Biology subjects

Ariizumi, T.

Publications and source records attributed to Ariizumi, T..

11 recordsLinked to original sources

bioRxiv2025

Evidence of Human adaptation for cluster 2 TMUV strain despite effective anti-viral responses.

Tembusu virus (TMUV) is an emerging Orthoflavivirus with potential zoonotic importance. To date, the biological differences among TMUV strains remain poorly understood. In this study, we compared the replication of a TMUV strain belonging to the cluster 1 and one belonging to the cluster 2 in human lung epithelial cells and further examined the replication characteristics of TMUV cluster 2 strain in both human and mosquito cell lines. The TMUV cluster 2 strain demonstrated a significant higher replication efficiency than the cluster 1 strain in human cells, indicating stronger adaptation to human-derived cells. Infection of human cells with the cluster 2 strain also induced robust innate immune response, including type I interferon and interferon-stimulated gene expression, associated with activation of the unfolded protein response via the PERK, and IRE1 pathways, reflecting an ER stress engagement. These findings suggest that TMUV cluster 2 strain exhibits enhanced replication capacity and more effectively modulates human host responses at the cellular level, underscoring its potential relevance in human health and the zoonotic risk it represents.

molecular biology↗

bioRxiv2025

Characterization and transcriptome analysis reveal abnormal pollen germination in cytoplasmic male sterile tomato

Cytoplasmic male sterility (CMS) is a phenomenon resulting from mitochondrial-nuclear incompatibility that is widely used in hybrid breeding. Although the mitochondrial gene orf137 has been identified as the causal CMS gene in tomatoes, its function remains unclear. In this study, we characterized the male-sterile phenotypes and analyzed the CMS pollen transcriptome. Microscopic and calcium imaging analyses revealed that CMS pollen exhibited abnormal germination from multiple apertures, accompanied by elevated calcium concentrations and vesicle accumulation, which are typically observed in pollen tube tips. RNA-Seq analysis revealed 440 differentially expressed genes, including four pectin methylesterase inhibitor (PMEI) genes that were highly expressed in the pollen. PME activity was significantly reduced in CMS pollen, suggesting its association with abnormal pollen germination. ATP and reactive oxygen species (ROS) levels, which are key mediators of mitochondrial retrograde signaling (MRS), remained unchanged in CMS pollen, and the expression of the mitochondrial stress marker AOX1a was not elevated. These findings suggest that orf137 triggers an alternative MRS pathway independent of ATP or ROS, potentially leading to PMEI upregulation and abnormal pollen germination. Our results reveal a previously unrecognized mechanism of CMS-induced male sterility in tomatoes involving nuclear gene regulation through unconventional mitochondrial signaling.

plant biology↗

bioRxiv2025

Relationship Between Open Reading Frame 320, a Gene Causing Male Sterility in Tomatoes, and Cytoplasmic Male Sterility in Potatoes

Cytoplasmic male sterility (CMS) is a phenotype wherein plants cannot develop normal male organs because of mitochondrial genes. Several cytoplasmic sterility factors are suggested to be involved in CMS phenotypes in potatoes (Solanum tuberosum); however, reports on the relevant mitochondrial genes remain scarce. Many potato cultivars carry mitochondrial genes that cause CMS, resulting in pollen sterility, thereby limiting their use as male parents in breeding. Therefore, identifying the causal genes is crucial for potato breeding. In this study, we focused on the T/{beta}-type cytoplasm, the most prevalent genome type of potato worldwide, to explore mitochondrial genes involved in CMS in potatoes. We identified a novel gene, open reading frame 320 (orf320), in potato genotypes with T/{beta}-type cytoplasm by comparing the mitochondrial genomes of potatoes. Functional analysis of tomatoes showed that overexpression of orf320 with a mitochondrial transit peptide induced male sterility phenotypes, including abnormal anther development and pollen abortion. Furthermore, an investigation of orf320 in 126 potato cultivars revealed that this gene is specific to the T/{beta}-type cytoplasm and is absent in investigated cultivars with other cytoplasmic types. These findings provide strong evidence that orf320 is a candidate CMS-causing gene in male sterility of T/{beta}-type cytoplasm, offering valuable insights for future potato breeding.

plant biology↗

bioRxiv2025

Simple and quantitative detection of double-stranded RNA as a signature of pan-virus infections using a luciferase-based biosensor

Viral infections produce double-stranded RNA (dsRNA) during replication, which trigger host innate immune responses. Immunoassays using anti-dsRNA antibodies have been widely employed to detect viral dsRNA. In this study, we used a luciferase-based dsRNA biosensor which consists of protein kinase R (PKR)-derived dsRNA binding domains fused to split luciferase subunits. Here, we demonstrate the use of the dsRNA biosensor to measure viral dsRNA in RNA specimens extracted from cells infected with Japanese encephalitis virus (JEV). Moreover, the biosensor reacts to a broad-spectrum of dsRNAs from infection with representatives of various viral families including positive- and negative-sense single-stranded RNA (ssRNA) viruses, dsRNA viruses, and DNA viruses. We validated the specific interaction between the dsRNA biosensor and viral RNA including subgenomic flavivirus RNA (sfRNA) through RNA immunoprecipitation. Additionally, we observed luminescence signals directly from lysates of JEV-infected cells after cell lysis and phase separation with Triton X-114. Finally, we used the biosensor to assess the activity of antiviral compounds. In summary, our results demonstrate that the luciferase-based dsRNA biosensor offers a simple, homogeneous, and high-throughput platform for quantifying viral replication, presenting a promising alternative to antibody-based dsRNA detection methods.

microbiology↗

bioRxiv2025

Artificial mutations in the nuclear gene encoding mitochondrial RNA polymerase restore pollen fertility in cytoplasmic male sterile tomato

Cytoplasmic male sterility (CMS) and restorer of fertility (Rf) are important traits in F1 hybrid breeding. However, the CMS/Rf system has not been used in tomatoes because of the limited resources of Rf lines. In this study, we performed mutagenesis in tomato CMS seeds and successfully obtained 13 suppressor mutants with pollen fertility. Using bulked segregant analysis and whole-genome sequencing for each suppressor mutant, we detected mutations associated with fertility restoration in the nuclear-encoded gene for the mitochondrial RNA polymerase termed SlRPOTm in four independent mutants created through mutagenesis. Furthermore, we found that the loss of function of SlRPOTm was associated with fertility restoration in the tomato CMS line. Expression analysis of orf137, a tomato CMS-causing gene, revealed that reduced expression of orf137 was associated with fertility restoration in tomato CMS. In addition, F1 plants carrying mutations in SlRPOTm were generated, and tomato fruit formation was comparable to that of normal F1 plants. This study demonstrates for the first time that the loss of function of mitochondrial RNA polymerase contributes to fertility restoration in CMS lines. Furthermore, it is possible to replace various tomato varieties with Rf lines using genome editing technology, which will promote tomato F1 breeding in the future.

plant biology↗

bioRxiv2025

Multiple fertility restorer loci for cytoplasmic male sterility caused by orf137 in tomato

Cytoplasmic male sterility (CMS) in plants is caused by incompatibility between nuclear and cytoplasmic genetic information. Fertility can be restored through the action of fertility restoration (RF) genes, which are usually present in the nucleus. CMS lines of tomato (Solanum lycopersicum) have been developed from asymmetric cell fusions, in these lines, cultivated tomato served as a nuclear donor and its wild relative, S. acaule, as a cytoplasm donor. Although RF genes are present in wild relatives of tomato, no genetic or genomic information on the RF genes is yet available. This study reports an RF genetic locus, RF1, on chromosome 1 of S. pimpinellifolium LA1670 and S. lycopersicum var. cerasiforme LA1673 that was revealed by bulked segregant analysis and sequencing. An additional RF locus, RF2, was identified on chromosome 2 of LA1670. A transgenic approach identified two other candidate genes that also restored fertility. The genomic sequence of S. cheesmaniae LA0166 was assembled using high-fidelity, long-read sequencing technology. Sequence comparisons identified further candidate RF genes on chromosome 1 of S. cheesmaniae LA0166. These results suggested that multiple gene loci control the fertility restoration trait in wild relatives of tomato.

plant biology↗

bioRxiv2023

Near-complete genome assembly of tomato (Solanum lycopersicum) cultivar Micro-Tom

We present a near-complete genome assembly of tomato (Solanum lycopersicum) cultivar Micro-Tom, which has been recognized as a model cultivar for fruit research. The genome DNA of Micro-Tom, provided by the National BioResource Project (NBRP) Tomato of Japan, was sequenced to obtain 72 Gb of high-fidelity long reads. These reads were assembled into 140 contigs, spanning 832.8 Mb, with an N50 length of 39.6 Mb. The contigs were aligned against the tomato reference genome sequence SL4.0 to establish a chromosome-level assembly. The genome assembly of Micro-Tom contained 98.5% complete BUSCOs and a total of 31,429 genes. Comparative genome structure analysis revealed that Micro-Tom possesses a cluster of rDNA genes spanning a 15 Mb stretch at the short arm of chromosome 2. This region was not found in the genome assemblies of previously sequenced tomato cultivars, possibly because of the inability of previous technologies to sequence such repetitive DNA. In conclusion, the near-complete genome assembly of Micro-Tom reported in this study would advance the genomics and genetics research on tomato and facilitate the breeding of improved tomato cultivars.

genomics↗

bioRxiv2023

Combination therapy with oral antiviral and anti-inflammatory drugs improves the efficacy of delayed treatment in severe COVID-19

Pulmonary infection with SARS-CoV-2 stimulates host immune responses and can also result in the progression of dysregulated and critical inflammation. Throughout the pandemic, the management and treatment of COVID-19 has been continuously updated with a range of antiviral drugs and immunomodulators. Monotherapy with oral antivirals has proven to be effective in the treatment of COVID-19. However, the treatment should be initiated in the early stages of infection to ensure beneficial therapeutic outcomes, and there is still room for further consideration on therapeutic strategies using antivirals. Here, we show that the oral antiviral ensitrelvir combined with the anti-inflammatory corticosteroid methylprednisolone has higher therapeutic effects and better outcomes in a delayed dosing model of SARS-CoV-2 infected hamsters compared to the monotherapy with ensitrelvir or methylprednisolone alone. Combination therapy with these drugs improved respiratory conditions and the development of pneumonia in hamsters even when the treatment was started after 2 days post infection. The combination therapy led to a differential histological and transcriptomic pattern in comparison to either of the monotherapies, with reduced lung damage and down-regulated expressions of genes involved in inflammatory response. Furthermore, we found that the combination treatment is effective in infection with both highly pathogenic delta and circulating omicron variants. Our results demonstrate the advantage of combination therapy with antiviral and corticosteroid drugs in COVID-19 treatment. Since both drugs are available as oral medications, this combination therapy could provide a clinical and potent therapeutic option for COVID-19.

microbiology↗

bioRxiv2022

Oral administration of S-217622, a SARS-CoV-2 main protease inhibitor, decreases viral load and accelerates recovery from clinical aspects of COVID-19

In parallel with vaccination, oral antiviral agents are highly anticipated to act as countermeasures for the treatment of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Oral antiviral medication demands not only high antiviral activity but also target specificity, favorable oral bioavailability, and high metabolic stability. Although a large number of compounds have been identified as potential inhibitors of SARS-CoV-2 infection in vitro, few have proven to be effective in vivo. Here, we show that oral administration of S-217622, a novel inhibitor of SARS-CoV-2 main protease (Mpro, also known as 3C-like protease), decreases viral load and ameliorates the disease severity in SARS-CoV-2-infected hamsters. S-217622 inhibited viral proliferation at low nanomolar to sub-micromolar concentrations in cells. Oral administration of S-217622 demonstrated eminent pharmacokinetic properties and accelerated recovery from acute SARS-CoV-2 infection in hamster recipients. Moreover, S-217622 exerted antiviral activity against SARS-CoV-2 variants of concern (VOCs), including the highly pathogenic Delta variant and the recently emerged Omicron variant. Overall, our study provides evidence that S-217622, an antiviral agent that is under evaluation in a phase II/III clinical trial, possesses remarkable antiviral potency and efficacy against SARS-CoV-2 and is a prospective oral therapeutic option for COVID-19.

microbiology↗

bioRxiv2021

Genome-wide cis-decoding for expression designing in tomato using cistrome data and explainable deep learning

In the evolutionary paths of plants, variations of the cis-regulatory elements (CREs) resulting in expression diversification have played a central role in driving the establishment of lineage-specific traits. However, it is difficult to predict expression behaviors from the CRE patterns to properly harness them, mainly because the biological processes are complex. In this study, we used cistrome datasets and explainable convolutional neural network (CNN) frameworks to predict genome-wide expression patterns in tomato fruits from the DNA sequences in gene regulatory regions. By fixing the effects of trans-elements using single cell-type spatiotemporal transcriptome data for the response variables, we developed a prediction model of a key expression pattern for the initiation of tomato fruit ripening. Feature visualization of the CNNs identified nucleotide residues critical to the objective expression pattern in each gene and their effects, were validated experimentally in ripening tomato fruits. This cis-decoding framework will not only contribute to understanding the regulatory networks derived from CREs and transcription factor interactions, but also provide a flexible way of designing alleles with optimized expression.

plant biology↗

bioRxiv2021

Organelle genome assembly uncovers the dynamic genome reorganization and cytoplasmic male sterility associated genes in tomato.

To identify cytoplasmic male sterility (CMS)-associated genes in tomato, we determined the genome sequences of mitochondria and chloroplasts in three CMS tomato lines derived from independent asymmetric cell fusions, their nuclear and cytoplasmic donors, and male fertile weedy cultivated tomato and wild relatives. The structures of the CMS mitochondrial genomes were highly divergent from those of the nuclear and cytoplasmic donors, and genes of the donors were mixed up in these genomes. On the other hand, the structures of CMS chloroplast genomes were moderately conserved across the donors, but CMS chloroplast genes were unexpectedly likely derived from the nuclear donors. Comparative analysis of the structures and contents of organelle genes and transcriptome analysis identified three genes that were uniquely present in the CMS lines, but not in the donor or fertile lines. RNA sequencing analysis indicated that these three genes transcriptionally expressed in anther, two of which were also expressed in pollen. They could be potential candidates for CMS-associated genes. This study suggests that organelle reorganization mechanisms after cell fusion events differ between mitochondria and chloroplasts, and provides insight into the development of new F1 hybrid breeding programs employing the CMS system in tomato.

plant biology↗