Showing papers by "Kazuki Saito published in 2022"

Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria

Abstract: Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation1,2. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes3-6. Here, using a genetic screen in Escherichia coli, we discovered a new rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNAs3) to rescue upstream ribosomes. SmrB is recruited to ribosomes and is activated by collisions. Cryo-electron microscopy structures of collided disomes from E. coli and Bacillus subtilis show distinct and conserved arrangements of individual ribosomes and the composite SmrB-binding site. These findings reveal the underlying mechanisms by which ribosome collisions trigger ribosome rescue in bacteria.

Ethanol-Mediated Novel Survival Strategy against Drought Stress in Plants

Abstract: Abstract Water scarcity is a serious agricultural problem causing significant losses to crop yield and product quality. The development of technologies to mitigate the damage caused by drought stress is essential for ensuring a sustainable food supply for the increasing global population. We herein report that the exogenous application of ethanol, an inexpensive and environmentally friendly chemical, significantly enhances drought tolerance in Arabidopsis thaliana, rice and wheat. The transcriptomic analyses of ethanol-treated plants revealed the upregulation of genes related to sucrose and starch metabolism, phenylpropanoids and glucosinolate biosynthesis, while metabolomic analysis showed an increased accumulation of sugars, glucosinolates and drought-tolerance-related amino acids. The phenotyping analysis indicated that drought-induced water loss was delayed in the ethanol-treated plants. Furthermore, ethanol treatment induced stomatal closure, resulting in decreased transpiration rate and increased leaf water contents under drought stress conditions. The ethanol treatment did not enhance drought tolerance in the mutant of ABI1, a negative regulator of abscisic acid (ABA) signaling in Arabidopsis, indicating that ABA signaling contributes to ethanol-mediated drought tolerance. The nuclear magnetic resonance analysis using 13C-labeled ethanol indicated that gluconeogenesis is involved in the accumulation of sugars. The ethanol treatment did not enhance the drought tolerance in the aldehyde dehydrogenase (aldh) triple mutant (aldh2b4/aldh2b7/aldh2c4). These results show that ABA signaling and acetic acid biosynthesis are involved in ethanol-mediated drought tolerance and that chemical priming through ethanol application regulates sugar accumulation and gluconeogenesis, leading to enhanced drought tolerance and sustained plant growth. These findings highlight a new survival strategy for increasing crop production under water-limited conditions.

Natural and induced variations in transcriptional regulator genes result in low‐nicotine phenotypes in tobacco

Abstract: SUMMARY In tobacco, the homologous ETHYLENE RESPONSE FACTOR (ERF) transcription factors ERF199 and ERF189 coordinate the transcription of multiple metabolic genes involved in nicotine biosynthesis. Natural alleles at the NIC1 and NIC2 loci greatly affect alkaloid accumulation and overlap with ERF199 and ERF189 in the tobacco genome, respectively. In this study, we identified several low‐nicotine tobacco varieties lacking ERF199 or ERF189 from a tobacco germplasm collection. We characterized the sequence of these new nic1 and nic2 alleles, as well as the previously defined alleles nic1‐1 and nic2‐1. Moreover, we examined the influence of different nic alleles on alkaloid contents and expression levels of genes related to nicotine biosynthesis. We also demonstrated that the deletion of a distal genomic region attenuates ERF199 expression, resulting in a moderately negative effect on the alkaloid phenotype. Our study provides new insights into the regulation of nicotine biosynthesis and novel genetic resources to breed low‐nicotine tobacco.

Tandem Gene Duplication of Dioxygenases Drives the Structural Diversity of Steroidal Glycoalkaloids in the Tomato Clade.

Abstract: Cultivated tomato (Solanum lycopersicum) contains α-tomatine, a steroidal glycoalkaloid (SGA), which functions as a defense compound to protect against pathogens and herbivores; interestingly, wild species in the tomato clade biosynthesize a variety of SGAs. In cultivated tomato the metabolic detoxification of α-tomatine during tomato fruit ripening is an important trait which aided in its domestication, and two distinct 2-oxoglutarate-dependent dioxygenases (DOXs), a C-23 hydroxylase of α-tomatine (Sl23DOX) and a C-27 hydroxylase of lycoperoside C (Sl27DOX), are key to this process. There are tandemly duplicated DOX genes on tomato chromosome 1, with high levels of similarity to Sl23DOX. While these DOX genes are rarely expressed in cultivated tomato tissues, the recombinant enzymes of Solyc01g006580 and Solyc01g006610 metabolized α-tomatine to habrochaitoside A and (20R)-20-hydroxytomatine, and were therefore named as habrochaitoside A synthase (HAS) and α-tomatine 20-hydroxylase (20DOX), respectively. Furthermore, 20DOX and HAS exist in the genome of wild tomato S. habrochaites accession LA1777, which accumulates habrochaitoside A in its fruits, and their expression patterns were in agreement with the SGA profiles in LA1777. These results indicate that the functional divergence of α-tomatine-metabolizing DOX enzymes results from gene duplication and the neofunctionalization of catalytic activity and gene expression, and this contributes to the structural diversity of SGAs in the tomato clade.

Skotomorphogenesis exploits threonine to promote hypocotyl elongation

Abstract: Abstract Abstract Mobilisation of seed storage reserves is important for seedling establishment in Arabidopsis. In this process, sucrose is synthesised from triacylglycerol via core metabolic processes. Mutants with defects in triacylglycerol-to-sucrose conversion display short etiolated seedlings. We found that whereas sucrose content in the indole-3-butyric acid response 10 (ibr10) mutant was significantly reduced, hypocotyl elongation in the dark was unaffected, questioning the role of IBR10 in this process. To dissect the metabolic complexity behind cell elongation, a quantitative-based phenotypic analysis combined with a multi-platform metabolomics approach was applied. We revealed that triacylglycerol and diacylglycerol breakdown were disrupted in ibr10, resulting in low sugar content and poor photosynthetic ability. Importantly, batch-learning self-organised map clustering revealed that threonine level was correlated with hypocotyl length. Consistently, exogenous threonine supply stimulated hypocotyl elongation, indicating that sucrose levels are not always correlated with etiolated seedling length, suggesting the contribution of amino acids in this process.

Chromosome-scale genome assembly of Glycyrrhiza uralensis revealed metabolic gene cluster centred specialized metabolites biosynthesis

Abstract: Abstract A high-quality genome assembly is imperative to explore the evolutionary basis of characteristic attributes that define chemotype and provide essential resources for a molecular breeding strategy for enhanced production of medicinal metabolites. Here, using single-molecule high-fidelity (HiFi) sequencing reads, we report chromosome-scale genome assembly for Chinese licorice (Glycyrrhiza uralensis), a widely used herbal and natural medicine. The entire genome assembly was achieved in eight chromosomes, with contig and scaffold N50 as 36.02 and 60.2 Mb, respectively. With only 17 assembly gaps and half of the chromosomes having no or one assembly gap, the presented genome assembly is among the best plant genomes to date. Our results showed an advantage of using highly accurate long-read HiFi sequencing data for assembling a highly heterozygous genome including its complexed repeat content. Additionally, our analysis revealed that G. uralensis experienced a recent whole-genome duplication at approximately 59.02 million years ago post a gamma (γ) whole-genome triplication event, which contributed to its present chemotype features. The metabolic gene cluster analysis identified 355 gene clusters, which included the entire biosynthesis pathway of glycyrrhizin. The genome assembly and its annotations provide an essential resource for licorice improvement through molecular breeding and the discovery of valuable genes for engineering bioactive components and understanding the evolution of specialized metabolites biosynthesis.

The ability of callus tissues induced from three Allium plants to accumulate health-beneficial natural products, S-alk(en)ylcysteine sulfoxides

Abstract: S-Alk(en)ylcysteine sulfoxides (CSOs), such as methiin, alliin, and isoalliin, are health-beneficial natural products biosynthesized in the genus Allium. Here, we report the induction of multiple callus tissue lines from three Allium vegetables, onion (A. cepa), Welsh onion (A. fistulosum), and Chinese chive (A. tuberosum), and their ability to accumulate CSOs. Callus tissues were initiated and maintained in the presence of picloram and 2-isopentenyladenine as auxin and cytokinin, respectively. For all plant species tested, the callus tissues almost exclusively accumulated methiin as CSO, while the intact plants contained a substantial amount of isoalliin together with methiin. These results suggest that the cellular developmental conditions and the regulatory mechanisms required for the biosynthesis of methiin are different from those of alliin and isoalliin. The methiin content in the callus tissues of onion and Welsh onion was much higher compared to that in the intact plants, and its cellular concentration could be estimated as 1.9-21.7 mM. The activity of alliinase that degrades CSOs in the callus tissues was much lower than that of the intact plants for onion and Welsh onion, but at similar levels as in the intact plants for Chinese chive. Our findings that the callus tissues of onion and Welsh onion showed high methiin content and low alliinase activity highlighted their potential as a plant-based system for methiin production.

Transcriptomic, Hormonomic and Metabolomic Analyses Highlighted the Common Modules Related to Photosynthesis, Sugar Metabolism and Cell Division in Parthenocarpic Tomato Fruits during Early Fruit Set

Abstract: Parthenocarpy, the pollination-independent fruit set, can raise the productivity of the fruit set even under adverse factors during the reproductive phase. The application of plant hormones stimulates parthenocarpy, but artificial hormones incur extra financial and labour costs to farmers and can induce the formation of deformed fruit. This study examines the performance of parthenocarpic mutants having no transcription factors of SlIAA9 and SlTAP3 and sldella that do not have the protein-coding gene, SlDELLA, in tomato (cv. Micro-Tom). At 0 day after the flowering (DAF) stage and DAFs after pollination, the sliaa9 mutant demonstrated increased pistil development compared to the other two mutants and wild type (WT). In contrast to WT and the other mutants, the sliaa9 mutant with pollination efficiently stimulated the build-up of auxin and GAs after flowering. Alterations in both transcript and metabolite profiles existed for WT with and without pollination, while the three mutants without pollination demonstrated the comparable metabolomic status of pollinated WT. Network analysis showed key modules linked to photosynthesis, sugar metabolism and cell proliferation. Equivalent modules were noticed in the famous parthenocarpic cultivars ‘Severianin’, particularly for emasculated samples. Our discovery indicates that controlling the genes and metabolites proffers future breeding policies for tomatoes.

Leiomyosarcoma arising from the ovarian vein as a gynecologic malignancy: Two case reports and a review of the literature

Abstract: Leiomyosarcoma arising from the ovarian vein has rarely been reported. Herein, we report two cases from a single institute. Given their direct connections to ovarian vessels, both leiomyosarcomas were initially suspected to be gynecological malignancies. In one case, leiomyosarcoma was discovered incidentally without any clinical symptoms; it had a close connection with the ovarian vein, was removed surgically, and the patient has survived for over 12 years. In another case, bowel obstruction caused by the tumor helped to identify metastatic leiomyosarcoma. Blood flow was supplied by the ovarian artery and grew into the lumen of the ovarian vein without invading adjacent organs. After surgical resection, the patient underwent 18 months of chemotherapy prior to palliative care. We propose that leiomyosarcoma arising from the ovarian vein should be treated as a gynecologic malignancy, especially if it develops in the lower abdomen.

Small Coil Antenna With Magnetic Sheet for Implantable Medical Device Communication in 40–60 MHz Band

Abstract: Low-frequency communication is one of the best ways to reduce signal attenuation from the human body, although slow data rates make stable wireless communication within the human body difficult. In this paper, we designed two coil antennas for wireless implant communication, including a small dual-band transmitting antenna that can be placed inside the human body and a corresponding receiving antenna that can be mounted on the abdomen of the human body. The proposed antenna is fed from a battery-powered impulse radio (IR) transceiver peaking at 10–60 MHz, and the antenna is designed to be wideband for higher data communication rate. Simulation and measurement of reflection and transmission coefficients confirmed operation at 40–60 MHz. In addition, a battery-powered IR transceiver is used to measure the transmission performance in a 2/3 muscle phantom. As a result, communication at a data rate of 20 Mbps is achieved at a distance of 90 mm in the 2/3 muscle phantom.

Endometrioid borderline ovarian tumor treated by laparoscopic surgery in an infertile patient with endometrioid cyst: a case report

Abstract: Objective: Endometrioid borderline ovarian tumor accounts for 0.2％ of all ovarian epithelial tumors, and 63％ of them are associated with endometriosis. In this report, we present a case of an infertile woman with ovarian endometrioma, which was diagnosed as an endometrioid borderline tumor postoperatively.

Out-of-pocket payment and patients’ treatment choice for assisted reproductive technology by household income: a conjoint analysis using an online social research panel in Japan

Abstract: Economic disparities affect access to assisted reproductive technology (ART) treatment in many countries. At the time of this survey, Japan provided partial reimbursement for ART treatment only for those in low- or middle-income classes due to limited governmental budgets. However, the optimal level of financial support by income class remains unclear.We conducted a conjoint analysis of ART in Japan in January 2020. We recruited 824 women with fertility problems aged 25 to 44 years via an online social research panel. They completed a questionnaire of 16 hypothetical scenarios measuring six relevant ART attributes (i.e., out-of-pocket payment, pregnancy rate, risk of adverse effects, number of visits to outpatient clinics, consultation hours and kindness of staff) and their relations to treatment choice.Mixed-effect logistic regression models showed that all six attributes significantly influenced treatment preferences, with participants valuing out-of-pocket payment the most, followed by pregnancy rates and kindness of staff. Significant interactions occurred between high household income (≥ 8 million JPY) and high out-of-pocket payment (≥ 500,000 JPY). However, the average marginal probability of the highest-income patients (i.e., ≥ 10 million JPY, ineligible for the subsidy) receiving ART treatment at the average cost of 400,000 JPY was 47%, compared to 56 - 61% of other income participants, who opted to receive ART at an average cost of 100,000 JPY after a 300,000 JPY subsidy.Our results suggest that out-of-pocket payment is the primary determinant in patients' decision to opt for ART treatment. High-income patients were more likely to choose treatment, even at a high cost, but their income-based ineligibility for government financial support might discourage some from receiving treatment.

Small Loop Shape Antenna for Generating a Localized Heating Region

Abstract: Microwave energy devices can coagulate biological tissues without generating surgical smoke. Therefore, we proposed the double-loop shape antenna for miniaturization and generating a localized heating region to adapt microwave energy device for robotic surgery. In order to evaluate the heating characteristics, numerical analysis and heating experiment were calculated. As a result, it is confirmed that the double-loop shape antenna with 10 mm rod can generate uniform heating region.

Development of Microwave Energy Device Generating Limited Coagulation Area

Abstract: あらまし 外科手術用エネルギーデバイスは,生体組織の凝固及び切開を同時に行うことが可能である.しか しながら,使用時に発生するサージカルスモークが課題である.これは,術野の妨害を招き,安全性低下の原因 である.一方,マイクロ波エネルギーデバイスはサージカルスモークを発生させずに生体組織の凝固が可能であ るため,微細な手技,特に,ロボット手術への応用が期待される.ロボット手術では微細な治療を実現するため, ロボットアームに取付けるデバイスは小形化が図られている.そのため,マイクロ波を放射するアンテナも小形 であることが求められる.しかしながら,アンテナサイズは,動作周波数によって決定される波長に依存するた め,小形化は容易ではない.更に目的部位以外への加熱を避けるために局所的な加熱が望ましい.そこで本研究 では,局所加熱が可能な小形のマイクロ波エネルギーデバイスを開発すべく,2 重ループ状アンテナを提案し, このアンテナによる加熱領域を電磁界解析より算出した SAR 分布で評価した.また,このアンテナを装備した 簡易的なシーリングデバイスを用いた加熱実験を行い,提案デバイスの有用性を評価した. キーワード マイクロ波,エネルギーデバイス,サージカルスモーク,ロボット手術,SAR

Identification of a regiospecific S-oxygenase for the production of marasmin in traditional medicinal plant Tulbaghia violacea.

Abstract: Marasmin [S-(methylthiomethyl)-L-cysteine-4-oxide] is a pharmaceutically valuable sulfur-containing compound produced by the traditional medicinal plant, Tulbaghia violacea. Here, we report the identification of an S-oxygenase, TvMAS1, that produces marasmin from its corresponding sulfide, S-(methylthiomethyl)-L-cysteine. The amino acid sequence of TvMAS1 showed high sequence similarity to known flavin-containing S-oxygenating monooxygenases in plants. Recombinant TvMAS1 catalyzed regiospecific S-oxygenation at S4 of S-(methylthiomethyl)-L-cysteine to yield marasmin, with an apparent K m value of 0.55 mM. TvMAS1 mRNA accumulated with S-(methylthiomethyl)-L-cysteine and marasmin in various organs of T. violacea. Our findings suggest that TvMAS1 catalyzes the S-oxygenation reaction during the last step of marasmin biosynthesis in T. violacea.

A RING membrane-anchor E3 ubiquitin ligase gene is co-expressed with steroidal glycoalkaloid biosynthesis genes in tomato.

Abstract: RING membrane-anchor (RMA) E3 ubiquitin ligases are involved in endoplasmic reticulum (ER)-associated protein degradation, which mediates the regulated destruction of ER-resident enzymes in various organisms. We determined that the transcription factor JASMONATE-RESPONSIVE ETHYLENE RESPONSE FACTOR 4 (JRE4) co-regulates the expression of the RMA-type ligase gene SlRMA1, but not its homolog SlRMA2, with steroidal glycoalkaloid biosynthesis genes in tomato, perhaps to prevent the overaccumulation of these metabolites.

Characteristics of an antenna generating a localized heating region for robotic surgery

Abstract: Microwave energy devices can coagulate biological tissues without generating surgical smoke. Therefore, we proposed the double-loop antenna for miniaturization and generating a localized heating to adapt microwave energy device for robotic surgery. The double-loop antenna consists of a double-loop and rod for changing the total antenna length. In order to evaluate the heating characteristics of our proposed antenna, the current distribution was calculated. As a result, it is confirmed that the combination of the double-loop and 10mm rod can achieve uniform heating.

A Jasmonate-Responsive ERF Transcription Factor Regulates Steroidal Glycoalkaloid Biosynthesis Genes in Eggplant

Abstract: Steroidal glycoalkaloids (SGAs) are a class of cholesterol-derived anti-nutritional defense compounds that are produced in species of the genus Solanum, such as tomato (S. lycopersicum), potato (S. tuberosum), and eggplant (S. melongena). However, the regulation of defense-related metabolites in eggplant remains underexplored. In tomato and potato, the JASMONATE-RESPONSIVE ETHYLENE RESPONSE FACTOR 4 (JRE4) transcription factor positively regulates a large number of genes involved in SGA biosynthesis. Here, we report that overexpression of eggplant JRE4 (SmJRE4) induces numerous metabolic genes involved in SGA biosynthesis in leaves. We demonstrate jasmonate-dependent induction of SmJRE4 and its downstream metabolic genes and show that ethylene treatment attenuates this induction. Our findings thus provide molecular insights into SGA biosynthesis and its regulation in this major crop.

Development of a High-Speed Implant Communication Module Deep Into the Human Body: Realized in the 10-60-MHz band with small antennas [Bioelectromagnetics]

Abstract: Implant sensors and robots are expected to sense biological information or images. They stay in the human body for a long time to make a diagnosis or move freely inside the body to perform remote treatment, such as excision of the affected area or drug injection. In this study, toward the aforementioned purpose, we developed a communication module with small antennas that use the 10-60-MHz band to enable high-speed implant communication to the deep part of the human body. A waveform equalization technique was also used to increase the transmission bandwidth limited by the small antennas and reduce the sizes of their implementation. As a result, an implant communication distance of 33 cm or more that can cover the entire human torso was achieved at a data rate of 20 Mb/s. Experimental results on a living swine also showed that the developed module is able to communicate deeper in the human body than all others reported in the literature at sufficiently high data rates. This article describes the development of the implant communication module and shows the current status of research by comparing its performance with others reported in the literature.