Details of a Researcher - Arakawa, Kazuharu

Papers - Arakawa, Kazuharu

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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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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

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

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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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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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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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

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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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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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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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

© 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

© 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

© 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

© 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

© 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

© 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

© 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

© 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

© 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

© 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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