Details of a Researcher - Arakawa, Kazuharu

Papers - Arakawa, Kazuharu

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Complete genome sequence of Solobacterium moorei 10714-02 isolated from the stool of a human colorectal cancer patient

Shinomiya A., Oshibuchi K., Yang J., Fukuda S., Arakawa K.

Microbiology Resource Announcements 15 ( 2 ) 2026.02

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Rhizospheric microbiomes differ between dormant and active Potaninia mongolica in the Gobi desert of Mongolia

Erdenetsetseg B., Arakawa K., Galipon J., Undrakhbold S., Fukuda S., Boldgiv B.

Scientific Reports 15 ( 1 ) 2025.12

Rhizospheric microbiomes differ between active and dormant plants due to changes in root activity and exudate production, especially under environmental stress. In arid regions, native plants such as Potaninia mongolica Maxim enter dormancy to survive harsh conditions. However, rhizospheric microbial and chemical differences between active and dormant states of plants remain poorly described. This study investigated rhizospheric microbial communities and soil chemical changes in the case of active and dormant P.mongolica plants. Rhizospheric soil samples were collected, and soil texture and chemical variables were analyzed. High-throughput sequencing targeting the 16S rRNA and ITS regions was conducted to profile bacterial and fungal communities, respectively. Results showed that the dominant fungal phyla were Ascomycota and Basidiomycota, while Proteobacteria and Actinobacteria were the dominant bacterial phyla in both plant states. Although bacterial diversity did not differ significantly between active and dormant plants (p > 0.05, Welch’s t-test), fungal diversity was significantly different. Among soil chemical variables, total nitrogen was notably elevated in the rhizosphere of dormant plants (mean = 7.93; SD = 5.91). These findings reveal differences in fungal community structure and nitrogen levels in the rhizosphere between active and dormant plant states. Understanding these interactions contributes to our knowledge of desert plant microbiome dynamics and may inform the use of microbial indicators or amendments to support vegetation restoration in arid environments.

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Genome-wide association study of plasma amino acids and Mendelian randomization for cardiometabolic traits

Toki R., Fushiki S., Kojima S., Sutoh Y., Otsuka-Yamasaki Y., Harada S., Iida M., Hirata A., Miyagawa N., Matsumoto M., Edagawa S., Miyake A., Kuwabara K., Hirayama A., Sugimoto M., Sato A., Amano K., Soga T., Tomita M., Arakawa K., Kinoshita K., Sakurai-Yageta M., Tamiya G., Ohmomo H., Shimizu A., Okamura T., Takebayashi T.

Scientific Reports 15 ( 1 ) 2025.12

Plasma amino acids (AAs) have emerged as promising biomarkers for metabolic disorders, yet their causality remains unclear. We aimed to investigate the genetic determinants of AA levels in a cohort of 10,333 individuals and their causal effects on cardiometabolic traits using Mendelian randomization (MR). Plasma levels of 20 AAs were quantified using capillary electrophoresis mass spectrometry. Genome-wide association studies were conducted using BOLT-LMM and heritability estimation via LDSC analysis. Causal effects of AAs on 11 cardiometabolic traits were examined using two-sample MR analyses. We identified 85 locus-metabolite associations across 43 genes for 18 AAs, including 44 novel loci linked to metabolic genes. Heritability for AAs was estimated at 16%. MR analysis demonstrated cystine to positively associate with systolic blood pressure (SBP) (β = 0.056, SE = 0.010), while serine indicated protective effects on SBP (β = − 0.040, SE = 0.011), diastolic BP (β = − 0.044, SE = 0.010), and coronary artery disease (odds ratio 0.888, SE = 0.028). We identified potentially novel genetic loci associated with AA levels and demonstrated robust causal associations between several AAs and cardiometabolic traits. These findings reinforce the importance of AAs as potential biomarkers and therapeutic targets in cardiometabolic health.

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Causal relationship between body mass index and insulin resistance: Linear and nonlinear Mendelian randomization study in a Japanese population

Ishida N., Harada S., Toki R., Hirata A., Matsumoto M., Miyagawa N., Iida M., Edagawa S., Miyake A., Kuwabara K., Shibuki T., Kato S., Arakawa K., Kinoshita K., Sakurai-Yageta M., Tamiya G., Nagashima K., Muraoka H., Sato Y., Takebayashi T.

Journal of Diabetes Investigation 16 ( 7 ) 1305 - 1314 2025.07

ISSN 20401116

Aims/Introduction: Obesity is a known risk factor for several chronic diseases, including type 2 diabetes mellitus, which results from increased insulin resistance and impaired insulin secretion. However, the association between obesity and insulin resistance in Asian populations has not yet been fully elucidated. Therefore, we aimed to investigate the causal relationship between body mass index (BMI) and glycemic traits using Mendelian randomization (MR). Materials and Methods: We performed individual-level MR analyses using genetic risk scores based on BMI-related variants in 3,745 individuals without diabetes mellitus from a Japanese cohort. We examined heterogeneity through subgroup analyses based on potential modifiers and determined the shape of the causal relationship using nonlinear MR analyses to further assess the impact of BMI on the homeostasis model assessment of insulin resistance (HOMA-IR). Results: MR analyses revealed a significant positive association between BMI and HOMA-IR (β = 0.077; 95% confidence interval, 0.014–0.141; P = 0.016; outcome variable was log-transformed and standardized). Additional analyses revealed heterogeneity among subgroups differentiated by age, sex, lifestyle habits, and cardiometabolic traits. Nonlinear MR analyses suggested a potential J-shaped causal relationship between BMI and HOMA-IR. Conclusions: Our findings demonstrated that obesity and low BMI may contribute to increased insulin resistance. Furthermore, the impact of BMI on insulin resistance could vary owing to effect modification. Managing BMI is crucial in individuals at high risk of increased insulin resistance and may have important implications for preventing type 2 diabetes, especially given the low insulin secretory capacity observed in East Asian populations.

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Uncommon N-Glycan Structures in Anhydrobiotic Tardigrades

Yagi H., Saito T., Guu S.Y., Yamakawa N., Shimamura S., Kondo S., Yagi-Utsumi M., Takai K., Furukawa J.I., Guérardel Y., Khoo K.H., Arakawa K., Kato K.

Molecular and Cellular Proteomics 24 ( 6 ) 2025.06

ISSN 15359476

We characterized the N-glycosylation profiles of anhydrobiotic tardigrades, Ramazzottius varieornatus and Hypsibius exemplaris, identifying high-mannose, paucimannose, and complex-type oligosaccharides, while hybrid-type glycans were undetectable. Notably, paucimannose-type oligosaccharides accounted for 39% of the N-glycans in R. varieornatus and 17% in H. exemplaris, with a substantial proportion of them exhibiting fucosylation of the innermost GlcNAc via an α1,6-linkage. This core fucosylation pattern, common to all animals, was observed alongside a distinctive glycosylation signature prominently observed in tardigrades: complex-type glycans lacking galactosylation but containing α1,3-fucosylated GlcNAc at non-reducing termini. This structure was more prevalent in H. exemplaris, with 22 out of 87 identified glycoproteins expressing the Fucα1,3-GlcNAc motif, including eight induced during anhydrobiosis. Key glycoproteins such as Cu/Zn-superoxide dismutase and papilin, implicated in oxidative stress protection and extracellular matrix remodeling, were among those modified. Comparative analyses reveal that non-reducing terminal α1,3-fucosylation in tardigrades is distinct from the mammalian Lewis X antigen and similar structures found in invertebrates, suggesting a unique substrate specificity of fucosyltransferases in these species. Genomic analysis identified homologs of FUT9 and FucTC, indicating potential candidates responsible for this glycosylation pattern. Our findings provide new insights into the molecular mechanisms of glycosylation in tardigrades and their relevance to their extreme stress tolerance.

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Genome assembly of the temporary socially parasitic spiny ant Polyrhachis lamellidens and its host Camponotus japonicus

Iwai H., Kurihara Y., Kono N., Hojo M.K., Yamaguchi K., Shigenobu S., Ozaki M., Koto A., Arakawa K.

DNA Research 32 ( 2 ) 2025.04

ISSN 13402838

Polyrhachis lamellidens is a temporary socially parasitic ant. The newly mated P. lamellidens queen takes over a colony of several Camponotus ant species and uses the labour of the host workers in the early stages of social parasitism. To facilitate genomic resources for these species, we assembled and annotated the chromosomal genome of P. lamellidens using the 10× Genomics linked-read and Hi-C sequencing, and the draft genome of its host, Camponotus japonicus, using long-read sequencing with the Revio system. The P. lamellidens chromosomal genome assembly is 214.1 Mb, 95.5% BUSCO completeness, and contains 13,703 protein-coding genes. The C. japonicus draft genome assembly is 314.2 Mb, 99.0% BUSCO completeness, and contains 11,207 protein-coding genes. Genome-wide phylogeny and synteny analysis confirmed the phylogenetic position of P. lamellidens and C. japonicus, and a high level of synteny with the genome of both ant species. In addition, P. lamellidens possesses nearly identical chemosensory proteins to its host, C. japonicus, and these genes tended to exhibit higher expression levels in the newly mated queen. The genome assemblies of P. lamellidens and its host C. japonicus provide a valuable resource for the molecular biological and bioinformatic basis for studying the strategy of social parasitism in ants.

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Pigment-dispersing factor neuropeptides act as multifunctional hormones and modulators in tardigrades

Dutta S., Hering L., Grollmann M.M., Metzendorf N., Gross V., Arakawa K., Neupert S., Stengl M., Herberg F.W., Mayer G.

Open Biology 15 ( 3 ) 2025.03

Pigment-dispersing factors (PDFs) are neuropeptides that play key roles in controlling the circadian rhythms in various insects, whereas their function remains elusive in other protostomes including tardigrades (water bears). Here we show that the three PDFs of the tardigrade Hypsibius exemplaris are co-localized in two pairs of inner lobe cells in the brain, whereas only one PDF occurs in four additional cerebral and two extracerebral cells. The axons of the inner lobe cells pass through the contralateral brain hemisphere, descend to the ventral nerve cord and terminate in two pairs of potential release sites in the posteriormost trunk ganglion. Using in vitro assays, we demonstrate that all three PDFs and their deorphanized receptor (PDFR) are functional. Widespread localization of PDFR suggests that tardigrade PDFs may act as multifunctional hormones and neuromodulators that control major functions including light detection, neural processing, locomotion, feeding, digestion, osmoregulation, growth, embryonic development and oogenesis/reproduction.

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Post-embryonic tail development through molting of the freshwater shrimp Neocaridina denticulata

Adachi H., Moritoki N., Shindo T., Arakawa K.

Iscience 28 ( 2 ) 2025.02

Neocaridina, a crustacean, exhibits distinctive tail morphogenesis during molting, making it a potential model for post-embryonic morphogenesis. After the first molting, two significant changes occur in the tail: the uropod branches are cleared and the telson undergoes convergent elongation. Cross-sectional analysis showed that uropod and telson branching begins immediately after hatching as cuticle branching. The surface structure of the developing tail suggested that telson elongation is achieved through anisotropic cuticle furrow extension during molting, linked to epithelial cell shape changes occurring post-hatching. An in vivo live imaging system with UV-LED resin revealed gradual telson contraction before molting. Additionally, a draft genome of Neocaridina denticulata was provided. This research enhances understanding of arthropod morphogenesis through molting and lays groundwork for further developmental and cytological studies in Neocaridina.

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Genome sequences of three Streptomyces isolated from the soil of soybean field in Tsuruoka, Japan

Sato R., Saito R., Takeda T., Sasaki N., Yuzawa S., Saito N., Arakawa K.

Microbiology Resource Announcements 14 ( 1 ) 2025.01

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Description and genome sequencing of Olios ishikawatodaorum n. sp. (Arachnida: Araneae: Sparassidae) from Aichi, Japan

Arakawa K., Kato N., Tanikawa A.

Acta Arachnologica 74 ( 1 ) 1 - 8 2025

ISSN 00015202

A new species of Olios, O. ishikawatodaorum n. sp. (♀♂) is described from Aichi Prefecture, Japan, with its annotated genome sequence. The assembled genome spans 3.7Gbp with contig N50 length of 413.4kbp. BUSCO 5 analysis indicates high completeness of the genome (93.8% complete + 3.5% partial = 97.3%), and 22,984 genes have been predicted using RNA-Seq data as evidence. The genome sheds light on neglected RTA clade spider genomics, and reveals a number of expanded gene families in this species. Fulllength or near-full-length spidroin sequences obtained from the genome showed the conservation of MaSp2 which is typically lost in the RTA clade, but whose presence may explain the unusually high supercontraction and strain at break in Sparassidae spiders.

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Correlating Mechanical Properties and Sequence Motifs in Artificial Spider Silk by Targeted Motif Substitution

Nakamura H., Ito Y., Sato R., Chi H., Sato C., Watanabe Y., Arakawa K.

ACS Biomaterials Science and Engineering 10 ( 12 ) 7394 - 7403 2024.12

The major ampullate silk of orb-weaving spiders is renowned for its exceptional mechanical properties, including high tensile strength and extensibility. The development of artificial spider silk presents a promising alternative to traditional fibers with significant environmental impacts. This study aims to elucidate the relationship between sequence motifs of natural spider silk and the mechanical properties of artificial spider silk. Using the Spider Silkome Database, we identified motifs correlated with specific physical properties and substituted them into MaSp2-based mini-spidroin BP1. We then measured the mechanical properties of the resulting recombinant artificial spider silk through tensile tests, observed structural properties via birefringence measurement and wide-angle X-ray scattering, and evaluated the water response through boiled water shrinkage tests. Introducing a positively correlated motif increased the tensile strength by 9.3%, while a negatively correlated motif decreased it by 5.1%, confirming the sequence-property relationship. These findings demonstrate that targeted motif substitution can effectively control the physical properties of artificial spider silk, facilitating the development of sustainable biomaterials with tailored mechanical properties for diverse industrial applications.

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Sexual dimorphism in the tardigrade Paramacrobiotus metropolitanus transcriptome

Sugiura K., Yoshida Y., Hayashi K., Arakawa K., Kunieda T., Matsumoto M.

Zoological Letters 10 ( 1 ) 2024.12

Background: In gonochoristic animals, the sex determination pathway induces different morphological and behavioral features that can be observed between sexes, a condition known as sexual dimorphism. While many components of this sex differentiation cascade show high levels of diversity, factors such as the Doublesex-Mab-3-Related Transcription factor (DMRT) are widely conserved across animal taxa. Species of the phylum Tardigrada exhibit remarkable diversity in morphology and behavior between sexes, suggesting a pathway regulating this dimorphism. Despite the wealth of genomic and zoological knowledge accumulated in recent studies, the sexual differences in tardigrades genomes have not been identified. In the present study, we focused on the gonochoristic species Paramacrobiotus metropolitanus and employed omics analyses to unravel the molecular basis of sexual dimorphism. Results: Transcriptome analysis between sex-identified specimens revealed numerous differentially expressed genes, of which approximately 2,000 male-biased genes were focused on 29 non-male-specific genomic loci. From these regions, we identified two Macrobiotidae family specific DMRT paralogs, which were significantly upregulated in males and lacked sex specific splicing variants. Furthermore, phylogenetic analysis indicated all tardigrade genomes lack the doublesex ortholog, suggesting doublesex emerged after the divergence of Tardigrada. In contrast to sex-specific expression, no evidence of genomic differences between the sexes was found. We also identified several anhydrobiosis genes that exhibit sex-biased expression, suggesting a possible mechanism for protection of sex-specific tissues against extreme stress. Conclusions: This study provides a comprehensive analysis for analyzing the genetic differences between sexes in tardigrades. The existence of male-biased, but not male-specific, genomic loci and identification of the family specific male-biased DMRT subfamily provides the foundation for understanding the sex determination cascade. In addition, sex-biased expression of several tardigrade-specific genes which are involved their stress tolerance suggests a potential role in protecting sex-specific tissue and gametes.

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Search for putative gene regulatory motifs in CAHS3, linked to anhydrobiosis in a tardigrade Ramazzottius varieornatus, in vivo and in silico

Ishikawa S., Tanaka S., Arakawa K.

Genes to Cells 29 ( 12 ) 1144 - 1153 2024.12

ISSN 13569597

Tardigrades possess the ability to enter an almost completely dehydrated state, anhydrobiosis. The CAHS (cytosolic abundant heat-soluble) protein family has been identified as one of the anhydrobiosis-related proteins. In particular, CAHS3 protein from an anhydrobiotic tardigrade, Ramazzottius varieornatus, shows heat-solubility and reversible condensation and is one of the most highly expressed among the CAHS paralogs. A recently developed tardigrade-specific vector showed tissue-specific expression of RvCAHS3 most pronounced in the epidermis in vivo, contrary to the idea that anhydrobiotic genes are uniformly expressed in all tardigrade cells. In this study, we investigated the regulation of RvCAHS3 gene expression through in vivo expression experiments using tardigrade vectors with a series of truncated upstream regions coupled with in silico analysis to identify the anhydrobiosis-related genes that are expressed under the same regulatory system as RvCAHS3. As a result, the 300–350 bp region upstream of RvCAHS3 is critical for regulating gene expression in tardigrade vector experiments, and three motifs conserved between two species of anhydrobiotic tardigrades were identified within a 500 bp region directly upstream of RvCAHS3 start codon. These motifs, which have also been identified upstream of other CAHS genes, could be associated with the regulatory system of anhydrobiosis-related genes in tardigrades.

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Posttranslational modifications in spider silk influence conformation and dimerization dynamics

Craig H.C., Malay A.D., Hayashi F., Mori M., Arakawa K., Numata K.

MRS Bulletin 49 ( 12 ) 1192 - 1204 2024.12

ISSN 08837694

Abstract: Spider silk is an archetypal biopolymer material with extreme tensile properties arising from its complex hierarchical assembly. While recent advances in sequencing have yielded abundant insights, relatively little is known concerning post-translational modifications (PTMs) in spider silk. Here, we probe the PTM landscape of dragline silk from the Jorō spider (Trichonephila clavata) using a combination of mass spectroscopy and solid-state nuclear magnetic resonance (NMR). The results reveal a wide array of potential modifications, including hydroxyproline, phosphorylation, and dityrosine cross-links, encompassing the different spidroin constituents. Notably, the MaSp3 repetitive region displayed numerous PTMs, whereas MaSp1 and MaSp2 variants showed distinct phosphorylation patterns in its terminal domains. The N-terminal domain (NTD) phosphorylation sites were found predominantly at the dimer interface, suggesting a modulatory function with respect to its pH-driven dimerization function, a hypothesis supported by studies using phosphomimetic NTD mutants. Possible roles of phosphoserine in limiting β-sheet formation, and hydroxyproline in disrupting β-turns are also discussed. Impact statement: Spider silk is an archetypal biomaterial that can outperform our most sophisticated artificial fibers. The secret to its mechanical properties lies in its complex hierarchical structure—encompassing the nano- to macroscales—that forms through a process of molecular self-assembly of the constituent spidroin proteins. While recent advances in "biomateriomics” have given us tremendous insights into the sequence–function relationships that determine spider silk behavior, the picture is still far from complete. One area that has received little attention is posttranslational modifications (PTMs). PTMs are ubiquitous biological phenomena that are crucial for providing dynamic control of the proteome, and effectively expand the structural and functional design space of proteins beyond that provided by the canonical amino acids. Here, we undertook a comprehensive analysis of PTMs from spider dragline silk fiber, which revealed numerous potential sites for a wide array of modifications. The results provide a fascinating window into additional layers of complexity underlying the mechanical behavior of spider silk, and suggest further avenues for creating novel, dynamically tunable, bioinspired materials.