on particle stability, multiplication, virulence, or infectivity depended on the specific mutation rather than on the ability to overcome the different resistance alleles, and effects on different traits were not correlated. Thus, the results do not provide evidence of links or trade-offs between particle stability, i.e., survival, and other components of virus fitness or virulence.IMPORTANCE The effect of survival on virus evolution remains underexplored, despite the fact that life history trade-offs may constrain virus evolution. We approached this topic by analyzing whether breaking of L-gene resistance in pepper by Pepper mild mottle virus, determined by coat protein (CP) mutations, is associated with reduced particle stability and survival. Resistance-breaking mutations affected particle stability by altering the interactions between CP subunits. However, the sense and magnitude of these effects were unrelated to the capacity to overcome different resistance alleles. Thus, resistance breaking was not traded with survival. Resistance-breaking mutations also affected virus fitness within the infected host, virulence, and infectivity in a mutation-specific manner. Comparison of the effects of CP mutations on these various traits indicates that there are neither trade-offs nor positive links between survival and other life history traits. These results demonstrate that trade-offs between life history traits may not be a general constraint in virus evolution.

Determinants of host species range in plant viruses

Prediction of pathogen emergence is an important field of research, both in human health and in agronomy. Most studies of pathogen emergence have focused on the ecological or anthropic factors involved rather than on the role of intrinsic pathogen properties. The capacity of pathogens to infect a large set of host species, i.e. to possess a large host range breadth (HRB), is tightly linked to their emergence propensity. Using an extensive plant virus database, we found that four traits related to virus genome or transmission properties were strongly and robustly linked to virus HRB. Broader host ranges were observed for viruses with single-stranded genomes, those with three genome segments and nematode-transmitted viruses. Also, two contrasted groups of seed-transmitted viruses were evidenced. Those with a single-stranded genome had larger HRB than non-seed-transmitted viruses, whereas those with a double-stranded genome (almost exclusively RNA) had an extremely small HRB. From the plant side, the family taxonomic rank appeared as a critical threshold for virus host range, with a highly significant increase in barriers to infection between plant families. Accordingly, the plant-virus infectivity matrix shows a dual structure pattern: a modular pattern mainly due to viruses specialized to infect plants of a given family and a nested pattern due to generalist viruses. These results contribute to a better prediction of virus host jumps and emergence risks.

Molecular Mapping of PMR1, a Novel Locus Conferring Resistance to Powdery Mildew in Pepper (Capsicum annuum)

Powdery mildew, caused by Leveillula taurica, is a major fungal disease affecting greenhouse-grown pepper (Capsicum annuum). Powdery mildew resistance has a complex mode of inheritance. In the present study, we investigated a novel powdery mildew resistance locus, PMR1, using two mapping populations: 102 'VK515' F_2:3 families (derived from a cross between resistant parental line 'VK515R' and susceptible parental line 'VK515S') and 80 'PM Singang' F₂ plants (derived from the F₁ 'PM Singang' commercial hybrid). Genetic analysis of the F_2:3 'VK515' and F₂ 'PM Singang' populations revealed a single dominant locus for inheritance of the powdery mildew resistance trait. Genetic mapping showed that the PMR1 locus is located on syntenic regions of pepper chromosome 4 in a 4-Mb region between markers CZ2_11628 and HRM4.1.6 in 'VK515R'. Six molecular markers including one SCAR marker and five SNP markers were localized to a region 0 cM from the PMR1 locus. Two putative nucleotide-binding site leucine-rich repeat (NBS-LRR)-type disease resistance genes were identified in this PMR1 region. Genotyping-by-sequencing (GBS) and genetic mapping analysis revealed suppressed recombination in the PMR1 region, perhaps due to alien introgression. In addition, a comparison of species-specific InDel markers as well as GBS-derived SNP markers indicated that C. baccatum represents a possible source of such alien introgression of powdery mildew resistance into 'VK515R'. The molecular markers developed in this study will be especially helpful for marker-assisted selection in pepper breeding programs for powdery mildew resistance.

Mutations That Determine Resistance Breaking in a Plant RNA Virus Have Pleiotropic Effects on Its Fitness That Depend on the Host Environment and on the Type, Single or Mixed, of Infection

Overcoming host resistance in gene-for-gene host-virus interactions is an important instance of host range expansion, which can be hindered by across-host fitness trade-offs. Trade-offs are generated by negative effects of host range mutations on the virus fitness in the original host, i.e., by antagonistic pleiotropy. It has been reported that different mutations in Pepper mild mottle virus (PMMoV) coat protein result in overcoming L-gene resistance in pepper. To analyze if resistance-breaking mutations in PMMoV result in antagonistic pleiotropy, all reported mutations determining the overcoming of L(3) and L(4) alleles were introduced in biologically active cDNA clones. Then, the parental and mutant virus genotypes were assayed in susceptible pepper genotypes with an L(+), L(1), or L(2) allele, in single and in mixed infections. Resistance-breaking mutations had pleiotropic effects on the virus fitness that, according to the specific mutation, the host genotype, and the type of infection, single or mixed with other virus genotypes, were antagonistic or positive. Thus, resistance-breaking mutations can generate fitness trade-offs both across hosts and across types of infection, and the frequency of host range mutants will depend on the genetic structure of the host population and on the frequency of mixed infections by different virus genotypes. Also, resistance-breaking mutations variously affected virulence, which may further influence the evolution of host range expansion.

IMPORTANCE

A major cause of virus emergence is host range expansion, which may be hindered by across-host fitness trade-offs caused by negative pleiotropy of host range mutations. An important instance of host range expansion is overcoming host resistance in gene-for-gene plant-virus interactions. We analyze here if mutations in the coat protein of Pepper mild mottle virus determining L-gene resistance-breaking in pepper have associated fitness penalties in susceptible host genotypes. Results show that pleiotropic effects of resistance-breaking mutations on virus fitness depend on the specific mutation, the susceptible host genotype, and the type of infection, single or mixed, with other virus genotypes. Accordingly, resistance-breaking mutations can have negative, positive, or no pleiotropic effects on virus fitness. These results underscore the complexity of host range expansion evolution and, specifically, the difficulty of predicting the overcoming of resistance factors in crops.

CaLecRK-S.5, a pepper L-type lectin receptor kinase gene, confers broad-spectrum resistance by activating priming

In Arabidopsis, several L-type lectin receptor kinases (LecRKs) have been identified as putative immune receptors. However, to date, there have been few analyses of LecRKs in crop plants. Virus-induced gene silencing of CaLecRK-S.5 verified the role of CaLecRK-S.5 in broad-spectrum resistance. Compared with control plants, CaLecRK-S.5-silenced plants showed reduced hypersensitive response, reactive oxygen species burst, secondary metabolite production, mitogen-activated protein kinase activation, and defense-related gene expression in response to Tobacco mosaic virus pathotype P0 (TMV-P0) infection. Suppression of CaLecRK-S.5 expression significantly enhanced the susceptibility to Pepper mild mottle virus pathotype P1,2,3, Xanthomonas campestris pv. vesicatoria, Phytophthora capsici, as well as TMV-P0 Additionally, β-aminobutyric acid treatment and a systemic acquired resistance assay revealed that CaLecRK-S.5 is involved in priming of plant immunity. Pre-treatment with β-aminobutyric acid before viral infection restored the reduced disease resistance phenotypes shown in CaLecRK-S.5-silenced plants. Systemic acquired resistance was also abolished in CaLecRK-S.5-silenced plants. Finally, RNA sequencing analysis indicated that CaLecRK-S.5 positively regulates plant immunity at the transcriptional level. Altogether, these results suggest that CaLecRK-S.5-mediated broad-spectrum resistance is associated with the regulation of priming.

Dominant resistance against plant viruses

To establish a successful infection plant viruses have to overcome a defense system composed of several layers. This review will overview the various strategies plants employ to combat viral infections with main emphasis on the current status of single dominant resistance (R) genes identified against plant viruses and the corresponding avirulence (Avr) genes identified so far. The most common models to explain the mode of action of dominant R genes will be presented. Finally, in brief the hypersensitive response (HR) and extreme resistance (ER), and the functional and structural similarity of R genes to sensors of innate immunity in mammalian cell systems will be described.

Host resistance selects for traits unrelated to resistance-breaking that affect fitness in a plant virus

The acquisition by parasites of the capacity to infect resistant host genotypes, that is, resistance-breaking, is predicted to be hindered by across-host fitness trade-offs. All analyses of costs of resistance-breaking in plant viruses have focused on within-host multiplication without considering other fitness components, which may limit understanding of virus evolution. We have reported that host range expansion of tobamoviruses on L-gene resistant pepper genotypes was associated with severe within-host multiplication penalties. Here, we analyze whether resistance-breaking costs might affect virus survival in the environment by comparing tobamovirus pathotypes differing in infectivity on L-gene resistance alleles. We predicted particle stability from structural models, analyzed particle stability in vitro, and quantified virus accumulation in different plant organs and virus survival in the soil. Survival in the soil differed among tobamovirus pathotypes and depended on differential stability of virus particles. Structure model analyses showed that amino acid changes in the virus coat protein (CP) responsible for resistance-breaking affected the strength of the axial interactions among CP subunits in the rod-shaped particle, thus determining its stability and survival. Pathotypes ranked differently for particle stability/survival and for within-host accumulation. Resistance-breaking costs in survival add to, or subtract from, costs in multiplication according to pathotype. Hence, differential pathotype survival should be considered along with differential multiplication to understand the evolution of the virus populations. Results also show that plant resistance, in addition to selecting for resistance-breaking and for decreased multiplication, also selects for changes in survival, a trait unrelated to the host-pathogen interaction that may condition host range expansion.

Coevolution and hierarchical interactions of Tomato mosaic virus and the resistance gene Tm-1

During antagonistic coevolution between viruses and their hosts, viruses have a major advantage by evolving more rapidly. Nevertheless, viruses and their hosts coexist and have coevolved, although the processes remain largely unknown. We previously identified Tm-1 that confers resistance to Tomato mosaic virus (ToMV), and revealed that it encodes a protein that binds ToMV replication proteins and inhibits RNA replication. Tm-1 was introgressed from a wild tomato species Solanum habrochaites into the cultivated tomato species Solanum lycopersicum. In this study, we analyzed Tm-1 alleles in S. habrochaites. Although most part of this gene was under purifying selection, a cluster of nonsynonymous substitutions in a small region important for inhibitory activity was identified, suggesting that the region is under positive selection. We then examined the resistance of S. habrochaites plants to ToMV. Approximately 60% of 149 individuals from 24 accessions were resistant to ToMV, while the others accumulated detectable levels of coat protein after inoculation. Unexpectedly, many S. habrochaites plants were observed in which even multiplication of the Tm-1-resistance-breaking ToMV mutant LT1 was inhibited. An amino acid change in the positively selected region of the Tm-1 protein was responsible for the inhibition of LT1 multiplication. This amino acid change allowed Tm-1 to bind LT1 replication proteins without losing the ability to bind replication proteins of wild-type ToMV. The antiviral spectra and biochemical properties suggest that Tm-1 has evolved by changing the strengths of its inhibitory activity rather than diversifying the recognition spectra. In the LT1-resistant S. habrochaites plants inoculated with LT1, mutant viruses emerged whose multiplication was not inhibited by the Tm-1 allele that confers resistance to LT1. However, the resistance-breaking mutants were less competitive than the parental strains in the absence of Tm-1. Based on these results, we discuss possible coevolutionary processes of ToMV and Tm-1.

Viruses rapidly evolve and adapt to their host organisms, and the evolutionary processes can be reproduced in the laboratory (experimental evolution). In contrast, cellular organisms (that can be viral hosts) evolve much more slowly than viruses, but the fact that they have antiviral systems suggests that viruses and their hosts have coevolved. To explore the coevolutionary histories of viruses and their hosts, we focused on Tm-1, a Solanum habrochaites gene that confers resistance to Tomato mosaic virus (ToMV). Based on analyses of the Tm-1 gene sequences in S. habrochaites, we demonstrated that a part of the gene has been under positive selection. Biochemical studies suggested that Tm-1 has evolved to strengthen its inhibitory activity rather than to diversify recognition spectra. In addition, experimental evolution analyses suggested that overcoming the Tm-1-mediated resistance by ToMV is associated with fitness costs. Based on these results, we discuss how ToMV and the plant resistance gene have coevolved.

Amino acids in Tobamovirus coat protein controlling pepper L(1a) gene-mediated resistance

In pepper plants (genus Capsicum), the resistance against Tobamovirus spp. is conferred by L gene alleles. The recently identified L variant L(1a) can recognize coat proteins (CPs) of Tobacco mild green mosaic virus Japanese strain (TMGMV-J) and Paprika mild mottle virus Japanese strain (PaMMV-J), but not of Pepper mild mottle virus (PMMoV), as the elicitor to induce resistance at 24 °C. Interestingly, L(1a) gene-mediated resistance against TMGMV-J, but not PaMMV-J, is retained at 30 °C. This observation led us to speculate that L(1a) can discriminate between CPs of TMGMV-J and PaMMV-J. In this study, we aimed to determine the region(s) in CP by which L(1a) distinguishes TMGMV-J from PaMMV-J. By using chimeric CPs consisting of TMGMV-J and PaMMV-J, we found that the chimeric TMGMV-J CP, whose residues in the β-sheet domain were replaced by those of PaMMV-J, lost its ability to induce L(1a) gene-mediated resistance at 30 °C. In contrast, the chimeric PaMMV-J CP with the β-sheet domain replaced by TMGMV-J CP was able to induce L(1a) gene-mediated resistance at 30 °C. Furthermore, viral particles were not detected in the leaves inoculated with either chimeric virus. These observations indicated that the amino acids within the β-sheet domain were involved in both the induction of L(1a) gene-mediated resistance and virion formation. Further analyses using chimeric CPs of TMGMV-J and PMMoV indicated that amino acids within the β-sheet domain alone were not sufficient for the induction of L(1a) gene-mediated resistance by TMGMV-J CP. These results suggest that multiple regions in Tobamovirus CP are implicated in the induction of L(1a) gene-mediated resistance.

Functional differentiation in the leucine-rich repeat domains of closely related plant virus-resistance proteins that recognize common avr proteins

The N' gene of Nicotiana sylvestris and L genes of Capsicum plants confer the resistance response accompanying the hypersensitive response (HR) elicited by tobamovirus coat proteins (CP) but with different viral specificities. Here, we report the identification of the N' gene. We amplified and cloned an N' candidate using polymerase chain reaction primers designed from L gene sequences. The N' candidate gene was a single 4143 base pairs fragment encoding a coiled-coil nucleotide-binding leucine-rich repeat (LRR)-type resistance protein of 1,380 amino acids. The candidate gene induced the HR in response to the coexpression of tobamovirus CP with the identical specificity as reported for N'. Analysis of N'-containing and tobamovirus-susceptible N. tabacum accessions supported the hypothesis that the candidate is the N' gene itself. Chimera analysis between N' and L(3) revealed that their LRR domains determine the spectrum of their tobamovirus CP recognition. Deletion and mutation analyses of N' and L(3) revealed that the conserved sequences in their C-terminal regions have important roles but contribute differentially to the recognition of common avirulence proteins. The results collectively suggest that Nicotiana N' and Capsicum L genes, which most likely evolved from a common ancestor, differentiated in their recognition specificity through changes in the structural requirements for LRR function.

Viruses of pepper crops in the Mediterranean basin: a remarkable stasis

Compared to other vegetable crops, the major viral constraints affecting pepper crops in the Mediterranean basin have been remarkably stable for the past 20 years. Among these viruses, the most prevalent ones are the seed-transmitted tobamoviruses; the aphid-transmitted Potato virus Y and Tobacco etch virus of the genus Potyvirus, and Cucumber mosaic virus member of the genus Cucumovirus; and thrips-transmitted tospoviruses. The last major viral emergence concerns the tospovirus Tomato spotted wilt virus (TSWV), which has undergone major outbreaks since the end of the 1980s and the worldwide dispersal of the thrips vector Frankliniella occidentalis from the western part of the USA. TSWV outbreaks in the Mediterranean area might have been the result of both viral introductions from Northern America and local reemergence of indigenous TSWV isolates. In addition to introductions of new viruses, resistance breakdowns constitute the second case of viral emergences. Notably, the pepper resistance gene Tsw toward TSWV has broken down a few years after its deployment in several Mediterranean countries while there has been an expansion of L³-resistance breaking pepper mild mottle tobamovirus isolates. Beyond the agronomical and economical concerns induced by the breakdowns of virus resistance genes in pepper, they also constitute original models to understand plant-virus interactions and (co)evolution.

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.

Rapid genetic diversification and high fitness penalties associated with pathogenicity evolution in a plant virus

Under the gene-for-gene model of host-pathogen coevolution, recognition of pathogen avirulence factors by host resistance factors triggers host defenses and limits infection. Theory predicts that the evolution of higher levels of pathogenicity will be associated with fitness penalties and that the cost of higher pathogenicity must be much smaller than that of not infecting the host. The analysis of pathogenicity costs is of academic and applied relevance, as these are determinants for the success of resistance genes bred into crops for disease control. However, most previous attempts of addressing this issue in plant pathogens yielded conflicting and inconclusive results. We have analyzed the costs of pathogenicity in pepper-infecting tobamoviruses defined by their ability to infect pepper plants with different alleles at the resistance locus L. We provide conclusive evidence of pathogenicity-associated costs by comparison of pathotype frequency with the fraction of the crop carrying the various resistance alleles, by timescaled phylogenies, and by temporal analyses of population dynamics and selection pressures using nucleotide sequences. In addition, experimental estimates of relative fitness under controlled conditions also provided evidence of high pathogenicity costs. These high pathogenicity costs may reflect intrinsic properties of plant virus genomes and should be considered in future models of host-parasite coevolution.

Single amino acid substitution in the methyltransferase domain of Paprika mild mottle virus replicase proteins confers the ability to overcome the high temperature-dependent Hk gene-mediated resistance in Capsicum plants

Capsicum plants harboring the Hk gene (Hk) show resistance to Paprika mild mottle virus (PaMMV) at 32 degrees C but not 24 degrees C. To identify the viral elicitor that activates the Hk-mediated resistance, several chimeric viral genomes were constructed between PaMMV and Tobacco mosaic virus-L. Infection patterns of these chimeric viruses in Hk-harboring plants revealed responsibility of PaMMV replicase genes for activation of the Hk-mediated resistance. The comparison of nucleotide sequence of replicase genes between PaMMV and PaHk1, an Hk-resistance-breaking strain of PaMMV, revealed that the adenine-to-uracil substitution at the nucleotide position 721 causes an amino acid change from threonine to serine at the 241st residue in the methyltransferase domain. Introduction of the A721U mutation into the replicase genes of parental PaMMV overcame the Hk resistance at 32 degrees C. The results indicate that Hk-mediated resistance is induced by PaMMV replicase proteins and that methyltransferase domain has a role in this elicitation.

Fine mapping and DNA fiber FISH analysis locates the tobamovirus resistance gene L3 of Capsicum chinense in a 400-kb region of R-like genes cluster embedded in highly repetitive sequences

The tobamovirus resistance gene L(3) of Capsicum chinense was mapped using an intra-specific F2 population (2,016 individuals) of Capsicum annuum cultivars, into one of which had been introduced the C. chinense L(3) gene, and an inter-specific F2 population (3,391 individuals) between C. chinense and Capsicum frutescence. Analysis of a BAC library with an AFLP marker closely linked to L(3)-resistance revealed the presence of homologs of the tomato disease resistance gene I2. Partial or full-length coding sequences were cloned by degenerate PCR from 35 different pepper I2 homologs and 17 genetic markers were generated in the inter-specific combination. The L(3) gene was mapped between I2 homolog marker IH1-04 and BAC-end marker 189D23M, and located within a region encompassing two different BAC contigs consisting of four and one clones, respectively. DNA fiber FISH analysis revealed that these two contigs are separated from each other by about 30 kb. DNA fiber FISH results and Southern blotting of the BAC clones suggested that the L(3) locus-containing region is rich in highly repetitive sequences. Southern blot analysis indicated that the two BAC contigs contain more than ten copies of the I2 homologs. In contrast to the inter-specific F2 population, no recombinant progeny were identified to have a crossover point within two BAC contigs consisting of seven and two clones in the intra-specific F2 population. Moreover, distribution of the crossover points differed between the two populations, suggesting linkage disequilibrium in the region containing the L locus.

Cooperative effect of two amino acid mutations in the coat protein of Pepper mild mottle virus overcomes L3-mediated resistance in Capsicum plants

We found that an L3 resistance-breaking field isolate of Pepper mild mottle virus (PMMoV), designated PMMoV-Is, had two amino acid changes in its coat protein (CP), namely leucine to phenylalanine at position 13 (L13F) and glycine to valine at position 66 (G66V), as compared with PMMoV-J, which induces a resistance response in L3-harboring Capsicum plants. The mutations were located to a CP domain corresponding to the outer surface of PMMoV particles in computational molecular modeling. Analyses of PMMoV CP mutants containing either or both of these amino acid changes revealed that both changes were required to efficiently overcome L3-mediated resistance with systemic necrosis induction. Although CP mutants containing either L13F or G66V could not efficiently overcome L3-mediated resistance, these amino acid changes had different effects on the elicitor activity of PMMoV CP. L13F caused a slight reduction in the elicitor activity, resulting in virus restriction to necrotic local lesions that were apparently larger than those induced by wild-type PMMoV, while G66V rendered wild-type PMMoV the ability to overcome L3-mediated resistance, albeit with a lower efficiency than PMMoV with both changes. These results suggest that a cooperative effect of the L13F and G66V mutations on the elicitor activity of CP is responsible for overcoming the L3-mediated resistance.

Genetics of plant virus resistance

Genetic resistance to plant viruses has been used for at least 80 years to control agricultural losses to viral diseases. To date, hundreds of naturally occurring genes for resistance to plant viruses have been reported from studies of both monocot and dicot crops, their wild relatives, and the plant model, Arabidopsis. The isolation and characterization of a few of these genes in the past decade have resulted in detailed knowledge of some of the molecules that are critical in determining the outcome of plant viral infection. In this chapter, we have catalogued genes for resistance to plant viruses and have summarized current knowledge regarding their identity and inheritance. Insofar as information is available, the genetic context, genomic organization, mechanisms of resistance and agricultural deployment of plant virus resistance genes are also discussed.

The coat protein of tobamovirus acts as elicitor of both L2 and L4 gene-mediated resistance in Capsicum

In Capsicum, the resistance conferred by the L(2) gene is effective against all of the pepper-infecting tobamoviruses except Pepper mild mottle virus (PMMoV), whereas that conferred by the L(4) gene is effective against them all. These resistances are expressed by a hypersensitive response, manifested through the formation of necrotic local lesions (NLLs) at the primary site of infection. The Capsicum L(2) gene confers resistance to Paprika mild mottle virus (PaMMV), while the L(4) gene is effective against both PaMMV and PMMoV. The PaMMV and PMMoV coat proteins (CPs) were expressed in Capsicum frutescens (L(2)L(2)) and Capsicum chacoense (L(4)L(4)) plants using the heterologous Potato virus X (PVX)-based expression system. In C. frutescens (L(2)L(2)) plants, the chimeric PVX virus containing the PaMMV CP was localized in the inoculated leaves and produced NLLs, whereas the chimeric PVX containing the PMMoV CP infected the plants systemically. Thus, the data indicated that the PaMMV CP is the only tobamovirus factor required for the induction of the host response mediated by the Capsicum L(2) resistance gene. In C. chacoense (L(4)L(4)) plants, both chimeric viruses were localized to the inoculated leaves and produced NLLs, indicating that either PaMMV or PMMoV CPs are required to elicit the L(4) gene-mediated host response. In addition, transient expression of PaMMV CP into C. frutescens (L(2)L(2)) leaves and PMMoV CP into C. chacoense (L(4)L(4)) leaves by biolistic co-bombardment with a beta-glucuronidase reporter gene led to the induction of cell death and the expression of host defence genes in both hosts. Thus, the tobamovirus CP is the elicitor of the Capsicum L(2) and L(4) gene-mediated hypersensitive response.

An analysis of the durability of resistance to plant viruses

ABSTRACT Genetic resistance often fails because a resistance-breaking (RB) pathogen genotype increases in frequency. On the basis of an analysis of cellular plant pathogens, it was recently proposed that the evolutionary potential of a pathogen is a major determinant of the durability of resistance. We test this hypothesis for plant viruses, which differ substantially from cellular pathogens in the nature, size, and expression of their genomes. Our analysis was based on 29 plant virus species that provide a good representation of the genetic and biological diversity of plant viruses. These 29 viruses were involved in 35 pathosystems, and 50 resistance factors deployed against them were analyzed. Resistance was found to be durable more often than not, in contrast with resistance to cellular plant pathogens. In a third of the analyzed pathosystems RB strains have not been reported, and in another third RB strains have been reported but have not become prevalent in the virus population. The evolutionary potential of the viruses in the 35 pathosystems was evaluated with a compound risk index based on three evolutionary factors: the population of the pathogen, the degree of recombination, and the amount of gene and genotype flow. Our analysis indicates that evolutionary potential may be an important determinant of the durability of resistance against plant viruses.

Screening and Field Trials of Virus Resistant Sources in Capsicum spp

Thirty-seven Capsicum accessions containing cultivated and wild species were screened for resistance to Cucumber mosaic virus (CMV), and were also investigated for their response to Tomato aspermy virus (TAV), Tomato mosaic virus (ToMV), Pepper mild mottle virus (PMMoV), and Tomato spotted wilt virus (TSWV). C. baccatum PI 439381-1-3 (PI 439381-1-3), C. frutescens LS 1839-2-4 (LS 1839-2-4), and C. frutescens cv. Tabasco (cv. Tabasco) showed a hypersensitive reaction against CMV-Y, and thus were not systemically infected. Only inoculated leaves of C. annuum cv. Sapporo-oonaga and cv. Nanbu-oonaga were infected with CMV-Y, and viral infection did not spread systemically. These five accessions (PI 439381-1-3, LS 1839-2-4, cv. Tabasco, cv. Sapporo-oonaga, and cv. Nanbu-oonaga) were considered resistant to CMV-Y. These accessions were also resistant to other CMV isolates, but not to the TAV isolate. PI 439381-1-3, LS1839-2-4, cv. Sapporo-oonaga, and cv. Nanbu-oonaga were susceptible to PMMoV, while PI 439381-1-3 and LS1839-2-4 showed systemic necrosis. All CMV-resistant accessions were susceptible to TSWV. Field tests of eight Capsicum accessions, including CMV, PMMoV, and/or TSWV-resistant accessions, demonstrated that most of the PI 439381-1-3 plants were not infected with CMV and PMMoV among the virus-infested fields. As occurred with mechanical inoculation, LS 1839-2-4, cv. Tabasco, cv. Sapporo-oonaga, and cv. Nanbu-oonaga were hard to infect with CMV in the field.

The complete nucleotide sequence and development of a differential detection assay for a pepper mild mottle virus (PMMoV) isolate that overcomes L3 resistance in pepper

The complete nucleotide sequence of the RNA genome of a Pepper Mild Mottle Virus (PMMoV) isolate that overcomes L3 resistance in pepper (Capsicum sp.) was determined and compared with the sequence of other Tobamoviruses. The RNA genome consists of 6357 nucleotides and contains four open reading frames. The 5' proximal ORF encodes a 128 kDa product that terminates in an amber codon which may be readthrough to produce a 180 kDa replication-associated protein (ORF 2). ORF 3 codes for the 28 kDa protein assumed to be involved in cell to cell spread of the virus. The last ORF encodes the coat protein (CP). Amino acid sequence comparison of the CP of this and other PMMoV isolates showed the same substitution (Met to Asn) as found in the Italian isolate of PMMoV and which is assumed to be responsible for L3-resistance breaking. RT-PCR using a common primer pair for PMMoV followed by restriction enzyme analysis with EcoRI allowed the discrimination of resistance breaking from non-L3 resistance breaking virus isolates.

Cymbidium ringspot tombusvirus coat protein coding sequence acts as an avirulent RNA

Avirulent genes either directly or indirectly produce elicitors that are recognized by specific receptors of plant resistance genes, leading to the induction of host defense responses such as hypersensitive reaction (HR). HR is characterized by the development of a necrotic lesion at the site of infection which results in confinement of the invader to this area. Artificial chimeras and mutants of cymbidium ringspot (CymRSV) and the pepper isolate of tomato bushy stunt (TBSV-P) tombusviruses were used to determine viral factors involved in the HR resistance phenotype of Datura stramonium upon infection with CymRSV. A series of constructs carrying deletions and frameshifts of the CymRSV coat protein (CP) undoubtedly clarified that an 860-nucleotide (nt)-long RNA sequence in the CymRSV CP coding region (between nt 2666 and 3526) is the elicitor of a very rapid HR-like response of D. stramonium which limits the virus spread. This finding provides the first evidence that an untranslatable RNA can trigger an HR-like resistance response in virus-infected plants. The effectiveness of the resistance response might indicate that other nonhost resistance could also be due to RNA-mediated HR. It is an appealing explanation that RNA-mediated HR has evolved as an alternative defense strategy against RNA viruses.

Mapping the virus and host genes involved in the resistance response in cucumber mosaic virus-Infected Arabidopsis thaliana

A yellow strain of cucumber mosaic virus (CMV) [CMV(Y)] induces a resistance response characterized by inhibition of virus systemic movement with development of necrotic local lesions in the virus-inoculated leaves of Arabidopsis thaliana ecotype C24. In this report, the avirulence determinant in the virus genome was defined and the resistance gene (RCY1) of C24 was genetically mapped. The response of C24 to CMV containing the chimeric RNA3 between CMV(Y) and a virulent strain of CMV indicated that the coat protein gene of CMV(Y) determined the localization of the virus in the inoculated leaves of C24. The RCY1 locus was mapped between two CAPS markers, DFR and T43968, which were located in the region containing genetically defined disease resistance genes and their homologues. These results indicate that the resistance response to CMV(Y) in C24 is determined by the combination of the coat protein gene and RCY1 on chromosome 5.

The multifunctional capsid proteins of plant RNA viruses

This article summarizes studies of viral coat (capsid) proteins (CPs) of RNA plant viruses. In addition, we discuss and seek to interpret the knowledge accumulated to data. CPs are named for their primary function; to encapsidate viral genomic nucleic acids. However, encapsidation is only one feature of an extremely diverse array of structural, functional, and ecological roles played during viral infection and spread. Herein, we consider the evolution of viral CPs and their multitude of interactions with factors encoded by the virus, host plant, or viral vector (biological transmission agent) that influence the infection and epidemiological facets of plant disease. In addition, applications of today's understanding of CPs in the protection of crops from viral infection and use in the manufacture of valuable compounds are considered.

The cylindrical inclusion gene of Turnip mosaic virus encodes a pathogenic determinant to the Brassica resistance gene TuRB01

The viral component of Turnip mosaic virus (TuMV) determining virulence to the Brassica napus TuRB01 dominant resistance allele has been identified. Sequence comparisons of an infectious cDNA clone of the UK 1 isolate of TuMV (avirulent on TuRB01) and a spontaneous mutant capable of infecting plants possessing TuRB01 suggested that a single nucleotide change in the cylindrical inclusion (CI) protein coding region (gene) of the virus was responsible for the altered phenotype. A second spontaneous mutation involved a different change in the CI gene. The construction of chimeric genomes and subsequent inoculations to plant lines segregating for TuRB01 confirmed the involvement of the CI gene in this interaction. Site-directed mutagenesis of the viral coat protein (CP) gene at the ninth nucleotide was carried out to investigate its interaction with TuRB01. The identity of this nucleotide in the CP gene did not affect the outcome of the viral infection. Both mutations identified in the CI gene caused amino acid changes in the C terminal third of the protein, outside any of the conserved sequences reported to be associated with helicase or cell-to-cell transport activities. This is the first example of a potyvirus CI gene acting as a determinant for a genotype-specific resistance interaction.

The amino terminus of the coat protein of Turnip crinkle virus is the AVR factor recognized by resistant arabidopsis

We have isolated three naturally occurring strains of Turnip crinkle virus (TCV) that break resistance in Di-17 Arabidopsis. Two mutations in the N terminus of the TCV coat protein, D4N and P5S, were shown to confer this phenotype. Thus, this region of the coat protein is involved in eliciting resistance responses in Arabidopsis.

Disease resistance gene analogs as candidates for QTLs involved in pepper-pathogen interactions

Whereas resistance genes (R-genes) governing qualitative resistance have been isolated and characterized, the biological roles of genes governing quantitative resistance (quantitave trait loci, QTLs) are still unknown. We hypothesized that genes at QTLs could share homologies with cloned R-genes. We used a PCR-based approach to isolate R-gene analogs (RGAs) with consensus primers corresponding with conserved domains of cloned R-genes: (i) the nucleotide binding site (NBS) and hydrophobic domain, and (ii) the kinase domain. PCR-amplified fragments were sequenced and mapped on a pepper intraspecific map. NBS-containing sequences of pepper, most similar to the N gene of tobacco, were classified into seven families and all mapped in a unique region covering 64 cM on the Noir chromosome. Kinase domain containing sequences and cloned R-gene homologs (Pto, Fen, Cf-2) were mapped on four different linkage groups. A QTL involved in partial resistance to cucumber mosaic virus (CMV) with an additive effect was closely linked or allelic to one NBS-type family. QTLs with epistatic effects were also detected at several RGA loci. The colocalizations between NBS-containing sequences and resistance QTLs suggest that the mechanisms of qualitative and quantitative resistance may be similar in some cases.Key words: Capsicum annuum, candidate gene, nucleotide binding site, kinase domain, quantitative trait loci.

Biochemical and molecular tools for the production of useful terpene products from pepper (Capsicum annuum)

Among other natural products such as colorants and flavorants, natural fungicides like the pepper phytoalexin capsidiol, and the related biochemical pathways, may be used for practical approaches. Key enzymes such as 3-hydroxy-3-methylglutaryl Coenzyme A: reductase, the farnesyl pyrophosphate synthase and and farnesyl pyrophosphate cyclases are known and some related genes have been isolated. However, specific enzymes for important and final modifications as methylation and others, are still to be studied. Construction of chimeric enzymes allowed already the synthesis of different products and the possibilities of designing new enzymes by gene manipulation to produce unknown and useful chemicals are open.

Tobacco mosaic virus virulence and avirulence

In celebration of a century of research on tobacco mosaic virus that initiated the science of virology, I review recent progress relative to earlier contributions concerning how viruses cause diseases of plants and how plants defend themselves from viruses.

Characterization of a pepper mild mottle tobamovirus strain capable of overcoming the L3 gene-mediated resistance, distinct from the resistance-breaking Italian isolate

Green pepper plants with the L3 resistance gene usually develop necrotic lesions on leaves infected with a Japanese strain of pepper mild mottle tobamovirus (PMMoV-J). A recently discovered strain, PMMoV-Ij, has the ability to overcome L3 resistance. Phytopathological responses of a variety of plant species to PMMoV-J and PMMoV-Ij were determined and the coat protein (CP) sequence comparisons revealed both amino acids 43 and 50 of PMMoV-Ij were unique. This led us to believe that substitutions at these residues would enable PMMoV-J to overcome L3 resistance. This was confirmed by Western blot (immunoblot) detection of PMMoV-J containing both point mutations in upper uninoculated leaves of resistant plants. Computer models suggest the critical residues in overcoming resistance lie in CP regions that putatively interact with other subunits. These results contribute to our understanding of the virus's ability to circumvent plant resistance.