Suppression of Jasmonic Acid-Mediated Defense by Viral-Inducible MicroRNA319 Facilitates Virus Infection in Rice

MicroRNAs (miRNAs) are pivotal modulators of plant development and host-virus interactions. However, the roles and action modes of specific miRNAs involved in viral infection and host susceptibility remain largely unclear. In this study, we show that Rice ragged stunt virus (RRSV) infection caused increased accumulation of miR319 but decreased expression of miR319-regulated TCP (TEOSINTE BRANCHED/CYCLOIDEA/PCF) genes, especially TCP21, in rice plants. Transgenic rice plants overexpressing miR319 or downregulating TCP21 exhibited disease-like phenotypes and showed significantly higher susceptibility to RRSV in comparison with the wild-type plants. In contrast, only mild disease symptoms were observed in RRSV-infected lines overexpressing TCP21 and especially in the transgenic plants overexpressing miR319-resistant TCP21. Both RRSV infection and overexpression of miR319 caused the decreased endogenous jasmonic acid (JA) levels along with downregulated expression of JA biosynthesis and signaling-related genes in rice. However, treatment of rice plants with methyl jasmonate alleviated disease symptoms caused by RRSV and reduced virus accumulation. Taken together, our results suggest that the induction of miR319 by RRSV infection in rice suppresses JA-mediated defense to facilitate virus infection and symptom development.

EPG Recordings Reveal Differential Feeding Behaviors in Sogatella furcifera in Response to Plant Virus Infection and Transmission Success

Plant viruses are primarily transmitted by insect vectors and virus infection may influence on the vectors' feeding behaviors. Using an electrical penetration graph, we detected that infection with the Southern rice black-streaked dwarf virus (SRBSDV) in the white-backed planthopper (WBPH) and in rice plants both altered the vector's feeding behavior. When viruliferous WBPH (carrying SRBSDV) were fed on uninfected plants, they spent more time in salivation and phloem sap ingestion than non-viruliferous insects. In comparison with uninfected plants, infected plants showed an arrestant effect on non-viruliferous WBPH for phloem sap ingestion. Differential feeding behaviors were also detected between the WBPH that inoculated or acquired SRBSDV and those that failed to. The WBPH that inoculated SRBSDV exhibited more probing bouts, salivation events and phloem sap ingestion events and longer salivation than those that failed to. The WBPH that acquired SRBSDV were quicker to reach phloem and spent more time in phloem sap ingestion than those that failed to. These behavior alterations in the vector may have adaptive advantages for SRBSDV transmission and spread success because greater salivation by viruliferous vectors on uninfected hosts will promote virus inoculation, whereas more sap ingestion by non-viruliferous vectors on infected hosts will promote virus acquisition.

Rice Reoviruses in Insect Vectors

Rice reoviruses, transmitted by leafhopper or planthopper vectors in a persistent propagative manner, seriously threaten the stability of rice production in Asia. Understanding the mechanisms that enable viral transmission by insect vectors is a key to controlling these viral diseases. This review describes current understanding of replication cycles of rice reoviruses in vector cell lines, transmission barriers, and molecular determinants of vector competence and persistent infection. Despite recent breakthroughs, such as the discoveries of actin-based tubule motility exploited by viruses to overcome transmission barriers and mutually beneficial relationships between viruses and bacterial symbionts, there are still many gaps in our knowledge of transmission mechanisms. Advances in genome sequencing, reverse genetics systems, and molecular technologies will help to address these problems. Investigating the multiple interaction systems among the virus, insect vector, insect symbiont, and plant during natural infection in the field is a central topic for future research on rice reoviruses.

Roles of the Laodelphax striatellus Down syndrome cell adhesion molecule in Rice stripe virus infection of its insect vector

The arthropod Down syndrome cell adhesion molecule (Dscam) mediates pathogen-specific recognition via an extensive protein isoform repertoire produced by alternative splicing. To date, most studies have focused on the subsequent pathogen-specific immune response, and few have investigated the entry into cells of viruses or endosymbionts. In the present study, we cloned and characterized the cDNA of Laodelphax striatellus Dscam (LsDscam) and investigated the function of LsDscam in rice stripe virus (RSV) infection and the influence on the endosymbiont Wolbachia. LsDscam displayed a typical Dscam domain architecture, including 10 immunoglobulin (Ig) domains, six fibronectin type III domains, one transmembrane domain and a cytoplasmic tail. Alternative splicing occurred at the N-termini of the Ig2 and Ig3 domains, the complete Ig7 domain, the transmembrane domain and the C-terminus, comprising 10, 51, 35, two and two variable exons, respectively. Potentially LsDscam could encode at least 71 400 unique isoforms and 17 850 types of extracellular regions. LsDscam was expressed in various L. striatellus tissues. Knockdown of LsDscam mRNA via RNA interference decreased the titres of both RSV and Wolbachia, but did not change the numbers of the extracellular symbiotic bacterium Acinetobacter rhizosphaerae. Specific Dscam isoforms may play roles in enhancing the infection of vector-borne viruses or endosymbionts.

Hairpin RNA Targeting Multiple Viral Genes Confers Strong Resistance to Rice Black-Streaked Dwarf Virus

Rice black-streaked dwarf virus (RBSDV) belongs to the genus Fijivirus in the family of Reoviridae and causes severe yield loss in rice-producing areas in Asia. RNA silencing, as a natural defence mechanism against plant viruses, has been successfully exploited for engineering virus resistance in plants, including rice. In this study, we generated transgenic rice lines harbouring a hairpin RNA (hpRNA) construct targeting four RBSDV genes, S1, S2, S6 and S10, encoding the RNA-dependent RNA polymerase, the putative core protein, the RNA silencing suppressor and the outer capsid protein, respectively. Both field nursery and artificial inoculation assays of three generations of the transgenic lines showed that they had strong resistance to RBSDV infection. The RBSDV resistance in the segregating transgenic populations correlated perfectly with the presence of the hpRNA transgene. Furthermore, the hpRNA transgene was expressed in the highly resistant transgenic lines, giving rise to abundant levels of 21-24 nt small interfering RNA (siRNA). By small RNA deep sequencing, the RBSDV-resistant transgenic lines detected siRNAs from all four viral gene sequences in the hpRNA transgene, indicating that the whole chimeric fusion sequence can be efficiently processed by Dicer into siRNAs. Taken together, our results suggest that long hpRNA targeting multiple viral genes can be used to generate stable and durable virus resistance in rice, as well as other plant species.

A Signaling Cascade from miR444 to RDR1 in Rice Antiviral RNA Silencing Pathway

Plant RNA-DEPENDENT RNA POLYMERASE1 (RDR1) is a key component of the antiviral RNA-silencing pathway, contributing to the biogenesis of virus-derived small interfering RNAs. This enzyme also is responsible for producing virus-activated endogenous small interfering RNAs to stimulate the broad-spectrum antiviral activity through silencing host genes. The expression of RDR1 orthologs in various plants is usually induced by virus infection. However, the molecular mechanisms of activation of RDR1 expression in response to virus infection remain unknown. Here, we show that a monocot-specific microRNA, miR444, is a key factor in relaying the antiviral signaling from virus infection to OsRDR1 expression. The expression of miR444 is enhanced by infection with Rice stripe virus (RSV), and overexpression of miR444 improves rice (Oryza sativa) resistance against RSV infection accompanied by the up-regulation of OsRDR1 expression. We further show that three miR444 targets, the MIKC(C)-type MADS box proteins OsMADS23, OsMADS27a, and OsMADS57, form homodimers and heterodimers between them to repress the expression of OsRDR1 by directly binding to the CArG motifs of its promoter. Consequently, an increased level of miR444 diminishes the repressive roles of OsMADS23, OsMADS27a, and OsMADS57 on OsRDR1 transcription, thus activating the OsRDR1-dependent antiviral RNA-silencing pathway. We also show that overexpression of miR444-resistant OsMADS57 reduced OsRDR1 expression and rice resistance against RSV infection, and knockout of OsRDR1 reduced rice resistance against RSV infection. In conclusion, our results reveal a molecular cascade in the rice antiviral pathway in which miR444 and its MADS box targets directly control OsRDR1 transcription.

Different pathogenicities of Rice stripe virus from the insect vector and from viruliferous plants

Persistent plant viruses usually depend on insects for their transmission; they cannot be transmitted between plants or through mechanical inoculation. However, the mechanism by which persistent viruses become pathogenic in insect vectors remains unknown. In this study, we used Rice stripe virus (RSV), its insect vector Laodelphax striatellus and host plant (Oryza sativa) to explore how persistent viruses acquire pathogenicity from insect vectors. RSV acquired phytopathogenicity in both the alimentary tract and the salivary gland of L. striatellus. We mechanically inoculated RSV into rice O. sativa leaves through midrib microinjection. Insect-derived RSV induced a typical stripe symptom, whereas plant-derived RSV only produced chlorosis in rice leaves. Insect-derived RSV had higher expression of genes rdrp, ns2, nsvc2, sp and nsvc4 than plant-derived RSV, and the latter had higher expression of genes cp and ns3 than the former in rice leaves. Different from plant-derived RSV, insect-derived RSV damaged grana stacks within the chloroplast and inhibited photosynthesis by suppressing the photosystem II subunit psbp. This study not only presented a convenient method to mechanically inoculate RSV into plants, but also provided insights into the different pathogenic mechanisms of RSV from the insect vector and from viruliferous plants.

Organ-specific transcriptome response of the small brown planthopper toward rice stripe virus

Rice stripe virus (RSV) causes rice stripe disease and is transmitted by the small brown planthopper (Laodelphax striatellus, SBPH) in a persistent, circulative, and propagative manner. The alimentary canal and salivary gland of SBPH play important roles in viral replication and transmission. However, little is known about the underlying molecular functions of these two organs in the interaction between RSV and SBPH. In this study, organ-specific transcriptomes of the alimentary canal and salivary gland were analyzed in viruliferous and naïve SBPH. The number of differentially expressed unigenes in the alimentary canal was considerably greater than that in the salivary gland after RSV infection, and only 23 unigenes were co-regulated in the two organs. In the alimentary canal, genes involved in lysosome, digestion and detoxification were activated upon RSV infection, whereas the genes related to DNA replication and repair were suppressed. RSV activated RNA transport and repressed the MAPK, mTOR, Wnt, and TGF-beta signaling pathways in the salivary gland. The overall immune reaction toward RSV was much stronger in the salivary gland than in the alimentary canal. RSV activated the pattern recognition molecules and Toll pathway in the salivary gland but inhibited these two reactions in the alimentary canal. The responses from reactive oxygen and the immune-responsive effectors were stronger in the salivary gland than in the alimentary canal after RSV infection. These findings provide clues on the roles of the two organs in confronting RSV infection and aid in the understanding of the interaction between RSV and SBPHs.

Viruliferous rate of small brown planthopper is a good indicator of rice stripe disease epidemics

Rice stripe virus (RSV), its vector insect (small brown planthopper, SBPH) and climatic conditions in Jiangsu, China were monitored between 2002 and 2012 to determine key biotic and abiotic factors driving epidemics of the disease. Average disease severity, disease incidence and viruliferous rate of SBPH peaked in 2004 and then gradually decreased. Disease severity of RSV was positively correlated with viruliferous rate of the vector but not with the population density of the insect, suggesting that the proportion of vectors infected by the virus rather than the absolute number of vectors plays an important role in RSV epidemics and could be used for disease forecasting. The finding of a positive correlation of disease severity and viruliferous rate among years suggests that local infection is likely the main source of primary inoculum of RSV. Of the two main climatic factors, temperature plays a more important role than rainfall in RSV epidemics.

Study of the long-distance migration of small brown planthoppers Laodelphax striatellus in China using next-generation sequencing

BACKGROUND

The small brown planthopper (Laodelphax striatellus) is a widespread insect pest of rice in East Asia. Previous studies have shown the long-distance migrations undertaken by L. striatellus, but have not provided molecular evidence to support this.

RESULTS

Long-distance immigration has occurred in the north-east coastal rice-growing region of China. Using the specific-locus amplified fragment sequencing technique, sequence data for 2.7 Gb of an abruptly increased population and 13 L. striatellus local populations from a range of regions in China that have serious rice stripe disease were obtained. A total of 2572 single nucleotide polymorphisms (SNPs) and 37 indels were detected, and the genotypes of many polymorphism sites were heterozygous in every sample, which indicated that there were rich genetic differences among the populations, and that the migration of insect pests accelerated the gene flow and increased the heterozygosity of L. striatellus populations. The genetic distance and the polymorphism markers among different populations showed that the abruptly increased population in Liaoning Province is close to several populations from Jiangsu Province and Shandong Province.

CONCLUSION

The vector that caused rice stripe disease in the north-east of China was an immigrant population; however, the population may be formed from several groups from different areas, such as Jiangsu and Shandong provinces.

Low Temperature Storage of Southern Rice Black-Streaked Dwarf Virus-Infected Rice Plants Cannot Sustain Virus Transmission by the Vector

Southern rice black-streaked dwarf virus (SRBSDV) is a novel virus transmitted by white-backed planthopper Sogatella furcifera (Hováth) (Hemiptera: Delphacidae). Due to low virus transmission efficiency by the planthopper, researchers are frequently confronted with shortage of viruliferous vectors or infected rice plants, especially in winter and the following spring. To find new ways to maintain virus-infected materials, viral rice plants were stored at -80°C for 45 or 140 d and evaluated as virus sources in virus transmission by the vector. SRBSDV virions were not degraded during storage at -80°C as indicated by reverse transcription-polymerase chain reaction and reverse transcription real-time PCR detection. The planthopper nymphs fed on the infected thawed plants for 48 h survived at about 40% and showed positive detection of SRBSDV, but they lost the virus after feeding for another 20 d (the circulative transmission period) on noninfected plants. Transmission electron microscope images indicated broken capsid of virions in infected thawed leaves in contrast to integrity capsid of virions in infected fresh leaves. These results show that low temperature storage of SRBSDV-infected rice plants cannot sustain virus transmission by white-backed planthopper.

Identification and regulation of host genes related to Rice stripe virus symptom production

Viral infections cause plant chlorosis, stunting, necrosis or other symptoms. The down-regulation of chloroplast-related genes (ChRGs) is assumed to be responsible for chlorosis. We identified the differentially expressed genes (DEGs) in Rice stripe virus (RSV)-infected Nicotiana benthamiana, and examined the contribution of 75 down-regulated DEGs to RSV symptoms by silencing them one by one using Tobacco rattle virus (TRV)-induced gene silencing. Silencing of 11 of the 75 down-regulated DEGs caused plant chlorosis, and nine of the 11 were ChRGs. Silencing of a down-regulated DEG encoding the eukaryotic translation initiation factor 4A (eIF4A) caused leaf-twisting and stunting that were visible on RSV-infected N. benthamiana. A region of RSV RNA4 was complementary to part of eIF4A mRNA and virus-derived small interfering (vsiRNAs) from that region were present in infected N. benthamiana. When expressed as artificial microRNAs, those vsiRNAs could target NbeIF4A mRNA for regulation. We provide experimental evidence supporting the association of ChRGs with chlorosis and show that eIF4A is involved in RSV symptom development. This is also the first report demonstrating that siRNA derived directly from a plant virus can target a host gene for regulation.

Integrative Analysis of the microRNAome and Transcriptome Illuminates the Response of Susceptible Rice Plants to Rice Stripe Virus

Rice stripe virus (RSV) is one of the most serious rice viruses in East Asia. To investigate how rice responds to RSV infection, we integrated miRNA expression with parallel mRNA transcription profiling by deep sequencing. A total of 570 miRNAs were identified of which 69 miRNAs (56 up-regulated and 13 down-regulated) were significantly modified by RSV infection. Digital gene expression (DGE) analysis showed that 1274 mRNAs (431 up-regulated and 843 down-regulated genes) were differentially expressed as a result of RSV infection. The differential expression of selected miRNAs and mRNAs was confirmed by qRT-PCR. Gene ontology (GO) and pathway enrichment analysis showed that a complex set of miRNA and mRNA networks were selectively regulated by RSV infection. In particular, 63 differentially expressed miRNAs were found to be significantly and negatively correlated with 160 target mRNAs. Interestingly, 22 up-regulated miRNAs were negatively correlated with 24 down-regulated mRNAs encoding disease resistance-related proteins, indicating that the host defense responses were selectively suppressed by RSV infection. The suppression of both osa-miR1423-5p- and osa-miR1870-5p-mediated resistance pathways was further confirmed by qRT-PCR. Chloroplast functions were also targeted by RSV, especially the zeaxanthin cycle, which would affect the stability of thylakoid membranes and the biosynthesis of ABA. All these modifications may contribute to viral symptom development and provide new insights into the pathogenicity mechanisms of RSV.

P2 of Rice grassy stunt virus (RGSV) and p6 and p9 of Rice ragged stunt virus (RRSV) isolates from Vietnam exert suppressor activity on the RNA silencing pathway

In Vietnam, the two main viruses that cause disease in rice are the Rice grassy stunt virus (RGSV) and the Rice ragged stunt virus (RRSV). Outbreaks of these two viruses have dramatically decreased rice production in Vietnam. Because natural resistance genes are unknown, an RNAi strategy may be an alternative method to develop resistance to RGSV and RRSV. However, this strategy will be efficient only if putative silencing suppressors encoded by the two viruses are neutralized. To identify these suppressors, we used the classical green fluorescent protein (GFP) agroinfiltration method in Nicotiana benthamiana. Then, we investigated the effects of viral candidate proteins on GFP expression and GFP siRNA accumulation and their interference with the short- or long-range signal of silencing. RGSV genes s2gp1, s5gp2, and s6gp1 and RRSV genes s5gp1, s6gp1, s9gp1, and s10gp1 were selected for viral silencing suppressor investigation according to their small molecular weight, the presence of cysteines, or the presence of a GW motif in related protein products. We confirmed that protein p6 of RRSV displays mild silencing suppressor activity and affects long-range silencing by delaying the systemic silencing signal. In addition, we identified two new silencing suppressors that displayed mild activity: p2 of RGSV and p9 of RRSV.

Interaction of HSP20 with a viral RdRp changes its sub-cellular localization and distribution pattern in plants

Small heat shock proteins (sHSPs) perform a fundamental role in protecting cells against a wide array of stresses but their biological function during viral infection remains unknown. Rice stripe virus (RSV) causes a severe disease of rice in Eastern Asia. OsHSP20 and its homologue (NbHSP20) were used as baits in yeast two-hybrid (YTH) assays to screen an RSV cDNA library and were found to interact with the viral RNA-dependent RNA polymerase (RdRp) of RSV. Interactions were confirmed by pull-down and BiFC assays. Further analysis showed that the N-terminus (residues 1-296) of the RdRp was crucial for the interaction between the HSP20s and viral RdRp and responsible for the alteration of the sub-cellular localization and distribution pattern of HSP20s in protoplasts of rice and epidermal cells of Nicotiana benthamiana. This is the first report that a plant virus or a viral protein alters the expression pattern or sub-cellular distribution of sHSPs.

Current Status of Proteomic Studies on Defense Responses in Rice

Biotic stresses are constraints to plant growth and development negatively impacting crop production. To counter such stresses, plants have developed stress-specific adaptations as well as simultaneous responses. The efficacy and magnitude of inducible adaptive responses are dependent on activation of signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification of proteins associated with defense mechanisms. Proteomics plays an important role in elucidating plant defense mechanisms by mining the differential regulation of proteins to various biotic stresses. Rice, one of the most widely cultivated food crops in world, is constantly challenged by a variety of biotic stresses, and high-throughput proteomics approaches have been employed to unravel the molecular mechanism of the biotic stresses-response in rice. In this review, we summarize the latest advances of proteomic studies on defense responses and discuss the potential relevance of the proteins identified by proteomic means in rice defense mechanism. Furthermore, we provide perspective for proteomics in unraveling the molecular mechanism of rice immunity.

Rice Responses and Resistance to Planthopper-Borne Viruses at Transcriptomic and Proteomic Levels

Rice (Oryza sativa) is one of the most important cereal crops in the world, especially in Asian areas. Rice virus diseases are considered as the most serious threat to rice yields. Most rice viruses are transmitted by hemipteran insects such as planthoppers and leafhoppers. In Asia five rice viruses are transmitted mainly by three planthopper species in a persistent manner: Rice stripe virus, Rice black-streaked dwarf virus, Rice ragged stunt virus, Rice grassy stunt virus, and Southern rice black-streaked dwarf virus. In rice antivirus studies, several individual genes have been shown to function in rice resistance to viruses. Since plant responses to viral infection are complex, system-level omic studies are required to fully understand the responses. Recently more and more omic studies have appeared in the literatures on relationships between planthoppers and viruses, employing microarray, RNA-Seq, small RNA deep sequencing, degradome sequencing, and proteomic analysis. In this paper, we review the current knowledge and progress of omic studies in rice plant responses and resistance to four planthopper-borned viruses. We also discuss progress in the omic study of the interactions of planthoppers and rice viruses. Future research directions and translational applications of fundamental knowledge of virus-vector-rice interactions are proposed.

Time-Course RNA-Seq Analysis Reveals Transcriptional Changes in Rice Plants Triggered by Rice stripe virus Infection

Rice stripe virus (RSV) has become a major pathogen of rice. To determine how the rice transcriptome is modified in response to RSV infection, we used RNA-Seq to perform a genome-wide gene expression analysis of a susceptible rice cultivar. The transcriptomes of RSV-infected samples were compared to those of mock-treated samples at 3, 7, and 15 days post-infection (dpi). From 8 to 11% of the genes were differentially expressed (>2-fold difference in expression) in RSV-infected vs. noninfected rice. Among them, 532 genes were differentially expressed at all three time points. Surprisingly, 37.6% of the 532 genes are related to transposons. Gene ontology enrichment analysis revealed that many chloroplast genes were down-regulated in infected plants at 3 and 15 dpi. Expression of genes associated with cell differentiation and flowering was significantly down-regulated in infected plants at 15 dpi. In contrast, most of the up-regulated genes in infected plants concern the cell wall, plasma membrane, and vacuole and are known to function in various metabolic pathways and stress responses. In addition, transcripts of diverse transcription factors gradually accumulated in infected plants with increasing infection time. We also confirmed that the expression of gene subsets (including NBS-LRR domain-containing genes, receptor-like kinase genes, and genes involving RNA silencing) was changed by RSV infection. Taken together, we demonstrated that down-regulation of genes related to photosynthesis and flowering was strongly associated with disease symptoms caused by RSV and that up-regulation of genes involved in metabolic pathways, stress responses, and transcription was related to host defense mechanisms.

Relation Between the Viral Load Accumulation of Southern Rice Black-Streaked Dwarf Virus and the Different Developmental Stages of Sogatella furcifera (Hemiptera: Delphacidae)

The white-backed planthopper, Sogatella furcifera (Horvath), is currently the only confirmed vector of Southern rice black-streaked dwarf virus (SRBSDV), which causes severe rice production losses in China. In this study, an absolute quantification qPCR method was used to detect viral gene mRNA expression levels at different developmental stages of white-backed planthoppers fed SRBSDV-infected rice plants. A comparison of viral copy numbers of the SRBSDV S10 gene at the same developmental stage indicated that the white-backed planthopper had higher viral copy numbers when the virus was acquired at the earlier developmental stages. The adult-stage white-backed planthoppers that had acquired the virus at the first-second nymphal stage displayed significantly higher viral titers than white-backed planthoppers that acquired the virus at the third-fourth nymphal stage, at the fifth nymphal stage, and at the adult stage. The fifth nymphal stage white-backed planthoppers that acquired the virus at the first-second nymphal stage displayed higher viral copy numbers than fifth nymphal stage white-backed planthoppers that acquired the virus at the third-fourth nymphal stage and at the fifth nymphal stage. The highest viral load value appeared in the middle adult stage. The annual immigration characteristics of white-backed planthoppers would be beneficial for the dispersal of SRBSDV because this virus could be transmitted far away following the migration of vigorous planthoppers. Therefore, investigating the change in the viral load at different life stages of SRBSDV-positive individuals is required to develop more effective control of the spread of SRBSDV in the field.

Brome mosaic virus Infection of Rice Results in Decreased Accumulation of RNA1

Brome mosaic virus (BMV) (the Russian strain) infects monocot plants and has been studied extensively in barley and wheat. Here, we report BMV can systemically infect rice (Oryza sativa var. japonica), including cultivars in which the genomes have been determined. The BMV capsid protein can be found throughout the inoculated plants. However, infection in rice exhibits delayed symptom expression or no symptoms when compared with wheat (Triticum aestivum). The sequences of BMV RNAs isolated from rice did not reveal any nucleotide changes in RNA1 or RNA2, while RNA3 had only one synonymous nucleotide change from the inoculum sequence. Preparations of purified BMV virions contained RNA1 at a significantly reduced level relative to the other two RNAs. Analysis of BMV RNA replication in rice revealed that minus-strand RNA1 was replicated at a reduced rate when compared with RNA2. Thus, rice appears to either inhibit RNA1 replication or lacks a sufficient amount of a factor needed to support efficient RNA1 replication.

Quantitative Analysis of Southern rice black-streaked dwarf virus in Sogatella furcifera and Virus Threshold for Transmission

We investigated Southern rice black-streaked dwarf virus (SRBSDV) accumulation in a vector insect, the whitebacked planthopper (Sogatella furcifera), to elucidate the association of virus accumulation in the vector with virus transmission efficiency. Real-time quantitative reverse transcription polymerase chain reaction analysis confirmed that this virus is transmitted in a persistent-propagative manner. SRBSDV was successfully transmitted by S. furcifera males in which RNA accumulation of the capsid protein gene of SRBSDV was >10(3) in the whole body of S. furcifera, indicating that the threshold accumulation of the virus RNA for virus transmission is 10(3) in an S. furcifera male. The SRBSDV detection rate in the immigrant population of S. furcifera was high in 2011 (39.5%); however, most of the insects contained fewer than 10(3) RNAs of the capsid protein gene. This result indicates that the risk of SRBSDV epidemics could be estimated from the proportion of virus-transmissible S. furcifera (i.e., S. furcifera that contained more than 10(3) RNAs of the virus capsid protein gene) rather than the SRBSDV detection rate in S. furcifera.

Interaction research on the antiviral molecule dufulin targeting on southern rice black streaked dwarf virus p9-1 nonstructural protein

Southern rice black streaked dwarf virus (SRBSDV) causes severe harm to rice production. Unfortunately, studies on effective antiviral drugs against SRBSDV and interaction mechanism of antiviral molecule targeting on SRBSDV have not been reported. This study found dufulin (DFL), an ideal anti-SRBSDV molecule, and investigated the interactions of DFL targeting on the nonstructural protein P9-1. The biological sequence information and bonding characterization of DFL to four kinds of P9-1 protein were described with fluorescence titration (FT) and microscale thermophoresis (MST) assays. The sequence analysis indicated that P9-1 had highly-conserved C- and N-terminal amino acid residues and a hypervariable region that differed from 131 aa to 160 aa. Consequently, wild-type (WT-His-P9-1), 23 C-terminal residues truncated (TR-ΔC23-His-P9-1), 6 N-terminal residues truncated (TR-ΔN6-His-P9-1), and Ser138 site-directed (MU-138-His-P9-1) mutant proteins were expressed. The FT and MST assay results indicated that DFL bounded to WT-His-P9-1 with micromole affinity and the 23 C-terminal amino acids were the potential targeting site. This system, which combines a complete sequence analysis, mutant protein expression, and binding action evaluating system, could further advance the understanding of the interaction abilities between antiviral drugs and their targets.

Rice stripe virus affects the viability of its vector offspring by changing developmental gene expression in embryos

Plant viruses may affect the viability and development process of their herbivore vectors. Small brown planthopper (SBPH) is main vector of Rice stripe virus (RSV), which causes serious rice stripe disease. Here, we reported the effects of RSV on SBPH offspring by crossing experiments between viruliferous and non-viruliferous strains. The life parameters of offspring from different cross combinations were compared. The hatchability of F1 progeny from viruliferous parents decreased significantly, and viruliferous rate was completely controlled by viruliferous maternal parent. To better elucidate the underlying biological mechanisms, the morphology of eggs, viral propagation and distribution in the eggs and expression profile of embryonic development genes were investigated. The results indicated that RSV replicated and accumulated in SBPH eggs resulting in developmental stunt or delay of partial eggs; in addition, RSV was only able to infect ovum but not sperm. According to the expression profile, expression of 13 developmental genes was regulated in the eggs from viruliferous parents, in which two important regulatory genes (Ls-Dorsal and Ls-CPO) were most significantly down-regulated. In general, RSV exerts an adverse effect on SBPH, which is unfavourable for the expansion of viruliferous populations. The viewpoint is also supported by systematic monitoring of SBPH viruliferous rate.

Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon

In eukaryotes, alternative splicing (AS) promotes transcriptome and proteome diversity. The extent of genome-wide AS changes occurring during a plant-microbe interaction is largely unknown. Here, using high-throughput, paired-end RNA sequencing, we generated an isoform-level spliceome map of Brachypodium distachyon infected with Panicum mosaic virus and its satellite virus. Overall, we detected ∼44,443 transcripts in B. distachyon, ∼30% more than those annotated in the reference genome. Expression of ∼28,900 transcripts was ≥2 fragments per kilobase of transcript per million mapped fragments, and ∼42% of multi-exonic genes were alternatively spliced. Comparative analysis of AS patterns in B. distachyon, rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), Arabidopsis thaliana, potato (Solanum tuberosum), Medicago truncatula, and poplar (Populus trichocarpa) revealed conserved ratios of the AS types between monocots and dicots. Virus infection quantitatively altered AS events in Brachypodium with little effect on the AS ratios. We discovered AS events for >100 immune-related genes encoding receptor-like kinases, NB-LRR resistance proteins, transcription factors, RNA silencing, and splicing-associated proteins. Cloning and molecular characterization of SCL33, a serine/arginine-rich splicing factor, identified multiple novel intron-retaining splice variants that are developmentally regulated and modulated during virus infection. B. distachyon SCL33 splicing patterns are also strikingly conserved compared with a distant Arabidopsis SCL33 ortholog. This analysis provides new insights into AS landscapes conserved among monocots and dicots and uncovered AS events in plant defense-related genes.

Interactions of Rice tungro bacilliform pararetrovirus and its protein P4 with plant RNA-silencing machinery

Small interfering RNA (siRNA)-directed gene silencing plays a major role in antiviral defense. Virus-derived siRNAs inhibit viral replication in infected cells and potentially move to neighboring cells, immunizing them from incoming virus. Viruses have evolved various ways to evade and suppress siRNA production or action. Here, we show that 21-, 22-, and 24-nucleotide (nt) viral siRNAs together constitute up to 19% of total small RNA population of Oryza sativa plants infected with Rice tungro bacilliform virus (RTBV) and cover both strands of the RTBV DNA genome. However, viral siRNA hotspots are restricted to a short noncoding region between transcription and reverse-transcription start sites. This region generates double-stranded RNA (dsRNA) precursors of siRNAs and, in pregenomic RNA, forms a stable secondary structure likely inaccessible to siRNA-directed cleavage. In transient assays, RTBV protein P4 suppressed cell-to-cell spread of silencing but enhanced cell-autonomous silencing, which correlated with reduced 21-nt siRNA levels and increased 22-nt siRNA levels. Our findings imply that RTBV generates decoy dsRNA that restricts siRNA production to the structured noncoding region and thereby protects other regions of the viral genome from repressive action of siRNAs, while the viral protein P4 interferes with cell-to-cell spread of antiviral silencing.