The nucleotide sequence of the coat protein genes and 3' non-coding regions of two resistance-breaking tobamoviruses in pepper shows that they are different viruses

Transcriptome profiling of pepper leaves by RNA-Seq during an incompatible and a compatible pepper-tobamovirus interaction

Upon virus infections, the rapid and comprehensive transcriptional reprogramming in host plant cells is critical to ward off virus attack. To uncover genes and defense pathways that are associated with virus resistance, we carried out the transcriptome-wide Illumina RNA-Seq analysis of pepper leaves harboring the L3 resistance gene at 4, 8, 24 and 48 h post-inoculation (hpi) with two tobamoviruses. Obuda pepper virus (ObPV) inoculation led to hypersensitive reaction (incompatible interaction), while Pepper mild mottle virus (PMMoV) inoculation resulted in a systemic infection without visible symptoms (compatible interaction). ObPV induced robust changes in the pepper transcriptome, whereas PMMoV showed much weaker effects. ObPV markedly suppressed genes related to photosynthesis, carbon fixation and photorespiration. On the other hand, genes associated with energy producing pathways, immune receptors, signaling cascades, transcription factors, pathogenesis-related proteins, enzymes of terpenoid biosynthesis and ethylene metabolism as well as glutathione S-transferases were markedly activated by ObPV. Genes related to photosynthesis and carbon fixation were slightly suppressed also by PMMoV. However, PMMoV did not influence significantly the disease signaling and defense pathways. RNA-Seq results were validated by real-time qPCR for ten pepper genes. Our findings provide a deeper insight into defense mechanisms underlying tobamovirus resistance in pepper.

Heterologous expression of pepper mild mottle virus coat protein encoding region and its application in immuno-diagnostics

Pepper mild mottle virus (PMMoV), a tobamovirus of family Virgaviridae affects the quality and quantity of Capsicum. PMMoV is highly contagious, capable of transmitting through infected seeds and soil. Symptoms are more severe when crop is infected at young stage but remain unnoticed when infection takes place at maturity. Therefore, cost effective diagnostic techniques are required for timely and accurate detection of virus. In present study, coat protein encoding region of PMMoV-HP1 isolate was cloned into expression vector system, pET28a and expressed in BL21, a protease deficient strain of Escherichia coli. The PMMoV-HP1 pathotype was identified as PMMoV-P₁₂ on the basis of coat protein amino acid sequence analysis in our previous study. The overexpression of recombinant coat protein of 26 kDa, corresponding to the expected 6X Histidine tag fused recombinant protein was purified using Ni-NTA columns from insoluble fraction. For antisera production, the purified recombinant protein was dialyzed ~ 24 h to remove urea and then used for raising polyclonal antisera. The specificity and sensitivity of antiserum obtained was demonstrated using different dilutions of antiserum for western blot assay and direct antigen coating enzyme linked immunosorbent assay (DAC-ELISA). In Western blot assay, the test antiserum reacted strongly both with PMMoV-CP in purified protein and native CP in crude sap from PMMoV infected pepper plants, whereas no reaction was observed with healthy plant sap. In DAC-ELISA antiserum dilution up to 1:1000 was capable of detecting the virus in infected sample. The absence of any cross reactivity of test antiserum was confirmed against tobacco mosaic virus, cucumber mosaic virus, tomato spotted wilt virus, pepper veinal mottle virus, potato virus Y and tomato yellow leaf curl virus antigen, known to infect capsicum.

Pepper mild mottle virus: A plant pathogen with a greater purpose in (waste)water treatment development and public health management

An enteric virus surrogate and reliable domestic wastewater tracer is needed to manage microbial quality of food and water as (waste)water reuse becomes more prevalent in response to population growth, urbanization, and climate change. Pepper mild mottle virus (PMMoV), a plant pathogen found at high concentrations in domestic wastewater, is a promising surrogate for enteric viruses that has been incorporated into over 29 water- and food-related microbial quality and technology investigations around the world. This review consolidates the available literature from across disciplines to provide guidance on the utility of PMMoV as either an enteric virus surrogate and/or domestic wastewater marker in various situations. Synthesis of the available research supports PMMoV as a useful enteric virus process indicator since its high concentrations in source water allow for identifying the extent of virus log-reductions in field, pilot, and full-scale (waste)water treatment systems. PMMoV reduction levels during many forms of wastewater treatment were less than or equal to the reduction of other viruses, suggesting this virus can serve as an enteric virus surrogate when evaluating new treatment technologies. PMMoV excels as an index virus for enteric viruses in environmental waters exposed to untreated domestic wastewater because it was detected more frequently and in higher concentrations than other human viruses in groundwater (72.2%) and surface waters (freshwater, 94.5% and coastal, 72.2%), with pathogen co-detection rates as high as 72.3%. Additionally, PMMoV is an important microbial source tracking marker, most appropriately associated with untreated domestic wastewater, where its pooled-specificity is 90% and pooled-sensitivity is 100%, as opposed to human feces where its pooled-sensitivity is only 11.3%. A limited number of studies have also suggested that PMMoV may be a useful index virus for enteric viruses in monitoring the microbial quality of fresh produce and shellfish, but further research is needed on these topics. Finally, future work is needed to fill in knowledge gaps regarding PMMoV's global specificity and sensitivity.

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.

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.

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.

A New Pathotype of Pepper mild mottle virus (PMMoV) Overcomes the L4 Resistance Genotype of Pepper Cultivars

The biological, serological, and molecular characteristics of a newly isolated L⁴ resistance-breaking isolate of Pepper mild mottle virus (PMMoV) were studied. The new pathotype of PMMoV is closely related to the Israeli pathotypes P_1,2 and P_1,2,3 of the virus; however, the mosaic symptoms caused by this new pathotype on pepper plants with an L⁴ genotype were more severe than the mild mosaic symptoms caused by other common pathotypes of the virus in susceptible plants. The predicted amino acid sequence of the putative coat protein (CP) of the newly described pathotype has two amino acid mismatches when compared with the CP of pathotype P_1,2, leucine to glutamine at position 47, and alanine to glycine at position 87. The CP of the new pathotype has one amino acid mismatch when compared with P_1,2,3, having alanine instead of glycine at position 87. Based on its biological characteristics, the new pathotype was designated P_1,2,3,4 of PMMoV-Is. A method is described for the differentiation among the three PMMoV pathotypes using restriction cleavage analysis of reverse-transcription polymerase chain reaction products made from virus-infected plants. An additional unique MnlI site in the CP gene of the newly isolated P_1,2,3,4 allows its distinction from the other two isolates, while BglI cleaved only products of the P_1,2 pathotype.

Pathogenicity of Pepper mild mottle virus Is Controlled by the RNA Silencing Suppression Activity of Its Replication Protein but Not the Viral Accumulation

ABSTRACT Pepper mild mottle virus (PMMoV) infects pepper plants, causing mosaic symptoms on the upper developing leaves. We investigated the relationship between a virus pathogenicity determinant domain and the appearance of mosaic symptoms. Genetically modified PMMoV mutants were constructed, which had a base substitution in the 130K replication protein gene causing an amino acid change or a truncation of the 3' terminal pseudoknot structure. Only one substitution mutant (at amino acid residue 349) failed to cause symptoms, although its accumulation was relatively high. Conversely, the pseudoknot mutants showed the lower accumulation, but they still caused mosaic symptoms as severe as the wild-type virus. Therefore, the level of virus accumulation in a plant does not necessarily correlate with the development of mosaic symptoms. The activity to suppress posttranscriptional gene silencing (PTGS) was impaired in the asymptomatic mutant. Consequently, pathogenicity causing mosaic symptoms should be controlled by combat between host PTGS and its suppression by the 130K replication protein rather than virus accumulation.

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.

Pepper mild mottle virus pathogenicity determinants and cross protection effect of attenuated mutants in pepper

To determine the pathogenicity domain and to apply cross protection, Pepper mild mottle virus (PMMoV) point-mutations in the replicase (REP) gene between the methyl-transferase and helicase domains, and deletions truncating pseudoknots in the 3' non-coding region (NCR), were constructed. Some mutants substituting a single amino acid in REP residue 348 exhibited mild symptoms in Nicotiana benthamiana or pepper plants. Accumulation of these mutants was higher than that of other REP mutants or wild-type PMMoV. Deletion mutants in the 3' NCR pseudoknot showed the lowest virus replication and accumulation among the mutants tested. Six attenuated mutants, which combined 3' NCR deletions and single or double REP substitution mutations were constructed to investigate cross protection effects on pepper plants. All six of the attenuated mutants showed milder symptom development than wild-type virus. These results suggest that REP and the pseudoknot in the 3' NCR are major pathogenicity determinants of the virus, and engineered PMMoV attenuated mutants can be useful for protection against the virus in pepper plants.

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.

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.

Transient expression of homologous hairpin RNA causes interference with plant virus infection and is overcome by a virus encoded suppressor of gene silencing

Specific post-transcriptional gene silencing (PTGS) of target genes can be induced in a variety of organisms by providing homologous double-stranded RNA (dsRNA) molecules. In plants, PTGS is part of a defense mechanism against virus infection. We have previously shown and patented that direct delivery to nontransgenic plants of dsRNA derived from viral sequences specifically interfere with virus infection. Here, we show that transient expression of constructs encoding hairpin RNA homologous to a rapidly replicating plant tobamovirus also interferes with virus multiplication in a sequence-dependent manner. A three-day lag period between delivery of hairpin RNA and virus into the same tissues completely block virus infectivity. Several hallmarks characteristic of PTGS were associated with viral interference mediated by hairpin RNA: high level of sequence identity between the hairpin RNA and the target RNA, presence of siRNAs in extracts derived from leaves infiltrated with hairpin RNA, and helper component-proteinase (HC-Pro) of potyviruses, a suppressor of PTGS, overcame interference. No evidence for a mobile silencing suppression signal induced by transient expression of HC-Pro was observed. The approach described here has the potential to be used as a versatile tool for studying the onset of PTGS in cases involving virus infection, in opposition to dsRNA-transgenic plants, which allow primarily for the study of PTGS maintenance.

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.

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.

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

In Capsicum, the resistance against tobamoviruses conferred by the L2 gene is effective against all but one of the known tobamoviruses. Pepper mild mottle virus (PMMoV) is the only virus which escapes its action. To identify the viral factors affecting induction of the hypersensitive reaction (HR) mediated by the Capsicum spp. L2 resistance gene, we have constructed chimeric viral genomes between paprika mild mottle virus (PaMMV) (a virus able to induce the HR) and PMMoV. A hybrid virus with the PaMMV coat protein gene substituted in the PMMoV-S sequences was able to elicit the HR in Capsicum frutescens (L2L2) plants. These data indicate that the sequences that affect induction of the HR mediated by the L2 resistance gene reside in the coat protein gene. Furthermore, a mutant that codes for a truncated coat protein was able to systemically spread in these plants. Thus, the elicitation of the host response requires the coat protein and not the RNA.

Accumulation kinetics of CMV RNA 3-encoded proteins and subcellular localization of the 3a protein in infected and transgenic tobacco plants

The complete nucleotide sequence of RNA 3 of a Spanish isolate of cucumber mosaic virus (CMV-24) has been determined. The encoded putative cell-to-cell movement protein (3a protein) and the coat protein are 279 and 218 amino acids long, respectively. The 3a protein was expressed in Escherichia coli using the vector pT7-7 and was used to raise an immunoserum. We have followed the time course of accumulation of the 3a protein, in parallel to that of the coat protein, and its subcellular localization as a function of time after CMV-24 infection on tobacco plants. The maximum accumulation level of the 3a protein was reached at early stages of infection, being detected in the cytosolic and the cell wall fractions. At later stages of infection, a decline in accumulation levels of the 3a protein was observed, and the protein was essentially associated with the cell wall fractions. These data were corroborated by immunocytochemistry performed in both infected and 3a-expressing transgenic tobacco plants.

Nucleotide sequence of Chinese rape mosaic virus (oilseed rape mosaic virus), a crucifer tobamovirus infectious on Arabidopsis thaliana

The complete nucleotide sequence of Chinese rape mosaic virus has been determined. The virus is a member of the tobamovirus genus of plant virus and is able to infect Arabidopsis thaliana (L.) Heynh systemically. The analysis of the sequence shows a gene array that seems to be characteristic of crucifer tobamoviruses and which is slightly different from the one most frequently found in tobamoviruses. Based on gene organization and on comparisons of sequence homologies between members of the tobamoviruses, a clustering of crucifer tobamoviruses is proposed that groups the presently known crucifer tobamovirus into two viruses with two strains each. A name change of Chinese rape mosaic virus to oilseed rape mosaic virus is proposed.

Rapid detection and differentiation of tobamoviruses infecting L-resistant genotypes of pepper by RT-PCR and restriction analysis

A procedure involving reverse transcription followed by polymerase chain reaction (RT-PCR) was developed for typing pathotypes of the tobamoviruses infecting the L-resistant genotypes of pepper. The method provides a much simpler alternative to the bioassay tests for the different Capsicum spp. genotypes previously used. Discrimination between the two pathotypes, P1,2 and P1,2,3, which cannot be differentiated by serological means, was achieved by restriction enzyme analysis of the PCR products. The assay also detects and distinguishes both pathotypes in a single mixed-infected plant. The procedure should be useful for the diagnosis and control of the disease and helpful to breeders and biotechnologists when producing and evaluating resistance in pepper plants.