An Immunological System for the Detection of Pepper mild mottle virus in Soil from Green Pepper Fields

Development and Application of Attenuated Plant Viruses as Biological Control Agents in Japan

In 1929, it was reported that yellowing symptoms caused by a tobacco mosaic virus (TMV) yellow mosaic isolate were suppressed in tobacco plants that were systemically infected with a TMV light green isolate. Similar to vaccination, the phenomenon of cross-protection involves a whole plant being infected with an attenuated virus and involves the same or a closely related virus species. Therefore, attenuated viruses function as biological control agents. In Japan, many studies have been performed on cross-protection. For example, the tomato mosaic virus (ToMV)-L11A strain is an attenuated isolate developed by researchers and shows high control efficiency against wild-type ToMV in commercial tomato crops. Recently, an attenuated isolate of zucchini yellow mosaic virus (ZYMV)-2002 was developed and registered as a biological pesticide to control cucumber mosaic disease. In addition, attenuated isolates of pepper mild mottle virus (PMMoV), cucumber mosaic virus (CMV), tobacco mild green mosaic virus (TMGMV), melon yellow spot virus (MYSV), and watermelon mosaic virus (WMV) have been developed in Japan. These attenuated viruses, sometimes called plant vaccines, can be used not only as single vaccines but also as multiple vaccines. In this review, we provide an overview of studies on attenuated plant viruses developed in Japan. We also discuss the application of the attenuated strains, including the production of vaccinated seedlings.

Pepper mild mottle virus can infect and traffick within Nicotiana benthamiana plants in non-virion forms

Virions are responsible for the long-distance transport of many viruses, such as Pepper mild mottle virus (PMMoV). Emerging evidence indicates viral traffic in the form of ribonucleoprotein complexes (RNP), yet comprehensive analysis is scarce. In this study, we inoculated plants with PMMoV-GFP, both with and without the coding sequence for the coat protein (CP). PMMoV-GFP was detected in systemic leaves, even in the absence of the CP, despite the presence of much smaller infection areas. Moreover, using leaf extracts from PMMoV-infected plants to perform a root-irrigation experiment, we confirmed that PMMoV can infect plants through root transmission. Diluting the leaf extracts significantly diminished infectivity, and attempts to compensate for the dilution of other components by adding virions above the original level proved ineffective. Our findings strongly indicate that PMMoV can infect and traffick within plants in non-virion forms. Future studies should aim to identify the specific forms involved.

High-throughput sequencing reveals the presence of novel and known viruses in diseased Paris yunnanensis

Paris spp. are important medicinal plant and main raw material for many Chinese patent medicines, but viral diseases have became serious problems in cultivation of this group of important medicinal plants in China. In this study, eight viruses were identified in the diseased plants of Paris yunnanensis by high-throughput sequencing (HTS) and RT-PCR. These viruses include three novel viruses (two potyviruses and one nepovirus), Hippeastrum chlorotic ringspot virus (HCRV), Lychnis mottle virus (LycMoV), Paris mosaic necrosis virus (PMNV), Paris virus 1 and pepper mild mottle virus. The three new viruses were tentatively named Paris potyvirus 3 (ParPV-3), Paris potyvirus 4 (ParPV-4), Paris nepovirus 1 (ParNV-1) and their complete genome sequences were determined. Sequence analyses showed ParPV-3 and ParPV-4 shared the highest amino acid (aa) sequence identities of 54.3% to each other and 53.0-57.8% to other known potyviruses. ParNV-1 had aa sequence identities of 28.8-63.7% at protease-polymerase (Pro-Pol) with other nepoviruses. Phylogenetic analyses further support that the three viruses are new members of their corresponding genera. Analyses of the partial sequences of HCRV and LycMoV infecting P. yunnanensis revealed they diverged from existing isolates by aa sequence identities of 97.1% at glycoprotein precursor of HCRV and 93.3% at polyprotein of LycMoV. These two viruses are reported for the first time in Paris spp. A total of 123 field samples collected from P. yunnanensis in four counties of Yunnan, Southwest China were tested by RT-PCR for detecting each of the eight viruses. Results showed that nearly half of the samples were positive for at least one of the eight viruses. Two potyviruses, ParPV-3 (26.8%) and PMNV (24.4%), were predominant and widely distributed in the fields, while other viruses occurred in low rates and/or had limited distribution. This study insights into the virome infecting P. yunnanensis and provides valuable information for diagnosis and control of viral diseases in P. yunnanensis.

Pepper Mild Mottle Virus Coat Protein as a Novel Target to Screen Antiviral Drugs

Pepper mild mottle virus (PMMoV) has caused serious economic losses to crop production in many countries. The coat protein (CP) of PMMoV is a multifunctional protein proved to be a determining factor in the assignment of virulence type. Therefore, we studied the interaction between drugs and PMMoV CP as a method to screen anti-PMMoV agents. In this study, vanisulfane (6f) exhibited good inactivation activity (68.5%) by biological activity screening. Meanwhile, the green fluorescent protein and PMMoV CP expression changes of vanisulfane against PMMoV were verified by western blot and qRT-PCR experiments. The affinity between vanisulfane and PMMoV CP was predicted to be the best by autodocking and molecular dynamics simulation. PMMoV CP was purified for the first time from the soluble fraction, and the strong affinity between vanisulfane and CP was further verified by interaction experiments. Therefore, this study found that vanisulfane is a potential anti-PMMoV drug targeting PMMoV CP.

First Discovery of Novel Cytosine Derivatives Containing a Sulfonamide Moiety as Potential Antiviral Agents

A series of cytosine derivatives containing a sulfonamide moiety were designed and synthesized, and their antiviral activities against pepper mild mottle virus (PMMoV) were systematically evaluated. Then, a three-dimensional quantitative structure-activity relationship (3D-QSAR) model was constructed to study the structure-activity relationship according to the pEC₅₀ of the compounds' protective activities. Next, compound A32 with preferable antiviral activity on PMMoV was obtained based on the CoMSIA and CoMFA models, with an EC₅₀ of 19.5 μg/mL, which was superior to the template molecule A25 (21.3 μg/mL) and ningnanmycin (214.0 μg/mL). In addition, further studies showed that the antiviral activity of compound A32 against PMMoV was in accord with the up-regulation of proteins expressed in the defense response and carbon fixation in photosynthetic organisms. These results indicated that cytosine derivatives containing a sulfonamide moiety could be used as novel potential antiviral agents for further research and development.

Defense Mechanism of Capsicum annuum L. Infected with Pepper Mild Mottle Virus Induced by Vanisulfane

Pepper mild mottle virus (PMMoV), an RNA virus, is one of the most devastating pathogens in pepper crops and has a significant influence on global crop yields. PMMoV poses a major threat to the global shortage of pepper plants and other Solanaceae crops due to the lack of an effective antiviral agent. In this study, we have developed a plant immune inducer (vanisulfane), as a "plant vaccine" that boosts plant immunity against PMMoV, and studied its resistance mechanism. The protective activity of vanisulfane against PMMoV was 59.4%. Vanisulfane can enhance the activity of defense enzymes and improve the content of chlorophyll, flavonoids, and total phenols for removing harmful free radicals from plants. Furthermore, vanisulfane was found to enhance defense genes. Label-free quantitative proteomics would tackle disease resistance pathways of vanisulfane. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, differentially abundant proteins (DAPs) are mainly involved in starch and sucrose metabolism, photosynthesis, MAPK signaling pathway, and oxidative phosphorylation pathway. These results are crucial for the discovery of new pesticides, understanding the improvement of plant immunity and the antiviral activity of plant immune inducers.

Identification of a Novel Quinvirus in the Family Betaflexiviridae That Infects Winter Wheat

Yellow mosaic disease in winter wheat is usually attributed to the infection by bymoviruses or furoviruses; however, there is still limited information on whether other viral agents are also associated with this disease. To investigate the wheat viromes associated with yellow mosaic disease, we carried out de novo RNA sequencing (RNA-seq) analyses of symptomatic and asymptomatic wheat-leaf samples obtained from a field in Hokkaido, Japan, in 2018 and 2019. The analyses revealed the infection by a novel betaflexivirus, which tentatively named wheat virus Q (WVQ), together with wheat yellow mosaic virus (WYMV, a bymovirus) and northern cereal mosaic virus (a cytorhabdovirus). Basic local alignment search tool (BLAST) analyses showed that the WVQ strains (of which there are at least three) were related to the members of the genus Foveavirus in the subfamily Quinvirinae (family Betaflexiviridae). In the phylogenetic tree, they form a clade distant from that of the foveaviruses, suggesting that WVQ is a member of a novel genus in the Quinvirinae. Laboratory tests confirmed that WVQ, like WYMV, is potentially transmitted through the soil to wheat plants. WVQ was also found to infect rye plants grown in the same field. Moreover, WVQ-derived small interfering RNAs accumulated in the infected wheat plants, indicating that WVQ infection induces antiviral RNA silencing responses. Given its common coexistence with WYMV, the impact of WVQ infection on yellow mosaic disease in the field warrants detailed investigation.

Transcriptomic and functional analyses reveal an antiviral role of autophagy during pepper mild mottle virus infection

BACKGROUND

Pepper mild mottle virus (PMMoV) is a member in the genus Tobamovirus and infects mainly solanaceous plants. However, the mechanism of virus-host interactions remains unclear. To explore the responses of pepper plants to PMMoV infection, we analyzed the transcriptomic changes in pepper plants after PMMoV infection using a high-throughput RNA sequencing approach and explored the roles of host autophagy in regulating PMMoV infection.

RESULTS

A total of 197 differentially expressed genes (DEGs) were obtained after PMMoV infection, including 172 significantly up-regulated genes and 25 down-regulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that most up-regulated DEGs were involved in plant abiotic and biotic stresses. Further analyses showed the expressions of multiple autophagy-related genes (ATGs) were increased after PMMoV infection in pepper and Nicotiana benthamiana plants. Through confocal microscopy and transmission electron microscopy, we have found that PMMoV infection in plant can induce autophagy, evidenced by the increased number of GFP-ATG8a fluorescent punctate and the appearance of double membrane autophagic structures in cells of N. benthamiana. Additionally, inhibition of autophagy significantly increased PMMoV RNA accumulation and aggravated systemic PMMoV symptoms through autophagy inhibitor (3-MA and E64d) treatment and silencing of NbATG expressions by a Tobacco rattle virus-induced gene silencing assays. These results indicated that autophagy played a positive role in plant resistance to PMMoV infection.

CONCLUSIONS

Taken together, our results provide a transcriptomic insight into pepper responding to PMMoV infection and reveal that autophagy induced by PMMoV infection has an antiviral role in regulating PMMoV infection. These results also help us to better understand the mechanism controlling PMMoV infection in plants and to develop better strategies for breeding projects for virus-resistant crops.

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.

Viral sequences required for efficient viral infection differ between two Chinese pepper mild mottle virus isolates

Pepper mild mottle virus (PMMoV) causes mosaic symptoms and malformation on both leaf and fruit of pepper, reduces considerable economical yields and poses threats to human health. In this study, infectious clone of PMMoV Huludao (HLD) isolate (pCB-PMMoV-HLD) was constructed and its infectious ablility in Nicotiana benthamiana was confirmed by virions observation and Northern blot analysis. The mutant PMMoV (HLD-fsCP) that cannot express coat protein (CP) showed reduced viral accumulation but can systemically infect N. benthamiana. We constructed several chimeric mutant viruses (ZA-HB-HC, HA-ZB-HC, HA-HB-ZC and HA-ZB-ZC) by sequences substitution between PMMoV-HLD and PMMoV Zhejiang isolates (PMMoV-ZJ) and analyzed their infectious abilities in N. benthamiana and Capsicum annuum. The results showed that the chimera virus expressed by pCB-ZA-HB-HC, pCB-HA-HB-ZC and pCB-HA-ZB-ZC, but not by pCB-HA-ZB-HC, exhibited reduced infectious ability compared with wild-type PMMoV-ZJ and PMMoV-HLD, which indicated that RNA sequences required for efficient infection of PMMoV differ between the two virus isolates. The differential requirement of viral RNA sequences for efficient PMMoV infection provided theoretical value to further understand the infection and pathogenesis of PMMoV.

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.

Atmospheric-pressure plasma irradiation can disrupt tobacco mosaic virus particles and RNAs to inactivate their infectivity

Low-temperature atmospheric-pressure air plasma is a source of charged and neutral gas species. In this study, N-carrying tobacco plants were inoculated with plasma irradiated and non-irradiated tobacco mosaic virus (TMV) solution, resulting in necrotic local lesions on non-irradiated, but not on irradiated, TMV-inoculated leaves. Virus particles were disrupted by plasma irradiation in an exposure-dependent manner, but the viral coat protein subunit was not. TMV RNA was also fragmented in a time-dependent manner. These results indicate that plasma irradiation of TMV can collapse viral particles to the subunit level, degrading TMV RNA and thereby leading to a loss of infectivity.

A single amino acid in the helicase domain of PMMoV-S is responsible for its enhanced accumulation in C. chinense (L(3)L(3)) plants at 32°C

In Capsicum chinense (L(3)L(3)) plants a higher accumulation of the tobamovirus Pepper mild mottle virus strain S (PMMoV-S) as compared to the Italian strain PMMoV-I is detected when plants are grown at 32°C. By using a reverse genetic approach, we have established that a single amino acid at position 898 in the helicase domain of the polymerase protein, outside of the conserved regions of the helicase, is critical for the higher accumulation of PMMoV-S observed. It also is necessary for both increased accumulation of viral RNA of both polarities in pepper protoplasts and enhanced cell-to-cell movement in C. chinense plants. The influence of thermoresistance of PMMoV-S, a P(1,2) pathotype, and its prevalence on pepper cultivars over PMMoV-I, a P(1,2,3), pathotype, is discussed.

Accumulation of Tobacco mosaic virus (TMV) at different depths clay and loamy sand textural soils due to tobacco waste application

The effects of tobacco waste (TW) application to the soil surface on the accumulation of Tobacco mosaic virus (TMV) in clay and loamy sand textural soils at various depths were investigated in two different fields. The tobacco waste had been found to be infected with TMV. Eighteen months after TW application to the soil surface, soils were sampled at 20 cm intervals through to 80 cm depth. The DAS-ELISA method was performed to determine infection of soil with TMV. The viruses persisted in clay soil for a long period compared with loamy sand soil. There was no accumulation of TMV at any depth of loamy sand soil in Experimental Field 2. TMV adsorption to soil particles in 0-60 cm depth of clay soil was determined in all TW treatments in Experimental Field 1. The highest ELISA Absorbance (A405) values in all treatments were determined in the 20-40 cm soil depth that had the highest clay content. ELISA A405 values of TMV at different depths of clay soil gave significant correlations with clay content (r = 0.793**), EC values (r = 0.421**) and soil pH (r = -0.405**). Adsorption of TMV to net negatively charged clay particle surfaces increased with increasing EC values of soil solution. Decreasing soil pH and infiltration rate increased adsorption of TMV to clay particles. Higher infiltration rate and lower clay content in loamy sand soil caused leaching of TMV from the soil profile.

Two Amino Acid Substitutions in the Coat Protein of Pepper mild mottle virus Are Responsible for Overcoming the L(4) Gene-Mediated Resistance in Capsicum spp

ABSTRACT The Capsicum spp. L genes (L(1) to L(4)) confer resistance to tobamoviruses. Currently, the L(4) gene from Capsicum chacoense is the most effective resistance gene and has been used widely in breeding programs in Japan which have developed new resistant cultivars against Pepper mild mottle virus (PMMoV). However, in 2004, mild mosaic symptoms began appearing on the leaves of commercial pepper plants in the field which possessed the L(4) resistance gene. Serological and biological assays on Capsicum spp. identified the causal virus strain as a previously unreported pathotype, P(1,2,3,4). PMMoV sequence analysis of the virus and site-directed mutagenesis using a PMMoV-J of the P(1,2) pathotype revealed that two amino acid substitutions in the coat protein, Gln to Arg at position 46 and Gly to Lys at position 85, were responsible for overcoming the L(4) resistance gene.