Shuhei Miyashita

• PhD
• Professor (Assistant) at Tohoku University

Genetic bottlenecks facilitate the fixation and extinction of variants in populations, and viral populations are no exception to this theory. To examine the existence of genetic bottlenecks in cell-to-cell movement of plant RNA viruses, we prepared constructs for Soil-borne wheat mosaic virus RNA2 vectors carrying two different fluorescent proteins...

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...

Recent studies on evolutionarily distant viral groups have shown that the number of viral genomes that establish cell infection after cell-to-cell transmission is unexpectedly small (1-20 genomes). This aspect of viral infection appears to be important for the adaptation and survival of viruses. To clarify how the number of viral genomes that estab...

Land plant genomes carry tens to hundreds of Resistance ( R ) genes to combat pathogens. The induction of antiviral R -gene-mediated resistance often results in a hypersensitive response (HR), which is characterized by virus containment in the initially infected tissues and programmed cell death (PCD) of the infected cells. Alternatively, systemic...

In evaluating the germination and growth of the seed resources of 322 cultivars of cowpea (Vigna unguiculata), we found the development of yellow symptoms on ~50% of the cotyledons of 10 cultivars. RNA-Seq analysis of total RNA extracted from symptomatic cotyledons indicated that the 10 cultivars were infected with the bean common mosaic virus (Pot...

The treatment of plants with non-thermal atmospheric-pressure plasma impacts several aspects of plant life. However, the effects of long-term plasma irradiation on crop cultivation are not enough investigated. The purpose of the current study is to address this subject. The growth of tomato plants, the preservation status of harvested tomato fruits...

Two Ralstonia phages, FLC1-1B and FLC4-3B, were isolated from leaf litter compost, using Ralstonia pseudosolanacearum, which is a causal agent of bacterial wilt disease, as a host. The genomic DNA sequences of FLC1-1B and FLC4-3B were determined and found to be 290,008 bp and 291,257 bp in length, respectively, and they were therefore classified as...

Two Ralstonia phages, FLC1-1B and FLC4-3B, were isolated from leaf litter compost, using Ralstonia pseudosolanacearum, which is a causal agent of bacterial wilt disease, as a host. The genomic DNA sequences of FLC1-1B and FLC4-3B were 290,008 bp and 291,257 bp, respectively, and they were therefore classified as jumbo phages. However, they did not...

The coat protein (CP) of the cucumber mosaic virus (CMV) yellow strain [CMV(Y)], but not the CMV B2 strain [CMV(B2)], serves as an avirulence determinant against the NB-LRR class RCY1 of Arabidopsis thaliana. To investigate the avirulence function, a series of binary vectors were constructed by partially exchanging the CP coding sequence between CM...

The coat protein (CP) of cucumber mosaic virus (CMV) yellow strain [CMV(Y)] but not CMV B2 strain [CMV(B2)], is an avirulence determinant against NB-LRR class RCY1 of Arabidopsis thaliana . To dissect the avirulent function, a series of binary vectors, which were constructed by partially exchanging CP-coding sequence between CMV(Y) and CMV(B2) or n...

Viruses with single-stranded, positive-sense (+) RNA genomes incur high numbers of errors during replication, thereby creating diversified genome populations from which new, better adapted viral variants can emerge. However, a definitive error rate is known for a relatively few (+) RNA plant viruses, due to challenges to account for perturbations c...

Induction of R-gene-mediated antiviral resistance results in phenotypically different responses depending on host R gene—virus combinations. The responses include a hypersensitive response (HR), in which virus infection is stopped within the initially infected tissues to form necrotic local lesions (NLLs) by induction of programmed-cell death (PCD)...

Viruses with single-stranded, positive-sense (+) RNA genomes incur high numbers of errors during replication, thereby creating diversified genome populations from which new, better adapted viral variants can emerge. However, a definitive error rate is known for a relatively few (+) RNA plant viruses, due to challenges to account for perturbations c...

Viruses are constantly subject to natural selection to enrich beneficial mutations and weed out deleterious ones. However, it remains unresolved as to how the phenotypic gains or losses brought about by these mutations cause the viral genomes carrying the very mutations to become more or less numerous. Previous investigations by us and others sugge...

Jumbo bacteriophages, which have genomic DNA larger than 200 k-bp, are attracting attention as potential biocontrol agents to suppress bacterial diseases in cultivated crops because they generally have a broader host range of phytopathogenic bacteria compared with ordinary bacteriophages. Thus, the identification of new jumbo phages from environmen...

Reactive nitrogen species (RNS) play an important role in plant immunity as signaling factors. We previously developed a plasma technology to partially convert air molecules into dinitrogen pentoxide (N2O5), an RNS whose physiological action is poorly understood. To reveal the function of N2O5 gas in plant immunity, Arabidopsis thaliana was exposed...

Cellular organisms purge lethal mutations as they occur (in haploids), or as soon as they become homozygous (in sexually reproducing diploids), thus making the mutation-carrying genomes the sole victims of lethality. How lethal mutations in viruses are purged remains an unresolved question because numerous viral genomes could potentially replicate...

Although several reports exist on the use of X-ray analysis in vegetables and fruits to examine internal disorders, cavities, and porosity, information on X-ray analysis of qualities, such as texture, is lacking as well as information on X-ray analysis of legumes. Therefore, this study aimed to perform X-ray analysis with sensory and rheometer test...

In this study, we developed an effective and stable technique for suppressing seedling rot of rice caused by Burkholderia glumae using bacterial communities cultured from nursery soils for organic farming (OF) of rice that have disease-suppressive activity. When culturable bacterial communities (CBCs) isolated from OF soils by growth on nutrient-ag...

A cucumber mosaic virus isolate, named Ho [CMV(Ho)], was isolated from a symptomless Arabidopsis halleri field sample containing low virus titers. An analysis of CMV(Ho) RNA molecules indicated that the virus isolate, besides the usual cucumovirus tripartite RNA genome, additionally contained defective RNA3 molecules and a satellite RNA. To study t...

Jumbo phages have DNA genomes larger than 200 kbp in large virions composed of an icosahedral head, tail, and other adsorption structures, and they are known to be abundant biological substances in nature. In this study, phages in leaf litter compost were screened for their potential to suppress rice seedling rot disease caused by the bacterium Bur...

In contrast to most Burkholderia species, which affect humans or animals, Burkholderia glumae is a bacterial pathogen of plants that causes panicle blight disease in rice seedlings, resulting in serious damage to rice cultivation. Attempts to combat this disease would benefit from research involving a phage known to attack this type of bacterium. S...

Many positive sense RNA viruses, especially those infecting plants, are known to experience stringent, stochastic population bottlenecks inside the cells they invade, but exactly how and why these populations become bottlenecked are unclear. A model proposed ten years ago advocates that such bottlenecks are evolutionarily favored because they cause...

The filamentous fungus Neurospora crassa is used as a model organism for genetics, developmental biology and molecular biology. Remarkably, it is not known to host or to be susceptible to infection with any viruses. Here, we identify diverse RNA viruses in N. crassa and other Neurospora species, and show that N. crassa supports the replication of t...

Systemic acquired resistance (SAR) is a broad-spectrum disease resistance response that can be induced upon infection from pathogens or by chemical treatment, such as with benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH). SAR involves priming for more robust activation of defence genes upon pathogen attack. Whether priming for SAR...

Many positive sense RNA viruses, especially those infecting plants, are known to experience stringent, stochastic population bottlenecks inside the cells they invade, but exactly how and why these populations become bottlenecked are unclear. A model proposed ten years ago advocates that such bottlenecks are evolutionarily favored because they cause...

When Arabidopsis thaliana ecotype Col-0 was inoculated with a series of reassortant viruses created by exchanging viral genomic RNAs between two strains of cucumber mosaic virus (CMV), CMV(Y), and CMV(H), cell death developed in the leaves inoculated with reassortant CMV carrying CMV(H) RNA1 encoding 1a protein, but not in noninoculated upper leave...

Exogenous application of L‐histidine enhances resistance to pathogens in tomato (Solanum lycopersicum) and Arabidopsis thaliana via activation of the ethylene (ET)‐dependent signaling pathway. In this study, the efficacy of L‐histidine for suppression of bacterial diseases in rice seedlings was investigated. Rice seeds were soaked in 10 mM L‐histid...

To protect against infection, plants have evolved multi-layered defense systems such as RNA silencing, salicylic acid (SA)-mediated resistance, resistance (R) protein-conferred resistance and defense priming. Antiviral defense systems seem to act in a coordinated manner in response to viral infection, but the underlying mechanisms are unknown excep...

CMV infected in Corchorus olitorius plants cultivated on a farm in Miyagi Prefecture, Japan, was analyzed via western blotting using antibody against the coat protein of cucumber mosaic virus (CMV). The virus was purified from Nicotiana benthamiana leaves rub-inoculated with a homogenate of infected C. olitorius containing CMV genomic RNA. The CMV...

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 w...

Zea mays has been historically imported to Japan via two independent geographical routes: into southern Japan by trading with Europe in the 16th century and into northern Japan by import from North America in the 19th century. Breeding to genetically improve on quality traits and high yields has led to the current domestic landraces in each region....

The outbreak of rice plant diseases can be effectively suppressed in organic farming systems. However, the mechanisms of disease suppression by organic farming systems are not well understood. When Burkholderia-infected rice seeds were sown and cultivated on nine organic-farmed soils which were supplied by nine independent organic rice farmers or s...

In Arabidopsis thaliana, RESISTANCE TO CMV(Y) (RCY1), which encodes a CC-NB-LRR class protein, confers the hypersensitive response (HR) to a yellow strain of cucumber mosaic virus [CMV(Y)]. A. thaliana ecotype Col-0 overexpressing RCY1 transgenes (Col::pRCY1-HA#13) shows extreme resistance (ER) to CMV(Y). To identify novel regulatory factors involv...

Ralstonia solanacearum causes bacterial wilt disease in Solanaceae spp. Expression of the Phytophthora inhibitor protease 1 (PIP1) gene, which encodes a papain-like extracellular cysteine protease, is induced in R. solanacearum-inoculated stem tissues of quantitatively resistant tomato cultivar LS-89, but not in susceptible cultivar Ponderosa. Phyt...

Most of the reported dominant disease-resistance genes in plants, R genes, encode NB-LRR immune receptors. Plant genomes carry many NB-LRR type R genes that recognize specific pathogens and induce resistance against them. Thus, this immune system in plants is thought to perform similar functions as the adaptive immune system in animals. In this rev...

The tobamovirus genome is a 5'-m(7)G-capped RNA that carries a tRNA-like structure at its 3'-terminus. The genomic RNA serves as the template for both translation and negative-strand RNA synthesis. The 5'- and 3'-untranslated regions (UTRs) of the genomic RNA contain elements that enhance translation, and the 3'-UTR also contains the elements neces...

Significance Replication of many positive-strand RNA viruses is cis -preferential: i.e., viral replicase proteins replicate genomic RNA molecules that have served as translation templates for their own synthesis, but not the other molecules in the same cell. Here, we show that tobacco mosaic virus replicase cotranslationally binds the 5′ untranslat...

Amino acid sequences under positive selection in the Tm-1 protein of S. habrochaites. 48 amino acid sequences of the Tm-1 protein from 24 S. habrochaites accessions were aligned. The positively selected region (79–112) is indicated. Identical amino acid residues to those of Tm-1GCR237 are indicated by dots. a and b indicate two sequences obtained f...

Amino acid sequence alignments of the Tm-1 protein from LT1-resistant S. habrochaites. Deduced amino acid sequences of the Tm-1 protein from three S. habrochaites plant individuals showing the LT1-resistant phenotypes (PI251304, PI365904, PI365906), GCR237 (LT1-susceptible but ToMV-L-resistant), and GCR26 (susceptible to both ToMV-L and LT1) are co...

Estimation of relative fitness of a virus variant to the other co-inoculated virus variant in plants. A model developed for estimation of relative fitness of a virus variant to a co-inoculated virus is schematically shown. The ratios of exclusive infections by one of the two variants and coinfection by the two variants were calculated by this model...

Estimation of relative fitness of ToMV derivatives in co-inoculated tomato plants. (DOCX)

Pyrosequencing examinations of the proportion of viral strains accumulated in co-inoculated protoplasts. (DOCX)

Eukaryotic positive-strand RNA viruses replicate their genomes in membrane-bound replication complexes composed of viral replication proteins and negative-strand RNA templates. These replication proteins are programmed to exhibit RNA polymerase and other replication-related activities only in replication complexes to avoid inducing double-stranded...

We have developed a modified yeast two-hybrid system using the GAL4 transcription activator by integrating a BD:bait gene (GAL4 binding domain:bait gene) into the host chromosome. Locus-specific integration by homologous recombination and use of a strong transcription promoter enabled uniform expression of the integrated BD:bait gene in all host ce...