Biology subjects

Masuda, S.

Publications and source records attributed to Masuda, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Two closely related RNA helicases, UAP56 and URH49, couple mRNA splicing and export pathways with their distinct complexes

Transcription and mRNA processing are integrated into appropriate mRNA export pathway(s) enabling fine-tuned gene expression. The closely related RNA helicases, UAP56 and URH49, form distinct complexes known as the apo-TREX and the apo-AREX complexes, respectively, which remodel into the ATP-TREX complexes, thus forming multiple mRNA export pathways. However, the mechanisms by which helicases and their complexes shape these pathways remain unclear. Here, we showed that UAP56 and URH49 play general roles in mRNA splicing ahead of export. Further analyses revealed three patterns of splicing regulation and their association with mRNA export: Type I, in which both helicases redundantly or synergistically regulate splicing within the same transcripts, associated with cooperative mRNA export; Type II, in which either helicase preferentially regulates splicing in distinct transcripts; and Type III, in which the helicases exert opposing splicing effects within the same transcripts. Type II and III regulation was associated with selective mRNA export. Moreover, we demonstrated that the distinct complex formation influenced the splicing patterns regulated by the two helicases. Our findings reveal an additional layer of transcriptome regulation mediated by UAP56, URH49, and their complexes, extending beyond their canonical roles in mRNA export.

molecular biology↗

bioRxiv2026

FGFR1-phosphate sensing and crystal-induced gasdermin D signaling in neutrophils drive vascular calcification in CKD

Chronic kidney disease (CKD) confers disproportionate cardiovascular risk. In non-dialysis CKD, calcification accumulates primarily within the intimal layer. Clinical studies indicate that intimal calcification correlates with hyperphosphatemia, yet the cellular and molecular pathways remain unclear. Given evidence that osteocytes sense phosphate via fibroblast growth factor receptor 1 (FGFR1), we hypothesized that FGFR1-expressing vascular immune cells, especially neutrophils, act as mediators linking high phosphate to plaque mineralization. In vitro, phosphate triggered FGFR1-dependent signaling in human and murine neutrophils, inducing neutrophil extracellular traps (NETs). Activated neutrophils promoted the depletion of Fetuin-A, a major inhibitor of calcium-phosphate complexation, creating a milieu permissive to mineral nucleation. Newly formed calcium-phosphate particles amplified NETs through gasdermin D (GSDMD), establishing a feed-forward loop that enhanced mineralization and endothelial injury in co-culture assays. Human arteriosclerotic plaques from CKD patients showed NETs markers co-localizing with calcified deposits. In vivo, pharmacological FGFR inhibition attenuated arterial intimal calcification and suppressed NET formation in CKD mice. These findings identify phosphate sensing via neutrophil FGFR1 and subsequent crystal-induced GSDMD signaling as drivers of intimal vascular calcification in CKD. Targeting phosphate-sensing pathways, NET formation, and neutrophil-driven mineralization may mitigate vascular calcification and reduce cardiovascular risk in CKD.

immunology↗

bioRxiv2026

Integrating spatial and single-cell multi-omics analysis of induced pluripotent stem cell-derived cervical adenocarcinoma model

Human papillomavirus 18 (HPV18) preferentially infects cervical stem cell-like cells and is strongly associated with adenocarcinoma. However, the mechanisms underlying differentiation into cervical adenocarcinoma remain unclear due to the lack of appropriate experimental models. We aimed to establish a model of HPV18-associated cervical adenocarcinoma and elucidate its molecular and cellular differentiation mechanisms. HPV18 E6/E7 were introduced into induced pluripotent stem cell-derived reserve cell-like cells (iRCs) to generate tumor models. Spatial transcriptomics and single-cell multi-omics analyses were performed to integrate histological and molecular data. A distinct component (Gland_A) exhibited morphological and immunohistochemical features of cervical adenocarcinoma and was efficiently induced in iRC-18 tumors. Gland_A showed increased chromatin accessibility and elevated expression of FOXA1, FOXA2, and ALDH1A1. Analysis of clinical samples confirmed enrichment of ALDH1A1 in HPV-associated adenocarcinomas. This model recapitulates key features of HPV18-associated cervical adenocarcinoma and provides insights into its differentiation mechanisms.

cancer biology↗

bioRxiv2025

Horizontal acquisition of nicotine catabolism gene cluster drives the assembly of tobacco root microbiota community

BackgroundPlant roots are hotspots for interactions with soil microbes, where a characteristic bacterial community structure is formed. Plant specialized metabolites often play pivotal roles in this assembly process. However, the molecular basis underlying root microbiota responses to these bioactive compounds, and how such metabolic interactions shape the assembly of host-specific root microbiota, remain largely unknown. Nicotine is a toxic alkaloid predominantly produced by the genus Nicotiana, and the genus Arthrobacter is known as one of the nicotine-degrading bacteria in the tobacco root microbiota. In this study, we used the tobacco-Arthrobacter interaction system as a model and integrated comparative genomics and experimental genetic manipulation assays to uncover the role of bacterial catabolism capacity for host specialized metabolites in shaping host-specific root microbiota. ResultsNicotine catabolism genes are uniquely found in the Arthrobacter strains derived from nicotine-containing environments, and this restricted gene distribution is driven by a plasmid-mediated horizontal gene transfer. To assess the ecological consequences of this genomic adaptation in Arthrobacter fitness in tobacco roots, we conducted adaptation assays under both in vitro and in planta conditions using genetically manipulated Arthrobacter and tobacco mutants, which are impaired in nicotine catabolism and biosynthesis, respectively. Nicotine improves Arthrobacter colonization to the tobacco roots through both catabolism-dependent and catabolism-independent mechanisms. Bacterial community analysis using a synthetic community approach further demonstrated that these metabolic interactions, mediated by tobacco nicotine biosynthesis and its catabolism by Arthrobacter, jointly affect root microbiota composition. ConclusionsOur findings illustrated that bacterial catabolic capacity toward host-derived plant specialized metabolites is key for successful root colonization. This metabolic adaptation is driven by plasmid-mediated horizontal gene transfer and ultimately shapes the structure of the overall root microbiota community.

microbiology↗

bioRxiv2025

NADPH phosphatase activity of Mesh1 controls sleep in Drosophila

Recent findings have shown that metazoans accumulate the bacterial second messenger guanosine tetraphosphate (ppGpp) and possess Mesh1, a gene encoding a ppGpp hydrolase domain. Mesh1 deficiency affects sleep behavior and eclosion under starvation in Drosopila, and ferroptosis in human cells. However, human Mesh1 also exhibits NADPH/NADP+ phosphatase activity in vitro, making it unclear whether these phenotypes result from loss of ppGpp hydrolysis, NADPH/NADP+ dephosphorylation, or both. To address this, we performed biochemical and genetic analysis of Drosophila Mesh1. We first found that Drosophila Mesh1 dephosphorylates NADPH, but not NADP+, in vitro. We subsequently sought to generate Drosophila Mesh1 point mutants specifically impaired in NADPH phosphatase activity. Based on structural data, we mutated W138 and R142, residues that are predicted to interact with NADPH but not ppGpp. W138 was replaced with phenylalanine results in complete loss of NADPH phosphatase activity with retained ppGpp hydrolase activity. Flies carrying the W138F mutation, introduced via genome editing, exhibited shortened total sleep and increased sleep fragmentation in behavioral assays, without changes in intracellular ppGpp levels. These results indicate that the NADPH phosphatase activity of Mesh1, and specifically the W138 residue, is essential for normal sleep regulation in Drosophila.

molecular biology↗

bioRxiv2025

From model to field: predictive design of microbial communities for resilient crop performance

Synthetic microbial communities (SynComs) represent a promising approach to enhance crop growth and stress resilience through microbiome engineering. However, the systematic design and field validation of SynComs remain limited. Here, we present a predictive framework for SynCom optimization, integrating plant phenotyping, microbial genomics, and machine learning. Using tomato as a model, we tested over 800 SynCom-temperature combinations consisting of root endophytic bacteria and rhizosphere metabolites. An Elastic Net regression model trained on plant biomass data accurately predicted the performance of unseen SynComs, with prediction accuracy plateauing at [~]5% (301/6144) of all possible SynCom-temperature combinations. Incorporating genomic features significantly improved model performance, whereas microbiome compositional data alone were not informative. We applied the model to design novel SynComs, which were tested in both laboratory and field conditions using a commercial tomato cultivar. The model-informed SynCom enhanced plant growth in field trials and improved heat stress tolerance under controlled laboratory conditions. Multi-omics analyses and feature importance metrics identified specific microbial taxa, including Sphingobium sp., whose enrichment was linked to host plant metabolite (e.g., tomatine) and stress-responsive gene expression. Our results demonstrate a scalable strategy for the predictive design of beneficial microbiomes to improve resilient crop performance under real-world conditions.

systems biology↗

bioRxiv2025

Establishment of spinocerebellar ataxia type 34 model mice accompanied by early glial activation and degeneration of cerebellar neurons

Spinocerebellar ataxia type 34 (SCA34) is an autosomal dominant neurodegenerative disease primarily characterized by progressive cerebellar atrophy and ataxia, frequently accompanied by cognitive dysfunction and erythrokeratodermia variabilis. In 2014, missense mutations in the gene encoding elongation of very long chain fatty acids protein 4 (ELOVL4) were identified as the causative gene for SCA34. ELOVL4, which is involved in the synthesis of very long chain fatty acids, is highly expressed in the cerebellum compared to other brain regions, with predominant expression in neurons. We attempted to establish a mouse model of SCA34 by expressing mutant ELOVL4 in cerebellar neurons using adeno-associated virus (AAV) vectors and to elucidate the underlying pathogenic mechanisms. Expression of W246G mutant ELOVL4 successfully induced progressive motor dysfunction beginning at two weeks post-AAV vector injection. Immunohistochemical analyses revealed that the degeneration of cerebellar Purkinje cells and neurons in the deep cerebellar nuclei (DCN) paralleled the observed motor decline. Importantly, microglial activation was detected in the molecular layer of the cerebellar cortices and the DCN prior to the onset of both neurodegeneration and motor dysfunction. Furthermore, after the onset of motor symptoms, the SCA34 model mice exhibited decreased synaptic inputs from climbing fibers to Purkinje cells, as well as reduced inputs from Purkinje cells to DCN neurons. These findings suggest that early microglial activation and the resulting synaptic disturbance are critical preceding events that lead to the progressive cerebellar neurodegeneration and motor dysfunction observed in this SCA34 mouse model.

neuroscience↗

bioRxiv2025

Diversity of exopolysaccharide cluster I in the Bradyrhizobium genus

Bradyrhizobium, the largest rhizobial genus, is characterized by variety exopolysaccharides (EPSs) components, depending on the species. However, several genes involved in EPS synthesis remain unknown. In this study, we investigated whether 186 Bradyrhizobium strains possess EPS cluster I, which is involved in the synthesis of a pentasaccharide EPS by B. diazoefficiense USDA110. Homologous genes involved in EPS synthesis were found to be absent in the B. elkanii and Photosynthetic Bradyrhizobium supergroups, other than the B. japonicus supergroup. These findings suggest that genes related to EPS synthesis are yet to be identified in the B. elkanii and Photosynthetic Bradyrhizobium supergroups.

microbiology↗

bioRxiv2025

Whole-genome sequencing of diverse 351 cultured prokaryotes including yet-unsequenced fastidious type strains

Genome sequences provide fundamental information for both basic and applied life sciences. Whole-genome sequencing is now requested for describing novel prokaryotic species and designating their type strains, which serve as representative and well-characterized strains of the species. Indeed, the number of sequenced prokaryotic genomes has been rapidly increasing. However, a considerable number of isolated strains, particularly "fastidious" type strains such as strict anaerobes and slow growers, remain without genome sequence information. Here we report the whole-genome sequencing of 290 bacterial and 61 archaeal strains, including fastidious type strains, obtained from Japan Collection of Microorganisms (JCM) using a combination of short- and long-read sequencing technologies. The dataset includes 284 type strain genomes and 235 complete genomes. Notably, in the dataset, genomes of over 200 strains, including over 150 type strains, had not been made publicly available. Comparative genomic analysis suggests that some strains need to be assigned to novel taxa or reclassified. Functional gene survey indicates that some strains possess previously unrecognized potential for carbon fixation or bioactive secondary metabolite production. Our dataset will contribute to more accurate taxonomic classification, fill gaps in the phylogeny of prokaryotes, and provide insights into their physiology and ecology.

microbiology↗

bioRxiv2025

Neofunctionalized RGF pathways drive haustorial organogenesis in parasitic plants

Parasitic plants initiate rapid de novo organogenesis of a specialized feeding structure called a haustorium upon contact with their hosts. Currently, little is known about the internal signals regulating haustorium development. Here, we identify root meristem growth factor (RGF) peptides in Phtheirospermum japonicum as endogenous inducers of prehaustorium formation. Treatment with specific RGF peptides in the absence of hosts triggered prehaustoria and induced expression of PjYUC3, a gene required for auxin biosynthesis and prehaustorium formation. CRISPR-mediated knockouts showed that PjRGFR1 and PjRGFR3, receptors activated by the haustorium specific RGF peptides PjRGF2 and PjRGF5, are essential for prehaustorium formation, revealing functional redundancy. Phylogenic analyses indicate that PjRGF2 is broadly conserved among Orobanchaceae, whereas PjRGF5 appears to have recently evolved through tandem multiplication and neofunctionalization. Our findings establish RGF peptides and their corresponding receptors as critical components of haustorium developmental signaling and provide insights into the evolutionary trajectories that shape plant parasitism. TeaserPlant peptide hormones regulate and induce the parasitic plant specialized organ for connecting to and feeding from the host.

plant biology↗

bioRxiv2023

Discovery of an isoflavone oxidative catabolic pathway in legume root microbiota

Isoflavones are major specialized metabolites found in legume plants, where they contribute to environmental adaptation. Isoflavones also play a role human health as promising therapeutic agents. This metabolite group is involved in interactions with soil microorganisms as initiation signals in rhizobial symbiosis and as modulators of the legume root microbiota. We previously reported that isoflavones enrich the Comamonadaceae, a predominant bacterial family in soybean roots, and that microorganisms in legume rhizosphere soil degrade isoflavones. However, the isoflavone catabolism pathway that underly the isoflavone-mediated legume-microbiota interactions have not yet been clarified. Here, we isolated Variovorax sp. strain V35, member of the Comamonadaceae that harbors isoflavone-degrading activity, from soybean roots and discovered a gene cluster responsible for isoflavone degradation named ifc. Strain V35 metabolizes isoflavones in a completely distinct oxidative manner from the reductive isoflavone metabolism pathway elucidated in the gut microbiota, in which resulting products enter the tricarboxylic acid cycle. The characterization of ifc mutants and heterologously expressed IFC enzymes revealed that isoflavones are catabolized via A-ring cleaving fission, which starts with hydroxylation at the 8-position of the A-ring. We further demonstrated that ifc genes are frequently found in bacterial strains isolated from legume plants, including mutualistic rhizobia, and contribute to detoxification of the antibacterial activity of isoflavones. Taken together, our findings reveal an oxidative catabolism pathway of isoflavone in the soybean root microbiota, providing molecular insights into isoflavone-mediated legume-microbiota interactions. SignificanceIsoflavones play pivotal roles in plant-environment interactions and in the maintenance and improvement of human health. Bacterial metabolism is a fundamental component of isoflavone-mediated interkingdom interactions. In the human gut, intestinal bacteria convert isoflavones into equol, a highly bioactive compound. However, the fate of isoflavones in the legume rhizosphere has not been elucidated, despite them being the key signaling molecules for nodule symbiosis and modulation of the legume root microbiota. Here, we discovered a novel isoflavone catabolism pathway in the soybean root microbiota and demonstrated the strong association between bacterial catabolic abilities and their interactions with host plants. Collectively, our findings provide new insights into bacterial isoflavone metabolism and a molecular understanding of legume-microbiota interactions.

plant biology↗

bioRxiv2023

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here, we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyze how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype with five complete sets of syntenic chromosomes (2n = 10x = 80) yet with a clear indication of subgenome dominance and highly diploidized gene contents. The male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbor three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. Novel gene evolution in recessive subgenomes is likely to be prevalent because duplicates were enriched with Nepenthes-specific genes with tissue-specific expression, including those expressed in trapping pitchers. Thus, subgenome dominance likely contributed to evolutionary novelty by allowing recessive subgenomes experiencing relaxed purifying selection to serve as a preferred host of novel tissue-specific duplicates. Our results provide insight into how polyploids, which may frequently be evolutionary dead-ends, have given rise to novel traits in exceptionally thriving high-ploidy lineages.

plant biology↗

bioRxiv2023

Genome and transcriptome analyses reveal genes involved in the formation of fine ridges on petal epidermal cells in Hibiscus trionum.

Hibiscus trionum, commonly known as the Flower of an Hour, is an easily cultivated plant in the Malvaceae family. The purple base part of its petal exhibits structural color due to the fine ridges on the epidermal cell surface, and the molecular mechanism of ridge formation has been actively investigated. We performed genome sequencing of H. trionum using a long-read sequencing technology with transcriptome and pathway analyses to identify candidate genes for fine structure formation. The ortholog of AtSHINE1, which is involved in the biosynthesis of cuticular wax in Arabidopsis thaliana, was significantly overexpressed in the iridescent tissue. In addition, orthologs of AtCUS2 and AtCYP77A, which contribute to cutin synthesis, were also overexpressed. Our results provide important insights into the formation of fine ridges on epidermal cells in plants using H. trionum as a model.

bioinformatics↗

bioRxiv2023

Uncovering plant microbiomes using long-read metagenomic sequencing

The microbiome of plants plays a pivotal role in their growth and health. Despite its importance, many fundamental questions about the microbiome remain largely unanswered, such as the identification of colonizing bacterial species, the genes they carry, and the location of these genes on chromosomes or plasmids. To gain insights into the genetic makeup of the rice leaf microbiome, we performed a metagenomic analysis using long-read sequences, and developed a genomic DNA extraction method that provides relatively intact DNA for long-read sequencing. 1.8 Gb reads were assembled into 26,067 contigs, including 136 circular sequences of less than 1 Mbp, as well as 172 large ([≥] 1 Mbp) sequences, six of which were circularized. Within these contigs, 669 complete 16S rRNA genes were clustered into 166 bacterial species, 130 of which showed low identity to previously defined sequences, suggesting that they represent novel species. The large circular contigs contain novel chromosomes and a megaplasmid, and most of the smaller circular contigs (<1 Mbp) were defined as novel plasmids or bacteriophages. One circular contig represents the complete chromosome of an uncultivated bacterium in the candidate phylum Candidatus Saccharibacteria. Our findings demonstrate the efficacy of long-read-based metagenomics for profiling microbial communities and discovering novel sequences in plant-microbiome studies.

microbiology↗

bioRxiv2023

Exon 44 skipping in Duchenne muscular dystrophy: NS-089/NCNP-02, a dual-targeting antisense oligonucleotide

Exon-skipping therapy mediated by antisense oligonucleotides (ASOs) is expected to provide a therapeutic option for Duchenne muscular dystrophy (DMD). ASOs for exon skipping reported so far target a single continuous sequence in or around the target exon. In the present study, we investigated ASOs for exon 44 skipping (applicable to approximately 6% of all DMD patients) to improve activity by using a novel ASO design incorporating two connected sequences. Phosphorodiamidate morpholino oligomers targeting two separate sequences in exon 44 were created to simultaneously target two splicing regulators in exon 44, and their exon 44 skipping was measured. NS-089/NCNP-02 showed the highest skipping activity among the oligomers. NS-089/NCNP-02 also induced exon 44 skipping and dystrophin protein expression in cells from a DMD patient to whom exon 44 skipping is applicable. We also assessed the in vivo activity of NS-089/NCNP-02 by intravenous administration to cynomolgus monkeys. NS-089/NCNP-02 induced exon 44 skipping in skeletal and cardiac muscle of cynomolgus monkeys. In conclusion, NS-089/NCNP-02, an ASO with a novel connected-sequence design, showed both in vitro and in vivo exon-skipping activity.

cell biology↗

bioRxiv2022

Complete loss of RelA and SpoT homologs in Arabidopsis reveals the importance of the plastidial stringent response in the interplay between chloroplast metabolism and plant defense response

The highly phosphorylated nucleotide, guanosine tetraphosphate (ppGpp), functions as a secondary messenger in bacteria and chloroplasts. The accumulation of ppGpp alters plastidial gene expression and metabolism, which are required for proper photosynthetic regulation and robust plant growth. However, because four plastid-localized ppGpp synthases/hydrolases function redundantly, the impact of the loss of ppGpp-dependent stringent response on plant physiology remains unclear. We used the CRISPR/Cas9 technology to generate an Arabidopsis thaliana mutant lacking all four ppGpp synthases/hydrolases, and characterized its phenotype. The mutant showed 20-fold less ppGpp levels than the wild type (WT) under normal growth conditions, and exhibited leaf chlorosis and increased expression of defense-related genes as well as salicylic acid and jasmonate levels upon transition to nitrogen-starvation conditions. These results demonstrate that proper levels of ppGpp in plastids are required for controlling not only plastid metabolism but also phytohormone signaling, which is essential for plant defense.

plant biology↗

bioRxiv2022

Development of a versatile high-throughput mutagenesis assay with multiplexed short read NGS using DNA-barcoded supF shuttle vector library amplified in non-SOS E. coli

A forward mutagenesis assay using the supF gene has been widely employed for the last several decades in studies addressing mutation frequencies and mutation spectra associated with various intrinsic and environmental mutagens. In this study, by using a supF shuttle vector and non-SOS-induced Escherichia coli with short read Next Generation Sequencing (NGS) technology, we present an advanced method for the study of mutations, which is simple, versatile, and cost-effective. We demonstrate the performance of our newly developed assay via pilot experiments with UV-irradiation, the results from which emerge more relevant than expected. The NGS data obtained from samples of the indicator E. coli grown on titer plates provides mutation frequency and spectrum data, and uncovers obscure mutations that cannot be detected by a conventional supF assay. Furthermore, a very small amount of NGS data from selection plates reveals the almost full spectrum of mutations in each specimen and offers us a novel insight into the mechanisms of mutagenesis, despite them being considered already well-known. We believe that the method presented here will contribute to future opportunities for research on mutagenesis, DNA repair, and cancer.

molecular biology↗

bioRxiv2020

Massive occurrence of benthic plastic debris at the abyssal seafloor beneath the Kuroshio Extension, the North West Pacific

The deep-sea is considered to be an ultimate sink for marine plastic debris. The abyssal (3500-6500 m) covers the bulk of the deep ocean floor yet little is known about the extent of plastic debris on the abyssal seafloor. We undertook a quantitative assessment of debris presents on the abyssal seafloor (5700-5800 m depth) beneath the Kuroshio Extension current system in the Northwest Pacific, which is one of the major transit points for massive amounts of debris sourced from Asia that are entering the North Pacific Ocean. The dominant type of debris was single-use plastics-mainly bags and food packaging. The density of plastic debris (average 4561 items km-2) in the abyssal zone was the highest recorded for an abyssal plain, suggesting that the deep-sea basin of the Northwest Pacific is a significant reservoir of plastic debris.

ecology↗