Papers - Arakawa, Kazuharu

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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We report the complete circular genome sequence (2,316,546 bp; 37.0% G + C) of Solobacterium moorei 10714-02, a gram-positive obligate anaerobe isolated from stool samples of a human colorectal cancer patient, differing from the typically linear chromosome of this species.

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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

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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

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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

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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

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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

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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

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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

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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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Streptomyces are Gram-positive bacteria typically found in the soil, with very large genomes and high GC content, and are known to produce a wide range of secondary metabolites. We isolated and sequenced the genomes of three Streptomyces bacteria from the soil of soybean field in Tsuruoka, Japan.

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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

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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

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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

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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

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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

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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.

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Complete genome sequence of Bulleidia sp. 10714-15 isolated from human colon cancer patients

Ikeda H., Oshibuchi K., Yang J., Fukuda S., Arakawa K.

Microbiology Resource Announcements 13 ( 12 )  2024.12

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Bulleidia sp. is a non-spore-forming, obligatory anaerobic, Gram-positive bacterium isolated from the stool samples of human colon cancer patients. We report the complete genome sequence of Bulleidia sp. 10714-15, comprising a single linear chromosome of 2,218,984 bp with a G + C content of 36.6%.

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Complete genome sequence of polylactic acid degrading Rhodopseudomonas palustris strain R1 isolated from rice field soil

Ito L., Masui M., Galipon J., Arakawa K.

Microbiology Resource Announcements 13 ( 11 )  2024.11

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Rhodopseudomonas palustris R1 is a phototrophic, purple, non-sulfur Gram-negative bacterium first isolated from the soils of rice fields, known for its polylactic acid degradability. Here, we present the complete circular genome sequence of this bacterium, spanning 5.32 Mbp and 4,949 protein-coding sequences.

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Complete genome sequences of two Paenibacillus isolated from pegmatite in Fukushima, Japan

Yamamoto P.K., Fujimoto Y., Warashina T., Arakawa K.

Microbiology Resource Announcements 13 ( 11 )  2024.11

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The genus Paenibacillus comprises facultatively anaerobic, endospore-forming, Gram-positive eubacteria known for efficiently producing a diverse array of exoenzymes. We isolated and sequenced the complete genomes of two Paenibacillus bacteria from the pegmatite surface in the fourth ore body in the mine Wagu Kannon Mine, Fukushima Prefecture.

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Complete genome sequence of Serratia plymuthica SWSY-3.47

Takahashi H., Warashina T., Takahashi Y., Tanaka M., Suzuki K., Morita T., Arakawa K.

Microbiology Resource Announcements 13 ( 11 )  2024.11

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Serratia plymuthica strain SWSY-3.47 is a Gram-negative, rod-shaped bacteria isolated for its high chitinolytic activity. Here, we report the complete genome of this strain comprised of a single circular chromosome of 5,636,345 bp with a G + C content of 56.0%.

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Complete genome sequence of Mediterraneibacter gnavus strain RI1, isolated from human feces

Ichimura R., Tanaka K., Nakato G., Fukuda S., Arakawa K.

Microbiology Resource Announcements 13 ( 9 )  2024.09

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We report the complete genome sequence of Mediterraneibacter gnavus strain RI1, a Gram-positive anaerobic gut microbe isolated from human feces. The complete circular genome has a genome size of 3.25 Mb, with a G+C content of 42.6%.

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Complete genome sequence of Kitasatospora aureofaciens Tü117

Kato S., Yuzawa S., Takeda T., Arakawa K.

Microbiology Resource Announcements 13 ( 2 )  2024.02

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Actinobacteria produce about two-thirds of all naturally derived antibiotics currently in clinical use. Kitasatospora aureofaciens Tü117 is a species of Actinobacteria and produces α-lipomycin. We report the complete genome sequence of K. aureofaciens, composed of a single linear chromosome of 8,717,539 Mbp with a G + C content of 72.0%.

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Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet

Tsukimi T., Obana N., Shigemori S., Arakawa K., Miyauchi E., Yang J., Song I., Ashino Y., Wakayama M., Soga T., Tomita M., Ohno H., Mori H., Fukuda S.

Msystems 9 ( 2 )  2024.02

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Mammalian gut microbes colonize the intestinal tract of their host and adapt to establish a microbial ecosystem. The host diet changes the nutrient profile of the intestine and has a high impact on microbiota composition. Genetic mutations in Escherichia coli, a prevalent species in the human gut, allow for adaptation to the mammalian intestine, as reported in previous studies. However, the extent of colonization fitness in the intestine elevated by genetic mutation and the effects of diet change on these mutations in E. coli are still poorly known. Here, we show that notable mutations in sugar metabolism-related genes (gatC, araC, and malI) were detected in the E. coli K-12 genome just 2 weeks after colonization in the germ-free mouse intestine. In addition to elevated fitness by deletion of gatC, as previously reported, deletion of araC and malI also elevated E. coli fitness in the murine intestine in a host diet-dependent manner. In vitro cultures of medium containing nutrients abundant in the intestine (e.g., galactose, N-acetylglucosamine, and asparagine) also showed increased E. coli fitness after deletion of the genes-of-interest associated with their metabolism. Furthermore, the host diet was found to influence the developmental trajectory of gene mutations in E. coli. Taken together, we suggest that genetic mutations in E. coli are selected in response to the intestinal environment, which facilitates efficient utilization of nutrients abundant in the intestine under laboratory conditions. Our study offers some insight into the possible adaptation mechanisms of gut microbes.

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The Evolution of Temperature and Desiccation-Related Protein Families in Tardigrada Reveals a Complex Acquisition of Extremotolerance

Fleming J.F., Pisani D., Arakawa K.

Genome Biology and Evolution 16 ( 1 )  2024.01

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Tardigrada is an ecdysozoan lineage famed for its resilience. Tardigrades can tolerate high doses of radiation, low-oxygen environments, desiccation, and both high and low temperatures under a dormant state called "anhydrobiosis", which is a reversible halt of metabolism upon almost complete desiccation. A large amount of research has focused on the genetic pathways related to these capabilities, and a number of genes have been identified and linked to the extremotolerant response of tardigrades. However, the history of these genes is unclear, and the origins and history of extremotolerant genes within Tardigrada remain a mystery. Here, we generate the first phylogenies of six separate protein families linked with desiccation and radiation tolerance in Tardigrada: cytosolic abundant heat-soluble protein, mitochondrial abundant heat-soluble protein, secretory abundant heat-soluble protein, meiotic recombination 11 homolog, and the newly discovered Echiniscus testudo abundant heat-soluble proteins (alpha and beta). The high number of independent gene duplications found amongst the six gene families studied suggests that tardigrades have a complex history with numerous independent adaptations to cope with aridity within the limnoterrestrial environment. Our results suggest that tardigrades likely transitioned from a marine environment to a limnoterrestrial environment only twice, once in stem Eutardigrada and once in Heterotardigrada, which explains the unique adaptations to anhydrobiosis present in both classes.

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Complete genome sequence of Limnobacter thiooxidans CS-K2T, isolated from freshwater lake sediments in Bavaria, Germany

Naruki M., Watanabe A., Warashina T., Morita T., Arakawa K.

Microbiology Resource Announcements 13 ( 1 )  2024.01

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Limnobacter thiooxidans CS-K2^T is a Gram-negative bacterium first isolated from the sediment of the littoral zone of a freshwater lake in Germany. We here present the complete annotated genome sequence of this thiosulfate-oxidizing bacterium, spanning 3.54 Mb and encoding 3,192 protein-coding sequences.

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Reliability of Time-Series Plasma Metabolome Data over 6 Years in a Large-Scale Cohort Study

Miyake A., Harada S., Sugiyama D., Matsumoto M., Hirata A., Miyagawa N., Toki R., Edagawa S., Kuwabara K., Okamura T., Sato A., Amano K., Hirayama A., Sugimoto M., Soga T., Tomita M., Arakawa K., Takebayashi T., Iida M.

Metabolites 14 ( 1 )  2024.01

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Studies examining long-term longitudinal metabolomic data and their reliability in large-scale populations are limited. Therefore, we aimed to evaluate the reliability of repeated measurements of plasma metabolites in a prospective cohort setting and to explore intra-individual concentration changes at three time points over a 6-year period. The study participants included 2999 individuals (1317 men and 1682 women) from the Tsuruoka Metabolomics Cohort Study, who participated in all three surveys—at baseline, 3 years, and 6 years. In each survey, 94 plasma metabolites were quantified for each individual and quality control (QC) sample. The coefficients of variation of QC, intraclass correlation coefficients, and change rates of QC were calculated for each metabolite, and their reliability was classified into three categories: excellent, fair to good, and poor. Seventy-six percent (71/94) of metabolites were classified as fair to good or better. Of the 39 metabolites grouped as excellent, 29 (74%) in men and 26 (67%) in women showed significant intra-individual changes over 6 years. Overall, our study demonstrated a high degree of reliability for repeated metabolome measurements. Many highly reliable metabolites showed significant changes over the 6-year period, suggesting that repeated longitudinal metabolome measurements are useful for epidemiological studies.

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Possible roles of CAHS proteins from Tardigrade in osmotic stress tolerance in mammalian cells

Bino T., Goto Y., Maryu G., Arakawa K., Aoki K.

Cell Structure and Function 49 ( 2 ) 123 - 133 2024

ISSN  03867196

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Anhydrobiosis, a phenomenon in which organisms survive extreme dehydration by entering a reversible ametabolic state, is a remarkable example of survival strategies. This study focuses on anhydrobiosis in tardigrades, which are known for their resilience to severe environmental conditions. Tardigrades utilize several protective mechanisms against desiccation, notably the constitutive expression of cytoplasmic abundant heat soluble (CAHS) proteins in Ramazzottius varieornatus. These proteins share similarities in their amphiphatic alpha helices with late embryogenesis abundant (LEA) proteins, but differ significantly in their amino acid sequences. In this study, we further explored the functionality of CAHS proteins by analyzing their role in aggregation and tolerance to hyperosmotic stress in mammalian cells. Using live cell imaging, we examined the subcellular localization of several CAHS and LEA proteins in response to hyperosmotic stress. The expression of CAHS1, CAHS3, and CAHS8 tended to enhance the resilience to the hyperosmotic conditions. These findings not only deepen our understanding of the molecular mechanisms of anhydrobiosis but also highlight the potential of CAHS proteins as cryoprotectants.

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Transcriptome analysis of the tardigrade Hypsibius exemplaris exposed to the DNA-damaging agent bleomycin

Yoshida Y., Hirayama A., Arakawa K.

Proceedings of the Japan Academy Series B Physical and Biological Sciences 100 ( 7 ) 414 - 428 2024

ISSN  03862208

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Tardigrades are microscopic animals that are renowned for their capabilities of tolerating near-complete desiccation by entering an ametabolic state called anhydrobiosis. However, many species also show high tolerance against radiation in the active state as well, suggesting cross-tolerance via the anhydrobiosis mechanism. Previous studies utilized indirect DNA damaging agents to identify core components of the cross-tolerance machinery in species with high anhydrobiosis capacities. However, it was difficult to distinguish whether transcriptomic changes were specific to DNA damage or mutual with anhydrobiosis. To this end, we performed transcriptome analysis on bleomycin-exposed Hypsibius exemplaris. We observed induction of several tardigrade-specific gene families, including a previously identified novel antioxidative stress family, which may be a core component of the cross-tolerance mechanism. We also identified enrichment of the tryptophan metabolism pathway, for which metabolomic analysis suggested engagement of this pathway in stress tolerance. These results provide several candidates for the core component of cross-tolerance, as well as possible anhydrobiosis machinery.

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Complete genome sequence of PETase type IIa-harboring Marinobacter nanhaiticus D15-8W, isolated from a South China Sea sediment

Suzuki Y., Fukazawa A., Sugawara K., Galipon J., Arakawa K.

Microbiology Resource Announcements 12 ( 12 )  2023.12

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Marinobacter nanhaiticus D15-8W is known for its ability to metabolize polycyclic aromatic hydrocarbons. Here, we report the complete circular genome sequence of this strain to be 5,336,660 bp (G + C content, 58.6%; 4,869 protein-coding sequences) with one plasmid (69,655 bp).

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Complete genome sequence of Actinoplanes sichuanensis strain 03-723T

Kawashima T., Watanabe Y., Arakawa K.

Microbiology Resource Announcements 12 ( 12 )  2023.12

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A mesophilic bacterium Actinoplanes sichuanensis strain 03-723^T was previously isolated from soil by Sun et al. Here, we present a complete and annotated genome sequence of this strain, which has a total size of 12.1 Mbp with a G + C content of 70.1%.

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Two new species in Leptocheliidae (Crustacea: Peracarida: Tanaidacea) from Japan, with notes on their phylogenetic position and aspects of morphology

Sato A., Arakawa K., Kakui K.

Zoologischer Anzeiger 306   51 - 68 2023.09

ISSN  00445231

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We describe two new species of leptocheliid tanaidaceans, Chondrochelia sublitoralis sp. nov. and Neoleptochelia japonica sp. nov., from Japan. Chondrochelia individuals were collected from 113 to 185 m depth in the Kumano Sea. Chondrochelia sublitoralis sp. nov. resembles Chondrochelia africana, Chondrochelia corsica, Chondrochelia taitungensis, and Chondrochelia tanykeraia in having females with slender chelipeds but differs from them in the length ratio of antennular articles and the setal pattern on maxillipeds, cheliped, pereopods 4–6, and pleopods. Males differ from Chondrochelia durbanensis, for which information on females is lacking, in having pereopod-1 propodus lacking ventrodistal spiniform setae and a uniarticulate uropodal exopod. Chondrochelia sublitoralis sp. nov. varies intraspecifically in the number of female antennular articles, five in larger and four in smaller females. Neoleptochelia japonica sp. nov., collected from the coast of Okinawa Island, differ from Neoleptochelia javaensis (previously the sole species in Neoleptochelia) in the setal pattern on antennae, maxillipeds, cheliped, and pleopods in females; and that on the cheliped in males. Male pereopods 1–3 show a unique subchelate condition that we speculate may function for clasping during copulation. Several females in both species had the second thoracomere demarcated on the carapace, whereas others did not. Cytochrome c oxidase subunit I (COI) gene sequences determined for C. sublitoralis sp. nov. and N. japonica sp. nov. showed intraspecific K2P distances of 0–0.4% and 0–0.5%, respectively. We inferred the phylogenetic positions of the two species in Leptocheliidae based on COI data.

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Nondomain biopolymers: Flexible molecular strategies to acquire biological functions

Arakawa K., Hirose T., Inada T., Ito T., Kai T., Oyama M., Tomari Y., Yoda T., Nakagawa S.

Genes to Cells 28 ( 8 ) 539 - 552 2023.08

ISSN  13569597

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A long-standing assumption in molecular biology posits that the conservation of protein and nucleic acid sequences emphasizes the functional significance of biomolecules. These conserved sequences fold into distinct secondary and tertiary structures, enable highly specific molecular interactions, and regulate complex yet organized molecular processes within living cells. However, recent evidence suggests that biomolecules can also function through primary sequence regions that lack conservation across species or gene families. These regions typically do not form rigid structures, and their inherent flexibility is critical for their functional roles. This review examines the emerging roles and molecular mechanisms of “nondomain biomolecules,” whose functions are not easily predicted due to the absence of conserved functional domains. We propose the hypothesis that both domain- and nondomain-type molecules work together to enable flexible and efficient molecular processes within the highly crowded intracellular environment.

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Composition of Minor Ampullate Silk Makes Its Properties Different from Those of Major Ampullate Silk

Nakamura H., Kono N., Mori M., Masunaga H., Numata K., Arakawa K.

Biomacromolecules 24 ( 5 ) 2042 - 2051 2023.05

ISSN  15257797

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Spider’s minor ampullate silk, or MI-silk, exhibits distinct mechanical properties and water resistance compared to its major ampullate counterpart (MA-silk). The principal protein constituent of MI-silk is known as minor ampullate spidroin, or MiSp, and while its sequence has been deciphered and is thought to underlie the differences in properties with MA-silk, the composition of MI-silk and the relationship between its composition and properties remain elusive. In this study, we set out to investigate the mechanical properties, water resistance, and proteome of MA-silk and MI-silk from Araneus ventricosus and Trichonephila clavata. We also synthesized artificial fibers from major ampullate spidroin, MaSp1 and 2, and MiSp to compare their properties. Our proteomic analysis reveals that the MI-silk of both araneids is composed of MiSp, MaSp1, and spidroin constituting elements (SpiCEs). The absence of MaSp2 in the MI-silk proteome and the comparison of the water resistance of artificial fibers suggest that the presence of MaSp2 is the reason for the disparity in water resistance between MI-silk and MA-silk.

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In vivo expression vector derived from anhydrobiotic tardigrade genome enables live imaging in Eutardigrada

Tanaka S., Aoki K., Arakawa K.

Proceedings of the National Academy of Sciences of the United States of America 120 ( 5 )  2023.01

ISSN  00278424

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Water is essential for life, but anhydrobiotic tardigrades can survive almost complete dehydration. Anhydrobiosis has been a biological enigma for more than a century with respect to how organisms sustain life without water, but the few choices of genetic toolkits available in tardigrade research have been a challenging circumstance. Here, we report the development of an in vivo expression system for tardigrades. This transient transgenic technique is based on a plasmid vector (TardiVec) with promoters that originated from an anhydrobiotic tardigrade Ramazzottius varieornatus. It enables the introduction of GFP-fused proteins and genetically encoded indicators such as the Ca²⁺ indicator GCaMP into tardigrade cells; consequently, the dynamics of proteins and cells in tardigrades may be observed by fluorescence live imaging. This system is applicable for several tardigrades in the class Eutardigrada: the promoters of anhydrobiosis-related genes showed tissue-specific expression in this work. Surprisingly, promoters functioned similarly between multiple species, even for species with different modes of expression of anhydrobiosis-related genes, such as Hypsibius exemplaris, in which these genes are highly induced upon facing desiccation, and Thulinius ruffoi, which lacks anhydrobiotic capability. These results suggest that the highly dynamic expression changes in desiccation-induced species are regulated in trans. Tissue-specific expression of tardigrade-unique unstructured proteins also suggests differing anhydrobiosis machinery depending on the cell types. We believe that tardigrade transgenic technology opens up various experimental possibilities in tardigrade research, especially to explore anhydrobiosis mechanisms.

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Molecular mechanisms of the high performance of spider silks revealed through multi-omics analysis

Watanabe Y., Arakawa K.

Biophysics and Physicobiology 20 ( 1 )  2023

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Spider silk is considered a promising next-generation biomaterial due to its exceptional toughness, coupled with its renewability and biodegradability. Contrary to the conventional view that spider silk is mainly composed of two types of silk proteins (spidroins), MaSp1 and MaSp2, multi-omics strategies are increasingly revealing that the inclusion of complex components confers the higher mechanical properties to the material. In this review, we focus on several recent findings that report essential components and mechanisms that are necessary to reproduce the properties of natural spider silk. First, we discuss the discovery of MaSp3, a newly identified spidroin that is a major component in the composition of spider silk, in addition to the previously understood MaSp1 and MaSp2. Moreover, the role of the Spider-silk Constituting Element (SpiCE), which is present in trace amounts but has been found to significantly increase the tensile strength of artificial spider silk, is explored. We also delve into the process of spidroin fibril formation through liquid-liquid phase separation (LLPS) that forms the hierarchical structure of spider silk. In addition, we review the correlation between amino acid sequences and mechanical properties such as toughness and supercontraction, as revealed by an analysis of 1,000 spiders. In conclusion, these recent findings contribute to the comprehensive understanding of the mechanisms that give spider silk its high mechanical properties and help to improve artificial spider silk production.

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A Nanopore Sequencing Course for Graduate School Curriculum

Arakawa K.

Methods in Molecular Biology Clifton N J 2632   113 - 127 2023

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The high-throughput long-read sequencing has become affordable enough for any molecular biology lab to utilize genome sequencing in their research. Complete genome sequencing and assembly of bacterial genomes is one such application which is powerful yet simple enough for anyone without advanced molecular biology or bioinformatics skills to conduct on his/her own. High-throughput sequencing will eventually become a basic routine tool in molecular biology labs just like polymerase chain reaction and electrophoresis in a near future. To assist the use of such nanopore sequencing technologies, we designed a graduate school course to learn both the experimental and bioinformatic skills of complete bacterial genome sequencing and assembly.

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The Method of Eliminating the Wolbachia Endosymbiont Genomes from Insect Samples Prior to a Long-Read Sequencing

Takasuka K., Arakawa K.

Methods in Molecular Biology Clifton N J 2632   101 - 112 2023

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When extracting DNA of invertebrates for long-read sequencing, not only enough quantity and size of the DNA but, depending on the species, elimination of contamination of endosymbiotic Wolbachia genome also has to be achieved. These requirements become troublesome, especially in small-sized species with a limited number of individuals available for the experiment. In this chapter, using tiny parasitoid wasps (Reclinervellus nielseni) parasitizing spiders as hosts, we developed a method of eliminating the Wolbachia genomes by means of an antibiotic administration to adult wasps via honey solution. Twenty days of rifampicin treatment since their emergence from cocoons resulted in a significant decrease in the Wolbachia genomes while keeping good DNA conditions for nanopore sequencing. An adequate quantity of DNA was then gained by pooling several individuals. The method could be applied to other insects or invertebrates that can be maintained by laboratory feeding with liquid food.

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Ultralow-Input Genome Library Preparation for Nanopore Sequencing with Droplet MDA

Arakawa K.

Methods in Molecular Biology Clifton N J 2632   91 - 100 2023

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Genome sequencing of small species, such as those of meinofauna, can be challenging due to the extremely low input of genomic DNA. While nanopore sequencing is a promising technology for genome assembly due to its limitless long reads, recommended input of 1 μg for the Ligation Sequencing Kit often precludes the use of this technology. Here, I detail an unbiased droplet-based multiple displacement amplification of picogram order of DNA to realize nanopore sequencing with ultralow input of genomic DNA. For this purpose, a microfluidic chip of 10X Genomics Chromium Controller is utilized. With this method, over 10 μg of unbiased amplicons around 10 kbp in length can be obtained from as low as 50 μg of input DNA, which is enough for the construction of multiple sequencing libraries, or for the size selection of longer DNA fragments.

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Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades

Yoshida Y., Satoh T., Ota C., Tanaka S., Horikawa D.D., Tomita M., Kato K., Arakawa K.

BMC Genomics 23 ( 1 )  2022.12

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Background: Tardigrades are microscopic animals that are capable of tolerating extreme environments by entering a desiccated state of suspended animation known as anhydrobiosis. While antioxidative stress proteins, antiapoptotic pathways and tardigrade-specific intrinsically disordered proteins have been implicated in the anhydrobiotic machinery, conservation of these mechanisms is not universal within the phylum Tardigrada, suggesting the existence of overlooked components. Results: Here, we show that a novel Mn-dependent peroxidase is an important factor in tardigrade anhydrobiosis. Through time-series transcriptome analysis of Ramazzottius varieornatus specimens exposed to ultraviolet light and comparison with anhydrobiosis entry, we first identified several novel gene families without similarity to existing sequences that are induced rapidly after stress exposure. Among these, a single gene family with multiple orthologs that is highly conserved within the phylum Tardigrada and enhances oxidative stress tolerance when expressed in human cells was identified. Crystallographic study of this protein suggested Zn or Mn binding at the active site, and we further confirmed that this protein has Mn-dependent peroxidase activity in vitro. Conclusions: Our results demonstrated novel mechanisms for coping with oxidative stress that may be a fundamental mechanism of anhydrobiosis in tardigrades. Furthermore, localization of these sets of proteins mainly in the Golgi apparatus suggests an indispensable role of the Golgi stress response in desiccation tolerance.

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1000 spider silkomes: Linking sequences to silk physical properties

Arakawa K., Kono N., Malay A.D., Tateishi A., Ifuku N., Masunaga H., Sato R., Tsuchiya K., Ohtoshi R., Pedrazzoli D., Shinohara A., Ito Y., Nakamura H., Tanikawa A., Suzuki Y., Ichikawa T., Fujita S., Fujiwara M., Tomita M., Blamires S.J., Chuah J.A., Craig H., Foong C.P., Greco G., Guan J., Holland C., Kaplan D.L., Sudesh K., Mandal B.B., Norma-Rashid Y., Oktaviani N.A., Preda R.C., Pugno N.M., Rajkhowa R., Wang X., Yazawa K., Zheng Z., Numata K.

Science Advances 8 ( 41 )  2022.10

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Spider silks are among the toughest known materials and thus provide models for renewable, biodegradable, and sustainable biopolymers. However, the entirety of their diversity still remains elusive, and silks that exceed the performance limits of industrial fibers are constantly being found. We obtained transcriptome assemblies from 1098 species of spiders to comprehensively catalog silk gene sequences and measured the mechanical, thermal, structural, and hydration properties of the dragline silks of 446 species. The combination of these silk protein genotype-phenotype data revealed essential contributions of multicomponent structures with major ampullate spidroin 1 to 3 paralogs in high-performance dragline silks and numerous amino acid motifs contributing to each of the measured properties. We hope that our global sampling, comprehensive testing, integrated analysis, and open data will provide a solid starting point for future biomaterial designs.

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Complete Genome Sequence of Streptomyces albus Strain G153

Takeda T., Fukumitsu N., Yuzawa S., Arakawa K.

Microbiology Resource Announcements 11 ( 7 )  2022.07

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The genus Streptomyces is a promising source of biologically active secondary metabolites. Here, we report the complete genome sequence of Streptomyces albus strain G153. The assembled genome comprised a single linear chromosome of 6.9 Mbp with a G1C content of 73.3%.

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Complete Genome Sequences of Four Bacteria Isolated from the Gut of a Spiny Ant (Polyrhachis lamellidens)

Ishikawa S., Huang M., Tomita A., Kurihara Y., Watanabe R., Iwai H., Arakawa K.

Microbiology Resource Announcements 11 ( 7 )  2022.07

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We isolated and sequenced the complete genomes of four bacteria from the gut contents of a spiny ant (Polyrhachis lamellidens) sampled from a primeval beech forest in Yamagata Prefecture, Japan. The isolates belong to the genera Tsukamurella, Enterococcus, Lysinibacillus, and Streptomyces and provide insights into the functional roles of microbiomes of ants.

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Molecular Evidence of Chemical Disguise by the Socially Parasitic Spiny Ant Polyrhachis lamellidens (Hymenoptera: Formicidae) When Invading a Host Colony

Iwai H., Mori M., Tomita M., Kono N., Arakawa K.

Frontiers in Ecology and Evolution 10 2022.06

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While most ant species establish a colony independently, some socially parasitic ants build the foundation of their colony by invading other ant (host) colonies and utilizing their labor forces. Many socially parasitic ants disguise their cuticular hydrocarbon (CHC) profile, which is also known as signature mixture for nestmate discrimination, when invading the host colony. Since the strategy of chemical disguise is widespread in socially parasitic ants, elucidating the mechanism of chemical disguise will promote knowledge on the evolutionary history of social parasitism. However, detailed knowledge is still lacking, as the relevant information has only originated from circumstantial evidence, which was obtained from ecological observations. In this study, we investigated the mechanism of chemical disguise in a new queen of a temporary socially parasitic spiny ant (Polyrhachis lamellidens) by measuring its CHC profile, performing a tracing assay with labeled substances, and analyzing gene expression levels. First, after rubbing behavior was observed against the host workers, the CHC profile in P. lamellidens shifted to pronounced peaks that closely resembling that of the host workers. We also observed a reduction in aggressive behaviors by the host ant against P. lamellidens after rubbing behavior was performed. In addition, P. lamellidens acquired artificially-applied labeling substances from host workers through their rubbing behaviors, while gene expression profiling showed the expression of CHC synthesis-related genes did not change during this behavior. These results suggest that P. lamellidens directly obtains host CHCs through rubbing behavior, and these host CHCs enables P. lamellidens to remain disguised during colony invasion.

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Tardigrade Secretory-Abundant Heat-Soluble Protein Varies Entrance Propensity Depending on the Amino-Acid Sequence

Miyazawa K., Itoh S.G., Yoshida Y., Arakawa K., Okumura H.

Journal of Physical Chemistry B 126 ( 12 ) 2361 - 2368 2022.03

ISSN  15206106

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Secretory-abundant heat-soluble (SAHS) proteins, which constitute a protein family unique to tardigrades, are thought to be essential for anhydrobiosis. Our previous study has revealed that one of the SAHS proteins of Ramazzottius varieornatus (RvSAHS1) has a more flexible entrance than a mammalian fatty-acid-binding protein, which has a crystal structure similar to that of RvSAHS1. Recently, SAHS paralogs that are expressed abundantly and specifically in the early embryos of this tardigrade and Hypsibius exemplaris have been identified. Comparing these amino-acid sequences with that of RvSAHS1, we have found characteristic differences as I113F and D146T. In this study, we investigate I113F and D146T mutants' properties of RvSAHS1 using molecular dynamics simulations and compare the structures and fluctuations of their entrances with those of the wild type. The two mutants exhibit different properties at the entrance of the β-barrel structure. The I113F mutant tends to close the entrance more than the wild type due to the enhanced hydrophobic network inside the cavity. The D146T mutant, in contrast to the I113F mutant, tends to open the entrance. The mechanism by which this mutation opens the entrance is also discussed. Even though only a single mutation located far from the entrance is added to the wild type, there is a clear difference in the tendency to open and close the β-barrel entrance. It indicates that the entrance properties of the SAHS protein are sensitive to the amino-acid sequence.

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Initial parasitic behaviour of the temporary social parasitic ant Polyrhachis lamellidens can be induced by host-like cuticles in laboratory environment

Kurihara Y., Iwai H., Kono N., Tomita M., Arakawa K.

Biology Open 11 ( 3 )  2022.03

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Polyrhachis lamellidens is a temporary social parasitic species. When a newly mated queen encounters a host worker, it opens its jaws and then mounts and rubs the body of the host worker, called rubbing behaviour. This behaviour is different from aggressive behaviour and is considered to be a preparatory action before invasion of the host colony. However, it is unclear what cues trigger rubbing behaviour. Therefore, in this study, we used glass beads that imitated the insect body surfaces and searched for triggers. Although P. lamellidens did not respond to the cuticular compounds only, cuticular compounds and chitin coatings on glass beads elicited responses that were similar to those towards live samples. The rubbing behaviour of P. lamellidens was elicited in response to a cuticle-like surface that mimicked a procuticle by combining the compounds with chitin. These results suggest that host recognition and nest-mate recognition are supported by different mechanisms.

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Examples of Extreme Survival: Tardigrade Genomics and Molecular Anhydrobiology

Arakawa K.

Annual Review of Animal Biosciences 10   17 - 37 2022.02

ISSN  21658102

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Tardigrades are ubiquitous meiofauna that are especially renowned for their exceptional extremotolerance to various adverse environments, including pressure, temperature, and even ionizing radiation. This is achieved through a reversible halt of metabolism triggered by desiccation, a phenomenon called anhydrobiosis. Recent establishment of genome resources for two tardigrades, Hypsibius exemplaris and Ramazzottius varieornatus, accelerated research to uncover the molecular mechanisms behind anhydrobiosis, leading to the discovery of many tardigrade-unique proteins. This review focuses on the history, methods, discoveries, and current state and challenges regarding tardigrade genomics, with an emphasis on molecular anhydrobiology. Remaining questions and future perspectives regarding prospective approaches to fully elucidate the molecular machinery of this complex phenomenon are discussed.

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Liquid‒liquid phase separation seen in tardigrade anhydrobiosis and spider silk spinning

Arakawa K.

Seikagaku 94 ( 4 ) 537 - 547 2022

ISSN  00371017

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Darwin's bark spider shares a spidroin repertoire with Caerostris extrusa but achieves extraordinary silk toughness through gene expression

Kono N., Ohtoshi R., Malay A.D., Mori M., Masunaga H., Yoshida Y., Nakamura H., Numata K., Arakawa K.

Open Biology 11 ( 12 )  2021.12

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Spider silk is a protein-based material whose toughness suggests possible novel applications. A particularly fascinating example of silk toughness is provided by Darwin's bark spider (Caerostris darwini) found in Madagascar. This spider produces extraordinarily tough silk, with an average toughness of 350 MJ m -1 and over 50% extensibility, and can build river-bridging webs with a size of 2.8 m 2. Recent studies have suggested that specific spidroins expressed in C. darwini are responsible for the mechanical properties of its silk. Therefore, a more comprehensive investigation of spidroin sequences, silk thread protein contents and phylogenetic conservation among closely related species is required. Here, we conducted genomic, transcriptomic and proteomic analyses of C. darwini and its close relative Caerostris extrusa. A variety of spidroins and low-molecular-weight proteins were found in the dragline silk of these species; all of the genes encoding these proteins were conserved in both genomes, but their genes were more expressed in C. darwini. The potential to produce very tough silk is common in the genus Caerostris, and our results may suggest the existence of plasticity allowing silk mechanical properties to be changed by optimizing related gene expression in response to the environment.

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Comprehensive Transcriptome Sequencing of Tanaidacea with Proteomic Evidences for Their Silk

Kakui K., Fleming J.F., Mori M., Fujiwara Y., Arakawa K.

Genome Biology and Evolution 13 ( 12 )  2021.12

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Tanaidaceans are small benthic crustaceans that mainly inhabit diverse marine environments, and they comprise one of the most diverse and abundant macrofaunal groups in the deep sea. Tanaidacea is one of the most thread-dependent taxa in the Crustacea, constructing tubes, spun with their silk, for shelter. In this work, we sequenced and assembled the comprehensive transcriptome of 23 tanaidaceans encompassing 14 families and 4 superfamilies of Tanaidacea, and performed silk proteomics of Zeuxo ezoensis to search for its silk genes. As a result, we identified two families of silk proteins that are conserved across the four superfamilies. The long and repetitive nature of these silk genes resembles that of other silk-producing organisms, and the two families of proteins are similar in composition to silkworm and caddisworm fibroins, respectively. Moreover, the amino acid composition of the repetitive motifs of tanaidacean silk tends to be more hydrophilic, and therefore could be a useful resource in studying their unique adaptation of silk use in a marine environment. The availability of comprehensive transcriptome data in these taxa, coupled with proteomic evidence of their silk genes, will facilitate evolutionary and ecological studies.

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Desiccation-induced fibrous condensation of CAHS protein from an anhydrobiotic tardigrade

Yagi-Utsumi M., Aoki K., Watanabe H., Song C., Nishimura S., Satoh T., Yanaka S., Ganser C., Tanaka S., Schnapka V., Goh E.W., Furutani Y., Murata K., Uchihashi T., Arakawa K., Kato K.

Scientific Reports 11 ( 1 )  2021.12

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Anhydrobiosis, one of the most extensively studied forms of cryptobiosis, is induced in certain organisms as a response to desiccation. Anhydrobiotic species has been hypothesized to produce substances that can protect their biological components and/or cell membranes without water. In extremotolerant tardigrades, highly hydrophilic and heat-soluble protein families, cytosolic abundant heat-soluble (CAHS) proteins, have been identified, which are postulated to be integral parts of the tardigrades’ response to desiccation. In this study, to elucidate these protein functions, we performed in vitro and in vivo characterizations of the reversible self-assembling property of CAHS1 protein, a major isoform of CAHS proteins from Ramazzottius varieornatus, using a series of spectroscopic and microscopic techniques. We found that CAHS1 proteins homo-oligomerized via the C-terminal α-helical region and formed a hydrogel as their concentration increased. We also demonstrated that the overexpressed CAHS1 proteins formed condensates under desiccation-mimicking conditions. These data strongly suggested that, upon drying, the CAHS1 proteins form oligomers and eventually underwent sol–gel transition in tardigrade cytosols. Thus, it is proposed that the CAHS1 proteins form the cytosolic fibrous condensates, which presumably have variable mechanisms for the desiccation tolerance of tardigrades. These findings provide insights into molecular strategies of organisms to adapt to extreme environments.

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Shifts in morphology, gene expression, and selection underlie web loss in Hawaiian Tetragnatha spiders

Berger C.A., Brewer M.S., Kono N., Nakamura H., Arakawa K., Kennedy S.R., Wood H.M., Adams S.A., Gillespie R.G.

BMC Ecology and Evolution 21 ( 1 )  2021.12

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Background: A striking aspect of evolution is that it often converges on similar trajectories. Evolutionary convergence can occur in deep time or over short time scales, and is associated with the imposition of similar selective pressures. Repeated convergent events provide a framework to infer the genetic basis of adaptive traits. The current study examines the genetic basis of secondary web loss within web-building spiders (Araneoidea). Specifically, we use a lineage of spiders in the genus Tetragnatha (Tetragnathidae) that has diverged into two clades associated with the relatively recent (5 mya) colonization of, and subsequent adaptive radiation within, the Hawaiian Islands. One clade has adopted a cursorial lifestyle, and the other has retained the ancestral behavior of capturing prey with sticky orb webs. We explore how these behavioral phenotypes are reflected in the morphology of the spinning apparatus and internal silk glands, and the expression of silk genes. Several sister families to the Tetragnathidae have undergone similar web loss, so we also ask whether convergent patterns of selection can be detected in these lineages. Results: The cursorial clade has lost spigots associated with the sticky spiral of the orb web. This appears to have been accompanied by loss of silk glands themselves. We generated phylogenies of silk proteins (spidroins), which showed that the transcriptomes of cursorial Tetragnatha contain all major spidroins except for flagelliform. We also found an uncharacterized spidroin that has higher expression in cursorial species. We found evidence for convergent selection acting on this spidroin, as well as genes involved in protein metabolism, in the cursorial Tetragnatha and divergent cursorial lineages in the families Malkaridae and Mimetidae. Conclusions: Our results provide strong evidence that independent web loss events and the associated adoption of a cursorial lifestyle are based on similar genetic mechanisms. Many genes we identified as having evolved convergently are associated with protein synthesis, degradation, and processing, which are processes that play important roles in silk production. This study demonstrates, in the case of independent evolution of web loss, that similar selective pressures act on many of the same genes to produce the same phenotypes and behaviors.

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Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada

Murai Y., Yagi-Utsumi M., Fujiwara M., Tanaka S., Tomita M., Kato K., Arakawa K.

BMC Genomics 22 ( 1 )  2021.12

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Background: Many limno-terrestrial tardigrades can enter an ametabolic state, known as anhydrobiosis, upon desiccation, in which the animals can withstand extreme environments. Through genomics studies, molecular components of anhydrobiosis are beginning to be elucidated, such as the expansion of oxidative stress response genes, loss of stress signaling pathways, and gain of tardigrade-specific heat-soluble protein families designated CAHS and SAHS. However, to date, studies have predominantly investigated the class Eutardigrada, and molecular mechanisms in the remaining class, Heterotardigrada, still remains elusive. To address this gap in the research, we report a multiomics study of the heterotardigrade Echiniscus testudo, one of the most desiccation-tolerant species which is not yet culturable in laboratory conditions. Results: In order to elucidate the molecular basis of anhydrobiosis in E. testudo, we employed a multi-omics strategy encompassing genome sequencing, differential transcriptomics, and proteomics. Using ultra-low input library sequencing protocol from a single specimen, we sequenced and assembled the 153.7 Mbp genome annotated using RNA-Seq data. None of the previously identified tardigrade-specific abundant heat-soluble genes was conserved, while the loss and expansion of existing pathways were partly shared. Furthermore, we identified two families novel abundant heat-soluble proteins, which we named E. testudo Abundant Heat Soluble (EtAHS), that are predicted to contain large stretches of disordered regions. Likewise the AHS families in eutardigrada, EtAHS shows structural changes from random coil to alphahelix as the water content was decreased in vitro. These characteristics of EtAHS proteins are analogous to those of CAHS in eutardigrades, while there is no conservation at the sequence level. Conclusions: Our results suggest that Heterotardigrada have partly shared but distinct anhydrobiosis machinery compared with Eutardigrada, possibly due to convergent evolution within Tardigrada. (276/350).

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The balance of crystalline and amorphous regions in the fibroin structure underpins the tensile strength of bagworm silk

Kono N., Nakamura H., Tateishi A., Numata K., Arakawa K.

Zoological Letters 7 ( 1 )  2021.12

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Protein-based materials are considered versatile biomaterials, and their biodegradability is an advantage for sustainable development. Bagworm produces strong silk for use in unique situations throughout its life stages. Rigorous molecular analyses of Eumeta variegata suggested that the particular mechanical properties of its silk are due to the coexistence of poly-A and GA motifs. However, little molecular information on closely related species is available, and it is not understood how these properties were acquired evolutionarily or whether the motif combination is a conserved trait in other bagworms. Here, we performed a transcriptome analysis of two other bagworm species (Canephora pungelerii and Bambalina sp.) belonging to the family Psychidae to elucidate the relationship between the fibroin gene and silk properties. The obtained transcriptome assemblies and tensile tests indicated that the motif combination and silk properties were conserved among the bagworms. Furthermore, our analysis showed that C. pungelerii produces extraordinarily strong silk (breaking strength of 1.4 GPa) and indicated that the cause may be the C. pungelerii -specific balance of crystalline/amorphous regions in the H-fibroin repetitive domain. This particular H-fibroin architecture may have been evolutionarily acquired to produce strong thread to maintain bag stability during the relatively long development period of Canephora species relative to other bagworms.

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The evidence of temporary social parasitism by Polyrhachis lamellidens (Hymenoptera, Formicidae) in a Camponotus obscuripes colony (Hymenoptera, Formicidae)

Iwai H., Kurihara Y., Kono N., Tomita M., Arakawa K.

Insectes Sociaux 68 ( 4 ) 375 - 382 2021.11

ISSN  00201812

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Polyrhachis lamellidens is a temporary socially parasitic ant whose new queen utilizes other ant species in the early stages of colony foundation. Field observations and rearing experiments suggest that Camponotus japonicus is a host species of P. lamellidens. It is presumed that Camponotus obscuripes is also a host of P. lamellidens by rearing experiments and field observations; however, there are no records of P. lamellidens workers or brood coexisting in C. obscuripes colonies in field observations, and there is no clear evidence that C. obscuripes is a natural host of P. lamellidens. We conducted detailed field observations, behavioral tests, and rearing experiments to show that C. obscuripes is a host of temporary social parasites. We found colonies with P. lamellidens queens, workers, and larvae intermixed with C. obscuripes workers in the field. Behavioral tests showed that workers of both species in mixed colonies did not attack each other and maintained nestmate recognition ability, which suggests a collaborative nestmate relationship. Furthermore, a rearing experiment confirmed social parasitism by P. lamellidens among C. obscuripes by producing a mixed brood-producing colony. These are the first field and laboratory records of temporary social parasitism involving P. lamellidens and C. obscuripes.

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Tardigrade Secretory-Abundant Heat-Soluble Protein Has a Flexible β-Barrel Structure in Solution and Keeps This Structure in Dehydration

Miyazawa K., Itoh S.G., Watanabe H., Uchihashi T., Yanaka S., Yagi-Utsumi M., Kato K., Arakawa K., Okumura H.

Journal of Physical Chemistry B 125 ( 32 ) 9145 - 9154 2021.08

ISSN  15206106

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Secretory-abundant heat-soluble (SAHS) proteins are unique heat-soluble proteins of Tardigrada and are believed to play an essential role in anhydrobiosis, a latent state of life induced by desiccation. To investigate the dynamic properties, molecular dynamics (MD) simulations of a SAHS protein, RvSAHS1, were performed in solution and under dehydrating conditions. For comparison purposes, MD simulations of a human liver-type fatty-acid binding protein (LFABP) were performed in solution. Furthermore, high-speed atomic force microscopy observations were conducted to ascertain the results of the MD simulations. Three properties of RvSAHS1 were found as follows. (1) The entrance region of RvSAHS1 is more flexible and can be more extensive in solutions compared with that of a human LFABP because there is no salt bridge between the βD and βE strands. (2) The intrinsically disordered domain in the N-terminal region significantly fluctuates and can form an amphiphilic α-helix. (3) The size of the entrance region gets smaller along with dehydration, keeping the β-barrel structure. Overall, the obtained results provide atomic-level dynamics of SAHS proteins.

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Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk

Kono N., Nakamura H., Mori M., Yoshida Y., Ohtoshi R., Malay A.D., Pedrazzoli Moran D.A., Tomita M., Numata K., Arakawa K.

Proceedings of the National Academy of Sciences of the United States of America 118 ( 31 )  2021.08

ISSN  00278424

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Dragline silk of golden orb-weaver spiders (Nephilinae) is noted for its unsurpassed toughness, combining extraordinary extensibility and tensile strength, suggesting industrial application as a sustainable biopolymer material. To pinpoint the molecular composition of dragline silk and the roles of its constituents in achieving its mechanical properties, we report a multiomics approach, combining highquality genome sequencing and assembly, silk gland transcriptomics, and dragline silk proteomics of four Nephilinae spiders.We observed the consistent presence of the MaSp3B spidroin unique to this subfamily as well as several nonspidroin SpiCE proteins. Artificial synthesis and the combination of these components in vitro showed that the multicomponent nature of dragline silk, including MaSp3B and SpiCE, along with MaSp1 and MaSp2, is essential to realize the mechanical properties of spider dragline silk.

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New Tardigrade Opsins and Differential Expression Analyses Show Ontogenic Variation in Light Perception

Fleming J.F., Pisani D., Arakawa K.

Genome Biology and Evolution 13 ( 8 )  2021.08

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Opsins are light-sensitive proteins involved in many photoreceptive processes, including, but not limited to, vision and regulation of circadian rhythms. Arthropod (e.g., insects, spiders, centipedes, and crabs) opsins have been extensively researched, but the relationships and function of opsins found in lineages that are evolutionarily closely related to the arthropods remains unclear. Multiple, independent, opsin duplications are known in Tardigrada (the water bears), evidencing that protostome opsin duplications are not limited to the Arthropoda. However, the relationships, function, and expression of these new opsins are still unknown. Here, we use two tardigrade transcriptomes with deep coverage to greatly expand our knowledge of the diversity of tardigrade opsins. We reconstruct the phylogenetic relationships of the tardigrade opsins and investigate their ontogenetic expression. We found that while tardigrades have multiple opsins that evolved from lineage-specific duplications of well-understood arthropod opsins, their expression levels change during ontogeny such that most of these opsins are not co-temporally expressed. Co-temporal expression of multiple opsins underpins color vision in Arthropoda and Vertebrata. Our results clearly show duplications of both rhabdomeric and ciliary opsins within Tardigrada, forming clades specific to both the Heterotardigrada and Eutardigrada in addition to multiple independent duplications within genera. However, lack of co-temporal, ontogenetic, expression suggests that while tardigrades possess multiple opsins, they are unlikely to be able to distinguish color.

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Complete genome sequence of atopobiaceae bacterium strain p1, isolated from mouse feces

Watanabe Y., Takeuchi N., Yang J., Obana N., Morinaga K., Kusada H., Tamaki H., Fukuda S., Arakawa K.

Microbiology Resource Announcements 10 ( 28 )  2021.07

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Atopobiaceae bacterium strain P1 (Actinobacteria, Coriobacteriales) was isolated from mouse feces. Here, we report the complete genome sequence of this strain, which has a total size of 2,028,478bp and a G1C content of 58.6%.

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Complete genome sequences of two lysobacter strains, isolated from seawater (lysobacter caseinilyticus) and soil (lysobacter helvus) in south korea

Watanabe Y., Arakawa K.

Microbiology Resource Announcements 10 ( 28 )  2021.07

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Lysobacter species produce lysobactin, a depsipeptide antibiotic that is effective against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Staphylococcus aureus. Here, we report complete genome sequences of two Lysobacter strains, which were isolated from seawater (Lysobacter caseinilyticus) and soil (Lysobacter helvus) in South Korea.

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Proteomic evidence for the silk fibroin genes of spider mites (Order Trombidiformes: Family Tetranychidae)

Arakawa K., Mori M., Kono N., Suzuki T., Gotoh T., Shimano S.

Journal of Proteomics 239 2021.05

ISSN  18743919

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Spider mites are a group of arachnids belonging to Acari (mites and ticks), family Tetranychidae, known to produce nanoscale silk fibers characterized by a high Young's modulus. The silk fibroin gene of spider mites has been computationally predicted through genomic analysis of Tetranychus urticae Koch, but it has yet to be confirmed by proteomic evidence. In this work, we sequenced and assembled the transcriptome from two genera of spider mites, Tetranychus kanzawai Kishida and Panonychus citri (McGregor), and combined it with silk proteomics of T. urticae and P. citri to characterize the fibroin genes through comparative genomics and multiomics analysis. As a result, two fibroins were identified, which were different genes than those previously predicted by computational methods. The amino acid composition and secondary structure suggest similarity to aciniform or cylindrical spidroins of spider silk, which partly mirrors their mechanical properties, exhibiting a high Young's modulus. The availability of full-length fibroin sequences of spider mites facilitates the study of the evolution of silk genes that sometimes emerge in multiple lineages in a convergent manner and in the industrial application of artificial protein fibers through the study of the amino acid sequence and the resulting mechanical properties of these silks. Significance: Here we sequenced and assembled the transcriptome from two genera of spider mites, T. kanzawai and P. citri, and combined it with silk proteomics of T. urticae and P. citri to characterize the fibroin genes through comparative genomics and multiomics analysis. Spider mite silk is especially characterized by its extremely fine nano-scale diameter and high Young's modulus, even exceeding those of spider silks. The availability of full-length fibroin sequences of spider mites facilitates the study of the evolution of silk genes, which independently evolved in mites, insects, and spiders but yet show sequence convergence, and in the industrial application of artificial protein fibers through the study of the amino acid sequence and the resulting mechanical properties of these silks.

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Systematics of tardigrada: A reanalysis of tardigrade taxonomy with specific reference to Guil et al. (2019)

Fleming J.F., Arakawa K.

Zoologica Scripta 50 ( 3 ) 376 - 382 2021.05

ISSN  03003256

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The Tardigrada are a clade with a disputed and complex taxonomy. The three traditional tardigrade classes are the Heterotardigrada, Eutardigrada and the dubious, monotypic Mesotardigrada. A recent molecular study by Guil et al (Zoologica Scripta, 48, 2019, 120) suggested that the Apochela, previously considered an order of Eutardigrada, should become a new class, Apotardigrada, with the Parachela becoming THE new Eutardigrada. This new diagnosis was presented alongside compelling morphological evidence. Here, we test the assumptions of the molecular evidence for Apotardigrada by analysing tardigrade 18S and 28S data under four separate conditions, along with new BUSCO data, across both Bayesian- and maximum-likelihood phylogenetic approaches. We found variable conclusions regarding the status of Apotardigrada could be drawn by comparing the ribosomal RNA and BUSCO results, and caution against using branch length data to determine taxonomic hierarchy.

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Complete genome sequence of adlercreutzia equolifaciens subsp. celatus DSM 18785

Takahashi H., Yang J., Yamamoto H., Fukuda S., Arakawa K.

Microbiology Resource Announcements 10 ( 19 )  2021.05

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Adlercreutzia equolifaciens subsp. celatus DSM 18785 was isolated from the cecal contents of a rat and is an obligately anaerobic equol-producing bacterium. Here, we report the finished and annotated genome sequence of this organism, which has a genome size of 2, 929, 991 bp and a G1C content of 63.2%.

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Complete genome sequence of Geobacter sp. strain SVR, an antimonate-reducing bacterium isolated from antimony-rich mine soil

Warashina T., Yamamura S., Suzuki H., Amachi S., Arakawa K.

Microbiology Resource Announcements 10 ( 14 )  2021.04

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We report here the complete genome sequence of Geobacter sp. strain SVR, isolated from antimony mine soil in Nakase Mine, Hyogo Prefecture, Japan. SVR strains proliferate using antimonate [Sb(V)] as an electron acceptor, providing insights into the antimony reduction mechanism.

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Xanthurenic acid is the main pigment of trichonephila clavata gold dragline silk

Fujiwara M., Kono N., Hirayama A., Malay A.D., Nakamura H., Ohtoshi R., Numata K., Tomita M., Arakawa K.

Biomolecules 11 ( 4 )  2021.04

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Spider silk is a natural fiber with remarkable strength, toughness, and elasticity that is attracting attention as a biomaterial of the future. Golden orb-weaving spiders (Trichonephila clavata) construct large, strong webs using golden threads. To characterize the pigment of golden T. clavata dragline silk, we used liquid chromatography and mass spectrometric analysis. We found that the major pigment in the golden dragline silk of T. clavata was xanthurenic acid. To investigate the possible function of the pigment, we tested the effect of xanthurenic acid on bacterial growth using gram-negative Escherichia coli and gram-positive Bacillus subtilis. We found that xanthurenic acid had a slight antibacterial effect. Furthermore, to investigate the UV tolerance of the T. clavata threads bleached of their golden color, we conducted tensile deformation tests and scanning electron microscope observations. However, in these experiments, no significant effect was observed. We therefore speculate that golden orb-weaving spiders use the pigment for other purposes, such as to attract their prey in the sunlight.

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The complete mitochondrial genome of Trichonephila clavipes (Araneae: Araneidae)

Kono N., Nakamura H., Arakawa K.

Mitochondrial DNA Part B Resources 6 ( 10 ) 2986 - 2988 2021

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Trichonephila clavipes (Linnaeus, 1767) is known as a golden silk orb-weaver and belongs to the family Araneidae. T. clavipes is one of the few spider species whose genome has been reported and model organism for a molecular biology. Here, we present the complete mitochondrial genome sequence (mtDNA) of T. clavipes. The sequence was obtained using a long-read Nanopore technology and corrected with an Illumina technology. The circular genome is 14,902 bp in length, and the AT content was 77.21%. The T. clavipes mitochondrial genome contains 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The majority of PCGs were found on the heavy strain.

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Complete Genome Sequence of Bifidobacterium longum Strain Jih1, Isolated from Human Feces

Inoue H., Shibata S., Ii K., Inoue J., Fukuda S., Arakawa K.

Microbiology Resource Announcements (Microbiology Resource Announcements)  9 ( 22 )  2020.05

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Copyright © 2020 Inoue et al. We report the complete genome sequence of Bifidobacterium longum strain Jih1, isolated from human feces. The assembled genome comprised one circular chromosome of 2.37 Mb. The chromosome harbors 1,941 protein-coding genes.

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Complete genome sequence of halomonas meridiana strain eplume2, isolated from a hydrothermal plume in the northeast pacific ocean

Kurihara Y., Kawai S., Sakai A., Galipon J., Arakawa K.

Microbiology Resource Announcements (Microbiology Resource Announcements)  9 ( 20 )  2020.05

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© 2020 Kurihara et al. Halomonas meridiana strain Eplume2 (ATCC BAA-804) is a Gram-negative bacterium isolated from hydrothermal plume seawater in the Northeast Pacific Ocean at a depth of 2,000 m. Here, we report the complete genome sequence of this strain, which has a total size of 4.12 Mbp and a 56.6% G+C content.

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Complete Genome Sequences of Two Cutibacterium acnes Strains Isolated from an Orthopedic Surgical Site

Seo K., Tanaka K., Fukuda S., Arakawa K.

Microbiology Resource Announcements (Microbiology Resource Announcements)  9 ( 17 )  2020.04

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Copyright © 2020 Seo et al Cutibacterium acnes was reported as one of the most frequently isolated opportunistic pathogens among the skin microbiota. Here, we report two complete genome sequences of Cutibacterium acnes strains that were isolated from surgical (strain SZ1) and nonsurgical (strain SZ2) sites on the back of an orthopedic surgery patient.

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Distribution of Macrobiotus shonaicus Stec, Arakawa & Michalczyk, 2018 (Tardigrada: Eutardigrada: Macrobiotidae) in Japan

Sugiura K., Arakawa K., Matsumoto M.

Zootaxa (Zootaxa)  4767 ( 1 ) 56 - 70 2020.04

ISSN  11755326

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Copyright © 2020 Magnolia Press. To date, only seven species of Macrobiotidae (Parachela; Eutardigrada; Tardigrada) have been reported from Japan, including the recently described Macrobiotus shonaicus Stec et al., 2018 from the Shonai region of Japan. This species has flexible filaments on the egg processes and is known to proliferate only through sexual reproduction. Here, we report a multifaceted analysis of nine populations of M. shonaicus found on four Japanese islands. DNA sequencing of the cytochrome oxidase subunit I (COI) and internal transcribed spacer 2 (ITS-2) of the nine populations revealed 8 and 11 haplotypes, respectively. The extensive morphometric analysis showed considerably greater variability in the morphology of eggs than of animals. In addition to the morphological and molecular data, we confirmed the karyotype and found that all populations had a chromosome number of n = 6. Moreover, we observed and filmed mating behaviour between all studied populations of M. shonaicus. Our results clearly indicated that M. shonaicus is widely distributed throughout Japan.

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Complete genome sequence of Bacillus sp. Strain KH172Yl63, isolated from deep-sea sediment

Murai Y., Masuda T., Onuma Y., Evans-Yamamoto D., Takeuchi N., Mori H., Masuyama N., Ishiguro S., Yachie N., Arakawa K.

Microbiology Resource Announcements (Microbiology Resource Announcements)  9 ( 16 )  2020.04

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Copyright © 2020 Murai et al. Bacillus sp. strain KH172YL63 is a Gram-positive bacterium isolated from the deep-sea floor surface sediment at 3,308 m below sea level in the Nankai Trough in Japan. Here, we report the complete genome sequence of Bacillus sp. strain KH172YL63, which has a genome size of 4,251,700 bp and a G+C content of 44.8%.

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Complete genome sequence of halomonas meridiana strain Slthf1, isolated from a deep-sea thermal vent

Takahashi Y., Takahashi H., Galipon J., Arakawa K.

Microbiology Resource Announcements (Microbiology Resource Announcements)  9 ( 16 )  2020.04

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Copyright © 2020 Takahashi et al. Halomonas meridiana strain Slthf1 (ATCC BAA-801) is a Gram-negative bacterium that was isolated from a thermal vent in 1998. Here, we report the complete genome sequence of this strain, which has a 3.6-Mbp genome, containing 3,400 protein-coding sequences.

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Complete genome sequence of halomonas hydrothermalis strain slthf2, a halophilic bacterium isolated from a deep-sea hydrothermal-vent environment

Takeyama N., Huang M., Sato K., Galipon J., Arakawa K.

Microbiology Resource Announcements (Microbiology Resource Announcements)  9 ( 15 )  2020.04

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© 2020 Takeyama et al. Halomonas hydrothermalis strain Slthf2 is a Gram-negative bacterium isolated from low-temperature hydrothermal fluids in South Pacific Ocean vent fields located at 2,580-m depth. Here, we report the complete genome sequence of this strain, which has a genome size of 4.12 Mb, with a GC content of 53.2%.

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The unique antimicrobial recognition and signaling pathways in tardigrades with a comparison across ecdysozoa

Mapalo M.A., Arakawa K., Baker C.M., Persson D.K., Mirano-Bascos D., Giribet G.

G3: Genes, Genomes, Genetics (G3: Genes, Genomes, Genetics)  10 ( 3 ) 1137 - 1148 2020.03

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© 2020 Mapalo et al. Tardigrades are microscopic animals known to withstand unfavorable abiotic conditions. These animals are also constantly exposed to biotic stresses, including parasites and internal microbiomes. However, the tardigrade immune mechanisms against these biotic stresses are largely uncharacterized. Due to the contentious phylogenetic position of tardigrades, it is not intuitive whether they possess an immune system more similar to that of arthropods (e.g., Toll, Imd, and JNK pathways of the Drosophila melanogaster antimicrobial response) or to that of nematodes (e.g., the Tir-1/Nsy-1/Sek-1/Pmk-1/Atf-7 signaling cassette [called Tir-1 pathway here]) in Caenorhabditis elegans). In this study, comparative genomic analyses were conducted to mine homologs of canonical D. melanogaster and C. elegans immune pathway genes from eight tardigrades (Echiniscoides cf. sigismundi, Echiniscus testudo, Hypsibius exemplaris, Mesobiotus philippinicus, Milnesium tardigradum, Paramacrobiotus richtersi, Richtersius cf. coronifer, and Ramazzottius varieornatus) and four non-arthropod ecdysozoans (two onychophorans: Epiperipatus sp. and Opisthopatus kwazululandi; one nematomorph: Paragordius varius; and one priapulan: Priapulus caudatus) in order to provide insights into the tardigrade antimicrobial system. No homologs of the intracellular components of the Toll pathway were detected in any of the tardigrades examined. Likewise, no homologs of most of the Imd pathway genes were detected in any of the tardigrades or any of the other non-arthropod ecdysozoans. Both the JNK and Tir-1 pathways, on the other hand, were found to be conserved across ecdysozoans. Interestingly, tardigrades had no detectable homologs of NF-kB, the major activator of antimicrobial response gene expression. Instead, tardigrades appear to possess NF-kB distantly related NFAT homologs. Overall, our results show that tardigrades have a unique gene pathway repertoire that differs from that of other ecdysozoans. Our study also provides a framework for future studies on tardigrade immune responses.

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Simultaneous metabarcoding of eukaryotes and prokaryotes to elucidate the community structures within tardigrade microhabitats

Arakawa K.

Diversity (Diversity)  12 ( 3 )  2020.03

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© 2020 by the author. Tardigrades are microscopic invertebrates that can withstand complete desiccation, but their interspecies interactions with prokaryotes and eukaryotes within their microhabitat remain relatively unexplored. Here, I utilized combined metabarcoding of eukaryotes and prokaryotes to simultaneously identify entire community structures within xeric and mesic mosses that harbor tardigrades. The populations of organisms within the microecosystems were successfully determined in 45 xeric moss samples and 47 mesic moss samples. Organismal composition was largely consistent regardless of the moss/lichen substrate, but significantly varied in the two tested locations, possibly because of the differences in environmental humidity. Xeric mosses containing xerophilic tardigrades and other anhydrobiotic invertebrates tended to have significantly limited biological diversity and prokaryotic population dominated by cyanobacteria, suggesting a selection due to extreme desiccation. A combined metabarcoding approach to identify both eukaryotes and prokaryotes can successfully elucidate community structures within microscopic ecosystems, and this can be a potential approach to study the microecology of meiofauna, including tardigrades.

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A new redescription of Richtersius coronifer, supported by transcriptome, provides resources for describing concealed species diversity within the monotypic genus Richtersius (Eutardigrada)

Stec D., Krzywański Ł., Arakawa K., Michalczyk Ł.

Zoological Letters (Zoological Letters)  6 ( 1 )  2020.02

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© 2020 The Author(s). Richtersius coronifer, the nominal species for the family Richtersiidae and a popular laboratory model, exemplifies a common problem in modern tardigrade taxonomy. Despite undeniable progress in the field, many old and incomplete descriptions of taxa hinder both species delimitation and the estimation of species diversity and distribution. Although for over a century this species has been recorded throughout the world, recent research indicates that records to date are likely to represent a species complex rather than a single cosmopolitan species. However, in order to recognise and name species diversity within the complex, an integrative redescription of the nominal species is first needed. Here, we describe an R. coronifer population collected from Spitsbergen, i.e., one of the two localities mentioned in the original description, with detailed morphological and morphometric data associated with standard DNA sequences of four standard genetic markers (18S rRNA, 28S rRNA, ITS-2, and COI) and supported by transcriptome sequencing. We propose replacement of the neotype designated in 1981 by Maucci and Ramazzotti, as it is impossible to verify whether the existing neotype is conspecific with specimens studied by Richters in 1903 and 1904. Finally, using newly obtained cytochrome c oxidase subunit I (COI) sequences of populations from Spitsbergen, Italy, Poland, and Greece together with sequences deposited in GenBank (China, Greenland, Italy, Mongolia), we performed genetic species delimitation, which indicated seven distinct potential species within the genus Richtersius, in addition to the nominal taxon. This study marks a starting point for further research on the taxonomy of and species diversity within the genus. Moreover, this work has the potential to be the first tardigrade redescription to provide both genetic barcodes and a transcriptome of the species in question.

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Pre-treatment with D942, a furancarboxylic acid derivative, increases desiccation tolerance in an anhydrobiotic tardigrade Hypsibius exemplaris

Kondo K., Mori M., Tomita M., Arakawa K.

FEBS Open Bio (FEBS Open Bio)   2020

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© 2020 The Authors. Published by FEBS Press and John Wiley & Sons Ltd. The tardigrade Hypsibius exemplaris can undergo anhydrobiosis. Several chemicals that inhibit successful anhydrobiosis in H. exemplaris have been identified, and these chemicals inhibit the activity of signaling molecules. In the present study, we investigated whether upregulation of the activity of these signaling molecules could improve desiccation tolerance of H. exemplaris. Pre-treatment with an indirect activator of AMP-activated protein kinase [AMPK; which directly inhibits mammalian NAD(P)H dehydrogenase [quinone] 1 [NQO1] of mitochondrial complex I (D942)] significantly improved desiccation tolerance of H. exemplaris, whereas a direct activator of AMPK did not. To elucidate the underlying molecular mechanisms, we examined the proteome of tardigrades treated with D942. Two proteins, putative glutathione S-transferase and pirin-like protein, were upregulated by treatment. Both of these proteins are known to be associated with the response to oxidative stress. One of the downregulated proteins was serine/threonine-proteinphosphatase 2A (PP2A) 65-kDa regulatory subunit A alpha isoform, and it is interesting to note that PP2A activity was previously suggested to be required for successful anhydrobiosis in H. exemplaris. Taken together, our results suggest that D942 treatment may partially induce responses common to those of desiccation stress. The identification of a chemical that improves desiccation tolerance of H. exemplaris may facilitate further investigation into desiccation tolerance mechanisms.

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BioHackathon 2015: Semantics of data for life sciences and reproducible research

Katayama T., Vos R.A., Mishima H., Kawano S., Kawashima S., Kim J.D., Moriya Y., Tokimatsu T., Yamaguchi A., Yamamoto Y., Wu H., Amstutz P., Antezana E., Aoki N.P., Arakawa K., Bolleman J.T., Bolton E., Bonnal R.J.P., Bono H., Burger K., Chiba H., Cohen K.B., Deutsch E.W., Fernández-Breis J.T., Fu G., Fujisawa T., Fukushima A., García A., Goto N., Groza T., Hercus C., Hoehndorf R., Itaya K., Juty N., Kawashima T., Kim J.H., Kinjo A.R., Kotera M., Kozaki K., Kumagai S., Kushida T., Lütteke T., Matsubara M., Miyamoto J., Mohsen A., Mori H., Naito Y., Nakazato T., Nguyen-Xuan J., Nishida K., Nishida N., Nishide H., Ogishima S., Ohta T., Okuda S., Paten B., Perret J.L., Prathipati P., Prins P., Queralt-Rosinach N., Shinmachi D., Suzuki S., Tabata T., Takatsuki T., Taylor K., Thompson M., Uchiyama I., Vieira B., Wei C.H., Wilkinson M., Yamada I., Yamanaka R., Yoshitake K., Yoshizawa A.C., Dumontier M., Kosaki K., Takagi T.

F1000Research (F1000Research)  9 2020

ISSN  20461402

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© 2020 Vos RA et al. We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

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Base editors for simultaneous introduction of C-to-T and A-to-G mutations

Sakata R.C., Ishiguro S., Mori H., Tanaka M., Tatsuno K., Ueda H., Yamamoto S., Seki M., Masuyama N., Nishida K., Nishimasu H., Arakawa K., Kondo A., Nureki O., Tomita M., Aburatani H., Yachie N.

Nature Biotechnology (Nature Biotechnology)   2020

ISSN  10870156

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© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. We describe base editors that combine both cytosine and adenine base-editing functions. A codon-optimized fusion of the cytosine deaminase PmCDA1, the adenosine deaminase TadA and a Cas9 nickase (Target-ACEmax) showed a high median simultaneous C-to-T and A-to-G editing activity at 47 genomic targets. On-target as well as DNA and RNA off-target activities of Target-ACEmax were similar to those of existing single-function base editors.

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Comparison of the transcriptomes of two tardigrades with different hatching coordination

Yoshida Y., Sugiura K., Tomita M., Matsumoto M., Arakawa K.

BMC Developmental Biology (BMC Developmental Biology)  19 ( 1 )  2019.12

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© 2019 The Author(s). Background: Tardigrades are microscopic organisms, famous for their tolerance against extreme environments. The establishment of rearing systems of multiple species has allowed for comparison of tardigrade physiology, in particular in embryogenesis. Interestingly, in-lab cultures of limnic species showed smaller variation in hatching timing than terrestrial species, suggesting a hatching regulation mechanism acquired by adaptation to their habitat. Results: To this end, we screened for coordinated gene expression during the development of two species of tardigrades, Hypsibius exemplaris and Ramazzottius varieornatus, and observed induction of the arthropod molting pathway. Exposure of ecdysteroids and juvenile hormone analog affected egg hatching but not embryonic development in only the limnic H. exemplaris. Conclusion: These observations suggest a hatching regulation mechanism by the molting pathway in H. exemplaris.

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AMPK activity is required for the induction of anhydrobiosis in a tardigrade Hypsibius exemplaris, and its potential up-regulator is PP2A

Kondo K., Mori M., Tomita M., Arakawa K.

Genes to Cells (Genes to Cells)  24 ( 12 ) 768 - 780 2019.12

ISSN  13569597

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© 2019 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd The anhydrobiotic tardigrade, Hypsibius exemplaris, was previously considered to require de novo gene expression and protein phosphatase 1 (PP1) and protein phosphatase 2A (PP2A) activity for successful anhydrobiosis. These indicate that H. exemplaris has signal transduction systems responding to desiccation stress, with the involvement of phosphorylation events. To this end, we carried out time-series phosphoproteomics of H. exemplaris exposed to mild desiccation stress and detected 48 phosphoproteins with significant differential regulations. Among them, immediate and successive reduction of phosphorylation levels of AMP-activated protein kinase (AMPK) was observed. The subsequent chemical genetic approach showed that AMPK was activated during the preconditioning stage for anhydrobiosis, and inhibition of its activity impaired successful anhydrobiosis. As PP2A is known to dephosphorylate AMPK in other organisms, we suggested that decreased phosphorylation levels of AMPK upon mild desiccation stress were caused by dephosphorylation by PP2A. Accordingly, phosphoproteomics of animals pre-treated with the PP1/PP2A inhibitor cantharidic acid (CA) lacked the decrease in phosphorylation levels of AMPK. These observations suggest that AMPK activity is required for successful anhydrobiosis in H. exemplaris, and its phosphorylation state is possibly regulated by PP2A.

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The bagworm genome reveals a unique fibroin gene that provides high tensile strength

Kono N., Nakamura H., Ohtoshi R., Tomita M., Numata K., Arakawa K.

Communications Biology (Communications Biology)  2 ( 1 )  2019.12

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© 2019, The Author(s). Arthropod silk is known as a versatile tool, and its variability makes it an attractive biomaterial. Eumeta variegata is a bagworm moth (Lepidoptera, Psychidae) that uses silk throughout all life stages. Notably, the bagworm-specific uses of silk include larval development in a bag coated with silk and plant materials and the use of silk attachments to hang pupae. An understanding at the molecular level of bagworm silk, which enables such unique purposes, is an opportunity to expand the possibilities for artificial biomaterial design. However, very little is known about the bagworm fibroin gene and the mechanical properties of bagworm silk. Here, we report the bagworm genome, including a silk fibroin gene. The genome is approximately 700 Mbp in size, and the newly found fibroin gene has a unique repetitive motif. Furthermore, a mechanical property test demonstrates a phylogenetic relationship between the unique motif and tensile strength of bagworm silk.

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Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue

Kono N., Nakamura H., Ohtoshi R., Moran D., Shinohara A., Yoshida Y., Fujiwara M., Mori M., Tomita M., Arakawa K.

Scientific Reports (Scientific Reports)  9 ( 1 )  2019.12

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© 2019, The Author(s). Members of the family Araneidae are common orb-weaving spiders, and they produce several types of silks throughout their behaviors and lives, from reproduction to foraging. Egg sac, prey capture thread, or dragline silk possesses characteristic mechanical properties, and its variability makes it a highly attractive material for ecological, evolutional, and industrial fields. However, the complete set of constituents of silks produced by a single species is still unclear, and novel spidroin genes as well as other proteins are still being found. Here, we present the first genome in genus Araneus together with the full set of spidroin genes with unamplified long reads and confirmed with transcriptome of the silk glands and proteome analysis of the dragline silk. The catalogue includes the first full length sequence of a paralog of major ampullate spidroin MaSp3, and several spider silk-constituting elements designated SpiCE. Family-wide phylogenomic analysis of Araneidae suggests the relatively recent acquisition of these genes, and multiple-omics analyses demonstrate that these proteins are critical components in the abdominal spidroin gland and dragline silk, contributing to the outstanding mechanical properties of silk in this group of species.

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Patterns of population structure and complex haplotype sharing among field isolates of the green alga Chlamydomonas reinhardtii

Craig R.J., Böndel K.B., Arakawa K., Nakada T., Ito T., Bell G., Colegrave N., Keightley P.D., Ness R.W.

Molecular Ecology (Molecular Ecology)  28 ( 17 ) 3977 - 3993 2019.09

ISSN  09621083

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© 2019 John Wiley & Sons Ltd The nature of population structure in microbial eukaryotes has long been debated. Competing models have argued that microbial species are either ubiquitous, with high dispersal and low rates of speciation, or that for many species gene flow between populations is limited, resulting in evolutionary histories similar to those of macroorganisms. However, population genomic approaches have seldom been applied to this question. Here, we analyse whole-genome resequencing data for all 36 confirmed field isolates of the green alga Chlamydomonas reinhardtii. At a continental scale, we report evidence for putative allopatric divergence, between both North American and Japanese isolates, and two highly differentiated lineages within N. America. Conversely, at a local scale within the most densely sampled lineage, we find little evidence for either spatial or temporal structure. Taken together with evidence for ongoing admixture between the two N. American lineages, this lack of structure supports a role for substantial dispersal in C. reinhardtii and implies that between-lineage differentiation may be maintained by reproductive isolation and/or local adaptation. Our results therefore support a role for allopatric divergence in microbial eukaryotes, while also indicating that species may be ubiquitous at local scales. Despite the high genetic diversity observed within the most well-sampled lineage, we find that pairs of isolates share on average ~9% of their genomes in long haplotypes, even when isolates were sampled decades apart and from different locations. This proportion is several orders of magnitude higher than the Wright–Fisher expectation, raising many further questions concerning the evolutionary genetics of C. reinhardtii and microbial eukaryotes generally.

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Complete genome sequence of halophilic deep-sea bacterium halomonas axialensis strain Althf1

Tsurumaki M., Deno S., Galipon J., Arakawa K.

Microbiology Resource Announcements (Microbiology Resource Announcements)  8 ( 31 )  2019.08

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Copyright © 2019 Tsurumaki et al. Halomonas axialensis is a halophilic bacterial species discovered near a deep-sea hydrothermal vent. Here, we report the first single closed genome sequence of the original strain, Halomonas axialensis strain Althf1. The genome was assembled by Nanopore sequencing and consisted of a single chromosome of 3.6 Mbp with 56.8% G+C content.

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Complete genome sequence of halomonas sulfidaeris strain esulfide1 isolated from a metal sulfide rock at a depth of 2,200 meters, obtained using nanopore sequencing

Saito M., Nishigata A., Galipon J., Arakawa K.

Microbiology Resource Announcements (Microbiology Resource Announcements)  8 ( 23 )  2019.06

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Copyright © 2019 Saito et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. We report the complete genome sequence of Halomonas sulfidaeris ATCC BAA-803, isolated from a metal sulfide rock at a depth of 2,200 m in the Northeast Pacific Ocean. The assembled genome comprised one circular chromosome of 4.20 Mb and one large plasmid of 273 kb. The chromosome harbors 6,705 protein-coding genes.

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Nanopore sequencing: Review of potential applications in functional genomics

Kono N., Arakawa K.

Development Growth and Differentiation (Development Growth and Differentiation)  61 ( 5 ) 316 - 326 2019.06

ISSN  00121592

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© 2019 Japanese Society of Developmental Biologists Molecular biology has been led by various measurement technologies, and increased throughput has developed omics analysis. The development of massively parallel sequencing technology has enabled access to fundamental molecular data and revealed genomic and transcriptomic signatures. Nanopore sequencers have driven such evolution to the next stage. Oxford Nanopore Technologies Inc. provides a new type of single molecule sequencer using protein nanopore that realizes direct sequencing without DNA synthesizing or amplification. This nanopore sequencer can sequence an ultra-long read limited by the input nucleotide length, or can determine DNA/RNA modifications. Recently, many fields such as medicine, epidemiology, ecology, and education have benefited from this technology. In this review, we explain the features and functions of the nanopore sequencer, introduce various situations where it has been used as a critical technology, and expected future applications.

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Complete genome sequence of halomonas olivaria, a moderately halophilic bacterium isolated from olive processing effluents, obtained by nanopore sequencing

Nagata S., Ii K., Tsukimi T., Miura M., Galipon J., Arakawa K.

Microbiology Resource Announcements (Microbiology Resource Announcements)  8 ( 18 )  2019.05

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© 2019 Nagata et al. Here, we report the complete genome sequence of Halomonas olivaria strain TYRC17, a moderately halophilic, Gram-negative bacterium that was isolated from olive processing effluents. The 5-Mbp genome consists of 7,375 protein-coding sequences, including a variety of genes involved in tyrosol metabolism, nitrate respiration, and the production of polysaccharides.

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Complete genome sequence of Psychrobacter sp. Strain KH172YL61, isolated from deep-sea sediments in the Nankai Trough, Japan

Evans-Yamamoto D., Takeuchi N., Masuda T., Murai Y., Onuma Y., Mori H., Masuyama N., Ishiguro S., Yachie N., Arakawa K.

Microbiology Resource Announcements (Microbiology Resource Announcements)  8 ( 16 )  2019.04

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Copyright © 2019 Evans-Yamamoto et al. Psychrobacter sp. strain KH172YL61 is a Gram-negative bacterium isolated from deep-sea sediment in the Nankai Trough in Japan. Here, we report the complete genome sequence of this strain, which has a genome size of 3.19 Mb, with a GC content of 44.0%.

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Anti-tumor effects and potential therapeutic response biomarkers in α-emitting meta-²¹¹At-astato-benzylguanidine therapy for malignant pheochromocytoma explored by RNA-sequencing

Ohshima Y., Kono N., Yokota Y., Watanabe S., Sasaki I., Ishioka N.S., Sakashita T., Arakawa K.

Theranostics (Theranostics)  9 ( 6 ) 1538 - 1549 2019

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© Ivyspring International Publisher. Targeted α-particle therapy is a promising option for patients with malignant pheochromocytoma. Recent observations regarding meta-211At-astato-benzylguanidine (211At-MABG) in a pheochromocytoma mouse model showed a strong anti-tumor effect, though the molecular mechanism remains elusive. Here, we present the first comprehensive RNA-sequencing (RNA-seq) data for pheochromocytoma cells based on in vitro 211At-MABG administration experiments. Key genes and pathways in the tumor α-particle radiation response are also examined to obtain potential response biomarkers. Methods: We evaluated genome-wide transcriptional alterations in the rat pheochromocytoma cell line PC12 at 3, 6, and 12 h after 211At-MABG treatment; a control experiment using 60Co γ-ray irradiation was carried out to highlight 211At-MABG-specific gene expression. For comparisons, 10% and 80% iso-survival doses (0.8 and 0.1 kBq/mL for 211At-MABG and 10 and 1 Gy for 60Co γ-rays) were used. Results: Enrichment analysis of differentially expressed genes (DEGs) and analysis of the gene expression profiles of cell cycle checkpoints revealed similar modes of cell death via the p53-p21 signaling pathway after 211At-MABG treatment and γ-ray irradiation. The top list of ranked DEGs demonstrated the expression of key genes on the decrease in the survival following 211At-MABG exposure, and four potential genes (Mien1, Otub1, Vdac1 and Vegfa genes) of 211At-MABG therapy. Western blot analysis indicated increased expression of TSPO in 211At-MABG-treated cells, suggesting its potential as a PET imaging probe. Conclusion: Comprehensive RNA-seq revealed contrasting cellular responses to γ-ray and α-particle therapy, leading to the identification of four potential candidate genes that may serve as molecular imaging and 211At-MABG therapy targets.

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Comparison of Sexual Reproductive Behaviors in Two Species of Macrobiotidae (Tardigrada: Eutardigrada)

Sugiura K., Minato H., Suzuki A.C., Arakawa K., Kunieda T., Matsumoto M.

Zoological Science (Zoological Science)  36 ( 2 ) 120 - 127 2019

ISSN  02890003

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© 2019 Zoological Society of Japan. Reproductive strategy is an important aspect of biological diversity. In tardigrades, several reproductive modes, including sexual reproduction, are known. However, tardigrade mating behavior has been observed only rarely in most species, and in some cases, especially in the freely ovipositing eutardigrades, remains entirely unknown. In the present study, we cultured two sexually reproducing tardigrade species that lay eggs freely, Paramacrobiotus sp. TYO strain and Macrobiotus shonaicus, to investigate and compare their courtship, mating, and chromosome morphology. Mating behavior was observed and recorded in both species. The entire mating sequence, including courtship, was categorized into five discrete steps common to two species, as follows: [1] Tracking: the male tracks and orientates toward the female; [2] Touching: the male makes contact with the cloaca of the female; [3] Standstill: the female ceases movement until male ejaculation is complete; [4] Ejaculation: the male curls its caudal end and ejaculates into the cloaca from close range; [5] Contraction: the female contracts its ventral side after ejaculation to capture spermatozoa deposited in the external environment in close proximity to the cloaca. Some notable differences between the two species were observed in the steps 3-4. First, oviposition was observed at 40 min in Paramacrobiotus sp. TYO strain, and a few days after mating in M. shonaicus, respectively. Comparisons of chromosome morphology before and after mating indicated that oocytes are arrested at metaphase I in both species. Spermatozoa attach to the interior of the chorion of laid eggs.

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Comparative proteomic analysis of mitochondria isolated from Euglena gracilis under aerobic and hypoxic conditions

Tamaki S., Nishino K., Ogawa T., Maruta T., Sawa Y., Arakawa K., Ishikawa T.

PLoS ONE (PLoS ONE)  14 ( 12 )  2019

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© 2019 Tamaki et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The unicellular microalga Euglena gracilis produces wax esters for ATP acquisition under low-oxygen conditions. The regulatory mechanism of wax ester production is not yet understood. Indeed, our previous transcriptomic analysis showed that transcript levels of genes involved in the wax ester synthesis hardly changed under hypoxic conditions, suggesting contribution of post-transcriptional regulation. In this study, we conducted a proteome analysis of E. gracilis mitochondria, as this organelle employs the fatty-acid synthesis pathway under hypoxic conditions. Mitochondria were isolated from E. gracilis SM-ZK strain treated with both aerobic and hypoxic conditions and used for shotgun proteomic analysis. Three independent proteomic analyses succeeded in identifying a total of 714 non-redundant proteins. Of these, 229 were detected in common to all experiments, and 116 were significantly recognized as differentially expressed proteins. GO enrichment analysis suggested dynamic changes in mitochondrial metabolic pathways and redox reactions under aerobic and hypoxic conditions. Protein levels of bifunctional enzymes isocitrate lyase and malate synthase in glyoxylate cycle were 1.35-fold higher under hypoxic conditions. Abundances of the propionyl- CoA synthetic enzymes, succinyl-CoA synthetase and propionyl-CoA carboxylase, were also 1.35- and 1.47-fold higher, respectively, under hypoxic conditions. Protein levels of pyruvate: NADP+ oxidoreductase, a key enzyme for anaerobic synthesis of acetyl-CoA, which serves as a C2 donor for fatty acids, showed a 1.68-fold increase under hypoxic conditions, whereas those of pyruvate dehydrogenase subunits showed a 0.77-0.81-fold decrease. Protein levels of the fatty-acid synthesis enzymes, 3-ketoacyl-CoA thiolase isoforms (KAT1 and KAT2), 3-hydroxyacyl-CoA dehydrogenases, and acyl-CoA dehydrogenase were up-regulated by 1.20- to 1.42-fold in response to hypoxic treatment. Overall, our proteomic analysis revealed that wax ester synthesis-related enzymes are up-regulated at the protein level posttranscriptionally to promote wax ester production in E. gracilis under low-oxygen conditions.

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Molecular palaeontology illuminates the evolution of ecdysozoan vision

Fleming J., Kristensen R., Sørensen M., Park T., Arakawa K., Blaxter M., Rebecchi L., Guidetti R., Williams T., Roberts N., Vinther J., Pisani D.

Proceedings of the Royal Society B: Biological Sciences (Proceedings of the Royal Society B: Biological Sciences)  285 ( 1892 )  2018.12

ISSN  09628452

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© 2018 The Authors. Colour vision is known to have arisen only twice—once in Vertebrata and once within the Ecdysozoa, in Arthropoda. However, the evolutionary history of ecdysozoan vision is unclear. At the molecular level, visual pigments, composed of a chromophore and a protein belonging to the opsin family, have different spectral sensitivities and these mediate colour vision. At the morphological level, ecdysozoan vision is conveyed by eyes of variable levels of complexity; from the simple ocelli observed in the velvet worms (phylum Onychophora) to the marvellously complex eyes of insects, spiders, and crustaceans. Here, we explore the evolution of ecdysozoan vision at both the molecular and morphological level; combining analysis of a large-scale opsin dataset that includes previously unknown ecdysozoan opsins with morphological analyses of key Cambrian fossils with preserved eye structures. We found that while several non-arthropod ecdysozoan lineages have multiple opsins, arthropod multi-opsin vision evolved through a series of gene duplications that were fixed in a period of 35 – 71 million years (Ma) along the stem arthropod lineage. Our integrative study of the fossil and molecular record of vision indicates that fossils with more complex eyes were likely to have possessed a larger complement of opsin genes.

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Ultralow input genome sequencing library preparation from a single tardigrade specimen

Yoshida Y., Konno S., Nishino R., Murai Y., Tomita M., Arakawa K.

Journal of Visualized Experiments (Journal of Visualized Experiments)  2018 ( 137 )  2018.07

ISSN  1940087X

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© 2018 Journal of Visualized Experiments. Tardigrades are microscopic animals that enter an ametabolic state called anhydrobiosis when facing desiccation and can return to their original state when water is supplied. The genomic sequencing of microscopic animals such as tardigrades risks bacterial contamination that sometimes leads to erroneous interpretations, for example, regarding the extent of horizontal gene transfer in these animals. Here, we provide an ultralow input method to sequence the genome of the tardigrade, Hypsibius dujardini, from a single specimen. By employing rigorous washing and contaminant exclusion along with an efficient extraction of the 50 ~ 200 pg genomic DNA from a single individual, we constructed a library sequenced with a DNA sequencing instrument. These libraries were highly reproducible and unbiased, and an informatics analysis of the sequenced reads with other H. dujardini genomes showed a minimal amount of contamination. This method can be applied to unculturable tardigrades that could not be sequenced using previous methods.

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The complete mitochondrial genome of Echiniscus testudo (Heterotardigrada: Echiniscidae)

Arakawa K.

Mitochondrial DNA Part B: Resources (Mitochondrial DNA Part B: Resources)  3 ( 2 ) 810 - 811 2018.07

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© 2018, © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. The complete mitchondrial genome of Echiniscus testudo, a cosmopolitan heterotardigrade collected in Japan, has been sequenced using a single molecule real-time (SMRT) sequencing long read after whole genome amplification from a single individual. The genome has a total length of 15,817 bp, consisting of 13 protein-coding genes, 20 tRNA, 2 rRNA genes, and an AT-rich control region. The nucleotide composition was extremely AT-rich, with 78.41% AT. Being in a different class of the phylum Tardigrada, there is a large sequence divergence from the previously reported mitochondrial genome of the eutardigrade Ramazzottius varieornatus, but the gene order of protein-coding genes are mostly conserved. This is the first report of a complete mitochondrial genome of a heterotardigrade.

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The complete mitochondrial genome of Eumeta variegata (Lepidoptera: Psychidae)

Arakawa K., Kono N., Ohtoshi R., Nakamura H., Tomita M.

Mitochondrial DNA Part B: Resources (Mitochondrial DNA Part B: Resources)  3 ( 2 ) 812 - 813 2018.07

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© 2018, © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. The complete mitochondrial genome of Eumeta variegate, largest bagworm moth in Japan, has been sequenced using a nanopore sequencer as a single long read. The genome has a total length of 16,601 bp, consisting of 13 protein-coding genes, 20 tRNA, 2 rRNA genes, and an AT-rich control region. The nucleotide composition was extremely AT-rich, with 42.4% A, 40.4% T, 6.67% G, and 10.6% C. This is the second report of a complete mitochondrial genome of Psychidae, and the sequence information together with a phylogenetic analysis would provide a reference data in the future studies of Lepidoptera and Psychidae.

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Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago

Ohta T., Kawashima T., Shinozaki N.O., Dobashi A., Hiraoka S., Hoshino T., Kanno K., Kataoka T., Kawashima S., Matsui M., Nemoto W., Nishijima S., Suganuma N., Suzuki H., Taguchi Y.H., Takenaka Y., Tanigawa Y., Tsuneyoshi M., Yoshitake K., Sato Y., Yamashita R., Arakawa K., Iwasaki W.

Journal of Plant Research (Journal of Plant Research)  131 ( 4 ) 709 - 717 2018.07

ISSN  09189440

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© 2018, The Botanical Society of Japan and Springer Japan KK, part of Springer Nature. Recent studies have shown that environmental DNA is found almost everywhere. Flower petal surfaces are an attractive tissue to use for investigation of the dispersal of environmental DNA in nature as they are isolated from the external environment until the bud opens and only then can the petal surface accumulate environmental DNA. Here, we performed a crowdsourced experiment, the “Ohanami Project”, to obtain environmental DNA samples from petal surfaces of Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago during spring 2015. C. × yedoensis is the most popular garden cherry species in Japan and clones of this cultivar bloom simultaneously every spring. Data collection spanned almost every prefecture and totaled 577 DNA samples from 149 collaborators. Preliminary amplicon-sequencing analysis showed the rapid attachment of environmental DNA onto the petal surfaces. Notably, we found DNA of other common plant species in samples obtained from a wide distribution; this DNA likely originated from the pollen of the Japanese cedar. Our analysis supports our belief that petal surfaces after blossoming are a promising target to reveal the dynamics of environmental DNA in nature. The success of our experiment also shows that crowdsourced environmental DNA analyses have considerable value in ecological studies.

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An integrative description of Macrobiotus shonaicus sp. nov. (Tardigrada: Macrobiotidae) from Japan with notes on its phylogenetic position within the hufelandi group

Stec D., Arakawa K., Michalczyk Ł.

PLoS ONE (PLoS ONE)  13 ( 2 )  2018.02

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Copyright: © 2018 Stec et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Tardigrade research in Japan dates back over 100 years, and to date, 167 species of this ecdysozoan phylum have been reported from the country. Of these species, the Macrobiotus hufelandi complex has been represented only by the nominal taxon of this group, Macrobiotus hufelandi. In this article, a new species of the hufelandi group from Japan, Macrobiotus shonaicus sp. nov., is described using integrative taxonomy. In addition to the detailed morphological and morphometric data, obtained using phase contrast light microscopy (PCM) and scanning electron microscopy (SEM), we provide DNA sequences of four molecular markers (both nuclear and mitochondrial). The new species belongs to the persimilis subgroup and is most similar to M. anemone from USA, M. naskreckii from Mozambique, and M. patagonicus from Argentina, but it can be easily distinguished from these species by the presence of thin flexible filaments on terminal discs of the egg process. By the latter character, the new species is most similar to M. paulinae and M. polypiformis, but it can be easily distinguished from them by having a solid egg surface between egg processes (i.e., without pores or reticulum). A phylogenetic analysis of available DNA sequences of the COI marker for the hufelandi group revealed that the new species clusters with the two other species that exhibit filaments on egg process discs (M. paulinae and M. polypiformis) and with two species that have entire egg processes modified into filaments (M. kristenseni and M. scoticus). All five species form a clade distinct from all other sequenced species of the hufelandi group with typical mushroom- or inverted goblet-shaped egg processes, which may suggest that the ancestor of the five species with atypical egg processes had a mutation allowing derivations from the mushroom or inverted chalice-like shape of egg processes.

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Accelerated laboratory evolution reveals the influence of replication on the GC skew in Escherichia coli

Kono N., Tomita M., Arakawa K.

Genome Biology and Evolution (Genome Biology and Evolution)  10 ( 11 ) 3110 - 3117 2018

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© The Author(s) 2018. Most bacterial genomes display contrasting strand asymmetry in a variety of features, such as nucleotide composition and gene orientation, of the two replichores separated by the replication origin and terminus. The cause for the polarization is often attributed to mutations arising from the asymmetric replication machinery. Notably, a base compositional bias known as a GC skew is focused on as a footprint of the bacterial genome evolution driven by DNA replication. Previously, although a replication driven mutation pattern responsible for the GC skew formation or the related mathematical models have been well reported, an exact impact of the replication-related elements on the genomic structure is yet actively debated, and not confirmed experimentally. However, the GC skew formation is very time consuming and challenging in the laboratory. We, therefore, used cytosine deaminase as a DNA mutator, and by monitoring the mutations during an accelerated laboratory evolution procedure with Illumina sequencing, we enabled the trial and error of the GC skew formation in high resolution. Using this technology, we succeeded in reconfirming the influence of bacterial replication machinery on the genomic structure at high resolution.

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Evaluation of the impact of RNA preservation methods ofspiders for de novo transcriptome assembly

Kono, Nobuaki, Nakamura, Hiroyuki, Ito, Yusuke, Tomita, Masaru, Arakawa, Kazuharu

MOLECULAR ECOLOGY RESOURCES 16 ( 3 ) 662 - 672 2016.05

Research paper (scientific journal),  ISSN  1755-098X

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No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade

Arakawa, Kazuharu

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 113 ( 22 ) E3057 - E3057 2016.05

Research paper (scientific journal),  ISSN  0027-8424

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De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions

Yoshida, Yuta, Tomiyama, Takuya, Maruta, Takanori, Tomita, Masaru, Ishikawa, Takahiro, Arakawa, Kazuharu

BMC GENOMICS 17 2016.03

Research paper (scientific journal),  ISSN  1471-2164

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Merging Multiple Omics Datasets In Silico: Statistical Analyses and Data Interpretation

ARAKAWA Kazuharu, Tomita M

Methods Mil. Biol. 985   459-470 2013

Research paper (scientific journal), Joint Work

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Toshiaki Katayama*, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul JP Bonnal, Brad Chapman, Peter JA Cock, Tore Eriksson, Paul MK Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido, Young Joo Kim, Akira R Kinjo, Fumikazu Konishi, Kyung-Hoon Kwon, Alberto Labarga, Anna-Lena Lamprecht, Yu Lin, Pierre Lindenbaum, Luke McCarthy, Hideyuki Morita, Katsuhiko Murakami, Koji Nagao, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Pjotr Prins, Taro L Saito, Matthias Samwald, Venkata P Satagopam, Yasumasa Shigemoto, Richard Smith, Andrea Splendiani, Hideaki Sugawara, James Taylor, Rutger A Vos, David Withers, Chisato Yamasaki, Christ

Journal of Biomedical Semantics 4   6 2013

Research paper (scientific journal), Joint Work, Accepted

Measures of Compositional Strand Bias Related to Replication Machinery and its Applications

ARAKAWA Kazuharu, TOMITA Masaru

Current Genomics 13 ( 1 ) 4-15 2012

Research paper (scientific journal), Joint Work, Accepted

Validation of bacterial replication termination models using simulation of genomic mutations

KONO Nobuaki, ARAKAWA Kazuharu, TOMITA Masaru

PLoS One 7 ( 4 ) e34526 2012

Research paper (scientific journal), Joint Work, Accepted

Two families of novel abundant heat-soluble proteins in an anhydrobiotic tardigrade

Yamaguchi A, Tanaka S, Yamaguchi S, Kuwahara H, Takamura C, Ohmi S, Horikawa DD, Toyoda A, Katayama T, Arakawa K, Fujiyama A, Kubo T, Kunieda T

PLoS One 7 ( 8 ) e44209 2012

Research paper (scientific journal), Joint Work, Accepted

Metabolic flux analysis and visualization

TOYA Yoshihiro, KONO Nobuaki, ARAKAWA Kazuharu, TOMITA Masaru

Journal of Proteome Research 10 ( 8 ) 3313-3323 2011.08

Research paper (scientific journal), Joint Work, Accepted

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernandez JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T.

Journal of Biomedical Semantics 2 ( 1 ) 4 2011.08

Research paper (scientific journal), Joint Work

Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index

ARAKAWA Kazuharu, Suzuki H, Tomita M

BMC Genomics 10   640 2009.12

Research paper (scientific journal), Joint Work, Accepted

Pathway Projector: Web-based Zoomable Pathway Browser using KEGG Atlas and Google Maps API

Kono N, ARAKAWA Kazuharu, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M

PLoS One 4 ( 11 ) e7710 2009.11

Research paper (scientific journal), Joint Work, Accepted

A web server for interactive and zoomable Chaos Game Representation images

ARAKAWA Kazuharu,Oshita K, Tomita M

Source Code for Biology and Medicin 4   6 2009.09

Research paper (scientific journal), Joint Work, Accepted

Genome Projector: zoomable genome map with multiple views

ARAKAWA Kazuharu, TAMAKI, Satoshi, KONO, Nobuaki, KIDO, Nobuhiro, IKEGAMI Keita, OGAWA Ryu, TOMITA Masaru

BMC Bioinformatics 10   31 2009.01

Research paper (scientific journal), Joint Work

Visualizing Complex Omics Information - Scientific Visualization for Genomics and Systems Biology

ARAKAWA Kazuharu

BIOforum Europe 6   27-29 2008

Research paper (scientific journal), Joint Work

Comparative study of circadian oscillatory network models of Drosophila

ARAKAWA Kazuharu

Artificial Life 14 ( 1 ) 29-48 2008

Research paper (scientific journal), Joint Work, Accepted

Computational Genome Analysis Using The G-language System

ARAKAWA Kazuharu

Genes, Genomes and Genomics 2 ( 1 ) 1-13 2008

Research paper (scientific journal), Joint Work

Noise-reduction filtering for accurate detection of replication termini in bacterial genomes

ARAKAWA Kazuharu

Febs Letters 581 ( 2 ) 253-258 2007

Research paper (scientific journal), Joint Work, Accepted

Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes

ARAKAWA Kazuharu

Evolutionary Bioinformatics 3   279-286 2007

Research paper (scientific journal), Joint Work, Accepted

The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection

ARAKAWA Kazuharu

Evolutionary Bioinformatics 3   145-154 2007

Research paper (scientific journal), Joint Work, Accepted

Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics

ARAKAWA Kazuharu

Genomics Proteomics Bioinformatics 5 ( 1 ) 53-58 2007

Research paper (scientific journal), Joint Work, Accepted

Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations

ARAKAWA Kazuharu

Science 316 ( 5824 ) 593-597 2007

Research paper (scientific journal), Joint Work, Accepted

In Silico Screening of Archaeal tRNA-encoding Genes Having Multiple Introns with Bulge-Helix-Bulge Splicing Motifs

ARAKAWA Kazuharu

RNA 13 ( 5 ) 671-681 2007

Research paper (scientific journal), Joint Work, Accepted

Significance of the genomic properties of Chi sites validated from the distribution of all octamers in Escherichia coli

ARAKAWA Kazuharu

Gene 392 ( 1-2 ) 239-246 2007

Research paper (scientific journal), Joint Work, Accepted

Large-scale Modeling for Systems Biology

ARAKAWA Kazuharu

BIOforum Europe 10   54-55 2006

Research paper (scientific journal), Joint Work

KEGG-based pathway visualization tool for complex omics data

ARAKAWA Kazuharu

In Silico Biology 5   0039 2005

Research paper (scientific journal), Joint Work, Accepted

G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining

ARAKAWA Kazuharu

Bioinformatics 19 ( 2 ) 305-306 2003

Research paper (scientific journal), Joint Work, Accepted

The orientation bias of Chi sequences is a general tendency of G-rich oligomers

ARAKAWA Kazuharu

Gene 259 ( 1-2 ) 207-215 2000

Research paper (scientific journal), Joint Work, Accepted