Papers - HONDA Daisuke
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Yohei Ishibashi, Hatsumi Goda, Rie Hamaguchi, Keishi Sakaguchi, Takayoshi Sekiguchi, Yuko Ishiwata, Yuji Okita, Seiya Mochinaga, Shingo Ikeuchi, Takahiro Mizobuchi, Yoshitake Takao, Kazuki Mori, Kosuke Tashiro, Nozomu Okino, Daiske Honda, Masahiro Hayashi, Makoto Ito
Communications Biology 4 ( 1 ) 2021.12
Publisher：Springer Science and Business Media LLC
Abstract
The demand for n-3 long-chain polyunsaturated fatty acids (n-3LC-PUFAs), such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), will exceed their supply in the near future, and a sustainable source of n-3LC-PUFAs is needed. Thraustochytrids are marine protists characterized by anaerobic biosynthesis of DHA via polyunsaturated fatty acid synthase (PUFA-S). Analysis of a homemade draft genome database suggested that Parietichytrium sp. lacks PUFA-S but possesses all fatty acid elongase (ELO) and desaturase (DES) genes required for DHA synthesis. The reverse genetic approach and a tracing experiment using stable isotope-labeled fatty acids revealed that the ELO/DES pathway is the only DHA synthesis pathway in Parietichytrium sp. Disruption of the C20 fatty acid ELO (C20ELO) and ∆4 fatty acid DES (∆4DES) genes with expression of ω3 fatty acid DES in this thraustochytrid allowed the production of EPA and n-3docosapentaenoic acid (n-3DPA), respectively, at the highest level among known microbial sources using fed-batch culture.DOI： 10.1038/s42003-021-02857-w
Other Link： https://www.nature.com/articles/s42003-021-02857-w
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Draft Genome Sequence of Sicyoidochytrium minutum DNA Virus Strain 001 Reviewed
Yumi Murakoshi, Takayuki Shimeki, Daiske Honda, Yoshitake Takao
Microbiology Resource Announcements 10 ( 23 ) 2021.6
Publisher：American Society for Microbiology
Sicyoidochytrium minutum DNA virus strain 001 (SmDNAV 001) is a double-stranded DNA (dsDNA) virus that infects the marine fungoid protist Sicyoidochytrium minutum . We report the draft genome sequence of SmDNAV 001. The 236,345-bp genome contained 358 coding sequences (CDSs) and three tRNA-coding sequences.
DOI： 10.1128/mra.00418-21
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Taming chlorophylls by early eukaryotes underpinned algal interactions and the diversification of the eukaryotes on the oxygenated Earth. Reviewed International coauthorship
Kashiyama, Y., Yokoyama, A., Shiratori, T., Hess, S., Not, F., Bachy, C., Gutierrez-Rodriguez, A., Kawahara, J., Suzaki, T., Nakazawa, M., Ishikawa, T., Maruyama, M., Wang, M., Chen, M., Gong, Y., Seto, K., Kagami, M., Hamamoto, Y., Honda, D., Umetani, T., Shihongi, A., Kayama, M., Matsuda, M., Taira, J., Yabuki, A., Tsuchiya, M., Hirakawa, Y., Kawaguchi, A., Nomura, M., Nakamura, A., Namba, N., Matsumoto, M., Tanaka, T., Yoshino, T., Higuchi, R., Yamamoto, A., Maruyama, T., Yamaguchi, A., Uzuka, A., Miyagishima, S., Tanifuji, G., Kawachi, M., Kinoshita, Y., Tamiaki, H.
The ISME Journal 13 1899 - 1910 2019.2
Joint Work
DOI： 10.1038/s41396-019-0377-0
Other Link： https://www.nature.com/articles/s41396-019-0377-0
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Nutritional intake of Aplanochytrium (Labyrinthulea, Stramenopiles) from living diatoms revealed by culture experiments suggesting the new prey–predator interactions in the grazing food web of the marine ecosystem. Reviewed
Hamamoto, Y., Honda, D.
PLoS ONE 14 ( 1 ) e0208941 2019.1
Joint Work
Authorship：Last author, Corresponding author
DOI： 10.1371/journal.pone.0208941
Other Link： https://doi.org/10.1371/journal.pone.0208941
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Iwata I, Honda D.
Protist 169 ( 6 ) 978 - 979 2018.12
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Abe E, Ikeda K, Nutahara E, Hayashi M, Yamashita A, Taguchi R, Doi K, Honda D, Okino N, Ito M.
PLoS ONE 13 ( 8 ) e0203016 - e0203016 2018.8
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Elemental composition and ultrafine structure of the skeleton in shellbearing protists—A case study of phaeodarians and radiolarians Reviewed
Nakamura, Y., Iwata, I., Hori, R. S., Uchiyama, N., Tuji, A., Fujita, M. J., Honda, D., Ohfuji, H.
Journal of Structural Biology 204 45 - 51 2018.7
Joint Work
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Nutritional intake by ectoplasmic nets of Schizochytrium aggregatum (Labyrinthulomycetes, Stramenopiles). Reviewed
Iwata, I., Honda, D.
Protist 169 727 - 743 2018.6
Joint Work
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Possible aplanochytrid (Labyrinthulea) prey detected using 18S metagenetic diet analysis in the key copepod species Calanus sinicus in the coastal waters of the subtropical western North Pacific Reviewed
Hirai, J., Hamamoto, Y., Honda, D., Hidaka, K.
Plankton and Benthos Research 13 ( 2 ) 75 - 82 2018.5
Joint Work
DOI： 10.3800/pbr.13.75
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Proposal of Monorhizochytrium globosum gen. nov., comb. nov.(Stramenopiles, Labyrinthulomycetes) for former Thraustochytrium globosum based on morphological features and phylogenetic relationships Reviewed
Doi, K., Honda, D.
Phycological Research 65 ( 3 ) 188 - 201 2017.7
Joint Work
DOI： 10.1111/pre.12175
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Bothrosome formation in Schizochytrium aggregatum (Labyrinthulomycetes, Stramenopiles) during zoospore settlement Reviewed
Izumi Iwata, Kei Kimura, Yuji Tomaru, Taizo Motomura, Kanae Koike, Kazuhiko Koike, Daiske Honda
Protist 168 ( 2 ) 206 - 219 2017.4
Joint Work
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Ecological dynamics of two distinct viruses infecting marine eukaryotic decomposer thraustochytrids (Labyrinthulomycetes, Stramenopiles) Reviewed
Yoshitake Takao, Yuji Tomaru, Keizo Nagasaki, Daiske Honda
PLOS ONE 10 ( 7 ) e0133395 2015.7
Joint Work
DOI： 10.1371/journal.pone.0133395
Other Link： http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0133395
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Seasonal dynamics of culturable thraustochytrids (Labyrinthulomycetes, Stramenopiles) in estuarine and coastal waters Reviewed
Ueda, M., Nomura, Y., Doi, K., Nakajima, M., Honda, D.
Aquatic Microbial Ecology 74 187 - 204 2015.3
Joint Work
DOI： 10.3354/ame01736
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Novel lysophospholipid acyltransferase PLAT1 of Aurantiochytrium limacinum F26-b responsible for generation of palmitate-docosahexaenoate-phosphatidylcholine and phosphatidylethanolamine. Reviewed
Abe, E., Ikeda, K., Nutahara, E., Hayashi, M., Yamashita A., Taguchi, R., Doi K., Honda D., Okino N., Ito, M.
PLoS ONE 9 ( 8 ) e102377 2014.8
Joint Work
DOI： 10.1371/journal.pone.0102377
Other Link： http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102377
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Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea. Reviewed
Zhu, D., Tanabe, S., Xie, C., Honda, D., Sun, J., Ai, L.
International Journal of Systematic and Evolutionary Microbiology 64 1712 - 1717 2014.5
Joint Work
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TLC screening of thraustochytrid strains for squalene production. Reviewed
Nakazawa, A., Kokubun, Y., Matsuura, H., Yonezawa, N., Kose, R., Yoshida, M., Tanabe, Y., Kusuda, E., Thang, D. V., Ueda, M., Honda, D., Mahakhant, A., Kaya, K., Watanabe, M. M.
Journal of Applied Phycology 26 ( 1 ) 29 - 41 2014.2
Joint Work
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Effect of trace elements on growth of marine eukaryotes, tharaustochytrids Reviewed
Nagano N, Taoka Y, Honda D, Hayashi M.
Journal of Bioscience and Bioengineering 116 ( 3 ) 337 - 339 2013.9
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Analysis of delta-12-fatty acid desaturase function revealed that two distinct pathways are active for the synthesis of PUFAs in T. aureum ATCC 34304 Reviewed
Matsuda T, Sakaguchi K, Hamaguchi R, Kobayashi T, Abe E, Hama Y, Hayashi M, Honda D, Okita Y, Sugimoto S, Okino N, Ito M
Journal of Lipid Research 53 1210 - 1222 2012.2
Joint Work
DOI： 10.1194/jlr.M024935
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Versatile Transformation System That Is Applicable to both Multiple Transgene Expression and Gene Targeting for Thraustochytrids Reviewed
Sakaguchi K, Matsuda T, Kobayashi T, Ohara J, Hamaguchi R, Abe E, Nagano N, Hayashi M, Ueda M, Honda D, Okita Y, Taoka Y, Sugimoto S, Okino N, Ito M
Applied and Environmental Microbiology 78 ( 9 ) 3193 - 3202 2012.2
Joint Work
DOI： 10.1128/AEM.07129-11
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On the bio-rearrangement into fully saturated fatty acidscontaining triglyceride in Aurantiochytrium sp. Reviewed
Matsuura H, Nakazawa A, Ueda M, Honda D, Watanabe MM, Kaya K
Procedia Environmental Sciences 15 66 - 72 2012
Joint Work
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Optimization of culture conditions of the thraustochytrid Aurantiochytrium sp. strain 18W-13a for squalene production Reviewed
Nakazawa A, Matsuura H, Kose R, Kato S, Honda D, Inouye I, Kaya K, Watanabe MM
Bioresource Technology 109 287 - 291 2012
Joint Work
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Optimization of biomass and fatty acid production by Aurantiochytrium sp. strain 4W-1b Reviewed
Nakazawa A, Matsuura H, Kose R, Ito K, Ueda M, Honda D, Inouye I, Kaya K, Watanabe MM
Procedia Environmental Sciences 15 27 - 33 2012
Joint Work
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Thraustochytrid Aurantiochytrium sp. 18W-13a accumulates high amounts of squalene. Reviewed
Kaya, K., Nakazawa, A., Matsuura, H., Honda, D., Inouye, I., and Watanabe, M. M.
Bioscience, Biotechnology and Biochemistry 75 ( 11 ) 2246 - 2248 2011.11
Joint Work
DOI： 10.1271/bbb.110430
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Detection of genes involved in fatty acid elongation and desaturation in thraustochytrid marine eukaryotes. Reviewed
Nagano, N., Sakaguchi, K., Taoka, Y., Okita, Y., Honda, D., Ito, M., and Hayashi, M.
Journal of Oleo Science 60 ( 9 ) 475 - 481 2011.8
Joint Work
DOI： 10.5650/jos.60.475
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Increase of eicosapentaenoic acid in thraustochytrids through thraustochytrid ubiquitin promoter-driven expression of a fatty acid ∆5 desaturase gene. Reviewed
Kobayashi, T., Sakaguchi, K., Matsuda, T., Abe, E., Hama, Y., Hayashi, M., Honda, D., Okita, Y., Sugimoto, S., Okino, N., and Ito, M.
Applied and Environmental Microbiology 77 ( 11 ) 3870 - 3876 2011.6
Joint Work
DOI： 10.1128/AEM.02664-10
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Increase of EPA in Thraustochytrids through Expression of a Fatty Acid 5 Desaturase Gene driven by the Thraustochytrid Ubiquitin Promoter
Takumi Kobayashi, Keishi Sakaguchi, Takanori Matsuda, Eriko Abe, Yoichiro Hama, Masahiro Hayashi, Daisuke Honda, Yuji Okita, Shinichi Sugimoto, Nozomu Okino, Makoto Ito
Journal of Biochemistry 2011.1
Joint Work
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The distribution of extracellular cellulase activity in marine eukaryotes, thraustochytrids. Reviewed
Nagano, N., Matsui, S., Kuramura, T., Taoka, Y., Honda, D., and Hayashi, M.
Marine Biotechnology 13 133 - 136 2011
Joint Work
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Optimization of culture conditions for growth and docosahexaenoic acid production by a marine thraustochytrid, Aurantiochytrium limacinum mh0186. Reviewed
Nagano, N., Taoka, Y., Honda, D., and Hayashi, M.
Journal of Oleo Science 58 ( 12 ) 623 - 628 2009.11
Joint Work
DOI： 10.5650/jos.58.623
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Olpidiopsis bostrychiae sp. nov.: an endoparasitic oomycete that infects Bostrychia and other red algae (Rhodophyta). Reviewed
Sekimoto, S., Klochkova, T. A., West, J. A., Beakes, G. W., and Honda, D.
Phycologia 48 ( 6 ) 460 - 472 2009.10
Joint Work
DOI： 10.2216/08-11.1
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Labyrinthulomycetes phylogeny and its implications for the evolutionary loss of chloroplasts and gain of ectoplasmic gliding. Reviewed
Tsui, C. K. M., Marshall, W., Yokoyama, R., Honda, D., Lippmeier, J. C., Craven, K. D., Peterson, P. D., and Berbee, M. L.
Molecular Phylogenetics and Evolution 50 ( 1 ) 129 - 140 2009.1
Joint Work
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Isolation and characterization of a ∆5-desaturase from Oblongichytrium sp. Reviewed
Kumon, Y., Kamisaka, Y., Tomita, N., Kimura, K., Uemura, H., Yokochi, T., Yokoyama, R., and Honda, D.
Bioscience, Biotechnology, and Biochemistry 72 ( 8 ) 2224 - 2227 2008.8
Joint Work
DOI： 10.1271/bbb.80235
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The development, ultrastructural cytology, and molecular phylogeny of the basal oomycete Eurychasma dicksonii, infecting the filamentous phaeophyte algae Ectocarpus siliculosus and Pylaiella littoralis. Reviewed
Sekimoto, S., Beakes, G. W., Gachon, C. M. M., Müller, D. G., Küpper, F. C., and Honda, D.
Protist 159 ( 2 ) 299 - 318 2008.4
Joint Work
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Taxonomy, molecular phylogeny, and ultrastructural morphology of Olpidiopsis porphyrae sp. nov. (Oomycetes, straminipiles), a unicellular obligate endoparasite of Bangia and Porphyra spp. (Bangiales, Rhodophyta). Reviewed
Sekimoto, S., Yokoo, K., Kawamura, Y., and Honda, D.
Mycological Research 112 ( 3 ) 361 - 374 2008.3
Joint Work
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Morphological and phylogenetic studies on unicellular diazotrophic cyanobacteria (cyanophytes) isolated from the coastal water around Singapore. Reviewed
Ohki, K., Kamiya, M., Honda, D., Kumazawa, S., and Ho, K. K.
Journal of Phycology 44 ( 1 ) 142 - 151 2008.1
Joint Work
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Taxonomic rearrangement of the genus Ulkenia sensu lato phylogeny based on morphology, chemotaxonomical characteristics and 18S rRNA gene (Thraustochytriaceae, Labyrinthulomycetes): emendation for Ulkenia and erection of Botryochytrium, Parietichytrium and Sicyoichytrium gen. nov. Reviewed
Yokoyama, R., Salleh, B., Honda, D.
Mycoscience 48 ( 6 ) 329 - 341 2007.12
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Squashed ball-like dsDNA virus infecting a marine fungoid protist Sicyoidochytrium minutum (Thraustochytriaceae, Labyrinthulomycetes).（共著）
Takao, Y., Nagasaki, K., Honda, D.
Aquatic Microbial Ecology 49 2007.11
Joint Work
Aquatic Microbial Ecology 49: 101-108 (2007).
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Proposal of Pseudochattonella verruculosa gen. nov., comb. nov. (Dictyochophyceae) for a formar raphidophycean alga Chattonella verruculosa, based on 18S rDNA phylogeny and ultrastructural characteristics. Reviewed
55 ( 3 ) 185 - 192 2007.8
Joint Work
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Molecular phylogeny of an unidentified Haliphthoros-like marine oomycete and Haliphthoros milfordensis inferred from nuclear-encoded small and large subunit rRNA genes and mitochondrial-encoded cox2 gene.（共著） Reviewed
Sekimoto, S., Hatai, K., Honda, D.
Mycoscience 48 48 212 - 221 2007.8
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Taxonomic rearrangement of the genus Schizochytrium sensu lato based on morphology, chemotaxonomical characteristics and 18S rRNA gene phylogeny (Thraustochytriaceae, Labyrinthulomycetes): emendation for Schizochytrium and erection of Aurantiochytrium and Oblongichytrium gen. nov.（共著） Reviewed
Yokoyama, R., Honda, D.
Mycoscience 48 ( 4 ) 199 - 211 2007.8
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Takao Y, Tomaru Y, Nagasaki K, Sasakura Y, Yokoyama R, Honda D.
Plankton and Benthos Research 2 ( 2 ) 91 - 97 2007.5
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Homologs of the sexually induced gene 1 (sig1) product constitute the stramenopile mastigonemes. Reviewed
Honda, D., Shono, T., Kimura. K., Fujita, S., Iseki, M., Makino, Y., Murakami, A.
Protist 158 ( 1 ) 77 - 88 2007.1
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A new labyrinthulid isolate that produces only docosahexaenoic acid Reviewed
Kumon Y, Yokoyama R, Haque Z, Yokochi T, Honda D, Nakahara T.
Marine Biotechnology 8 ( 2 ) 170 - 177 2006
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Shirai Y, Takao Y, Mizumoto H, Tomaru Y, Honda D, Nagasaki K.
Journal of the Marine Biological Association of the United Kingdom 86 ( 3 ) 475 - 483 2006
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Takao Y, Mise K, Nagasaki K, Okuno T, Honda D.
Journal of General Virology 87 ( 3 ) 723 - 733 2006
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Yuasa T, Takahashi O, Dolven J.K, Mayama S, Matsuoka A, Honda D, Bj?rklund K.R.
Marine Micropaleontology 59 ( 2 ) 104 - 114 2006
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Phylogenetic analyses of the polycystine Radiolaria based on the 18S rDNA sequences of the Spumellariada and Nessellarida. （共著）
Yuasa T, Takahashi O, Honda D, Mayama S.
Eur. J. Protistol.41 2005.11
Joint Work
Eur. J. Protistol. 41: 287-298 (2005)
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Isolation and characterization of a novel single-stranded RNA virus (SssRNAV) infectious to a marine fungoid protist Schizochytrium sp. (Thraustochytriaceae, Labyrinthulae). （共著）
Yoshitake Takao, Keizo Nagasaki, Kazuyuki Mise, Tetsuro Okuno, Daiske Honda.
Applied and Environmental Microbiology71 2005.11
Joint Work
Applied and Environmental Microbiology 71: 4516-4522 (2005).
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養殖ノリに被害を与える壺状菌Olpidiopsis sp.（卵菌綱，クロミスタ界）のPCRによる早期検出．（共著）
横尾一成，関本訓士，川村嘉応，本多大輔
日本水産学会誌71 2005.11
Joint Work
日本水産学会誌71，917-922 (2005)
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Molecular phylogeny of solitary shell-bearing Polycystinea (Radiolaria).（共著）
Osamu Takahashi, Tomoko Yuasa, Daiske Honda, Shigeki Mayama.
Revue de Micropaleontologie47 2004.11
Joint Work
Revue de Micropaleontologie 47: 111-118 (2004)
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Grouping newly isolated docosahexaenoic acid-producing thraustochytrids based on their polyunsaturated fatty acid profiles and comparative analysis of 18S rRNA genes. （共著）
Jianzhong Huang, Tsunehiro Aki, Toshihiro Yokochi, Toro Nakahara, Daiske Honda, Seiji Kawamoto, Seiko Shigeta, Kazuhisa Ono, and Osamu Suzuki.
Marine Biotechnology 5 2003.11
Joint Work
Marine Biotechnology 5: 450-457 (2003)
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A new labyrinthulid isolate, which solely produces n-6 docosapentaenoic acid Reviewed
Kumon Y, Yokoyama R, Yokochi T, Honda D, Nakahara T.
Applied Microbiology and Biotechnology 63 ( 1 ) 22 - 28 2003
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Ultrastructure and taxonomy of pelagic golden flagellate Phaeomonas parva gen. et sp. nov. (Pinguiophyceae) with particular emphasis on the flagellar apparatus architecture. （共著）
Daiske Honda and Isao Inouye.
Phycological Research50 2002.11
Joint Work
Phycological Research 50: 75-89 (2002).
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The Pinguiophyceae classis nova, a new class of chromophyte algae whose members produce large amounts of omega-3 fatty acids. （共著）
Masanobu Kawachi, Isao Inouye, Daiske Honda, Charles J. O'Kelly, J. Craig Bailey, Robert R. Bidigare and Robert A. Andersen.
Phycological Research 50 2002.11
Joint Work
Phycological Research 50: 31-47 (2002).
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Phylogenetic analysis of psychrotrophic bacteria isolated from the Japan Trench, including a description of the deep-sea species Psychrobacter pacificensis sp. nov.（共著）
Maruyama, A., Honda, D., Yamamoto, H., Kitamura, K., Higashihara, T.
International Journal of Systematic and Evolutionary Microbiology50 2000.11
Joint Work
International Journal of Systematic and Evolutionary Microbiology 50: 835-846.
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A deeply branched novel phylotype found in Japanese paddy soils. Reviewed
HONDA Daiske
Microbiology 146 2309 - 2315 2000
Single Work
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Detection of seven major evolutionary lineages in Cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains.（共著）
Honda, D., Yokota, A., Sugiyama, J.
Journal of Molecular Evolution48 1999.11
Joint Work
Journal of Molecular Evolution 48: 723-739.
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Molecular phylogeny of labyrinthulids and thraustochytrids based on the sequencing of 18S ribosomal RNA gene. （共著）
Honda, D., Yokochi, T., Nakahara, T., Raghukumar, S., Nakagiri, A., Schaumann, K., Higashihara, T.
Journal of Eukaryotic Microbiology46 1999.11
Joint Work
Journal of Eukaryotic Microbiology 46: 637-647.
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Schizochytrium limacinum sp. nov., a new thraustochytrid from mangrove area in the west Pacific Ocean（共著）
Honda, D., Yokochi, T., Nakahara, T, Erata, M & Higashihara, T.
Mycological Research102 1998.11
Joint Work
Mycological Research 102: 439-448.
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Optimization of docosahexaenoic acid production by Schizochytrium limacinum SR21. （共著）
Yokochi, T., Honda, D., Higashihara, T. & Nakahara, T.
Applied Microbiology and Biotechnology 49 1998.11
Joint Work
Applied Microbiology and Biotechnology 49: 72-76.
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Production of docosahexaenoic and docosapentaenoic acids by Schizochytrium sp. isolated from Yap Islands. （共著）
Nakahara, T., Yokochi, T., Higashihara, T., Tanaka, S., Yaguchi, T. & Honda, D.
Journal of the American Oil Chemists' Society73 1996.11
Joint Work
Journal of the American Oil Chemists' Society 73: 1421-1426.
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Chrysocystis fragilis gen. nov., sp. nov. (Chrysophyceae, Sarcinochrysidales), with note on other macroscopic chrysophytes (golden algae) on Guam reefs.（共著）
Lobban, C.S., Honda, D., Chihara, M. & Schefter, M.
Micronesica28 91 - 102 1995.11
Joint Work
Micronesica 28: 91-102
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Ultrastructure and reconstruction of the flagellar apparatus architecture in Ankylochrysis lutea (Chrysophyceae, Sarcinochrysidales). Reviewed
Honda, D. and Inouye, I.
Phycologia 34 215 - 227 1995.3
Joint Work
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Sulcochrysis biplastida gen. et sp. nov.: Cell structure and absolute configuration of the flagellar apparatus of an enigmatic chromophyte alga. Reviewed
Honda, D., Kawachi, M. and Inouye, I.
Phycological Research 43 1 - 16 1995.3
Joint Work