Papers - HONDA Daisuke
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Nakazawa A, Matsuura H, Kose R, Kato S, Honda D, Inouye I, Kaya K, Watanabe MM
Bioresource Technology 109 287 - 291 2012
Joint Work
Optimum conditions of temperature, salinity and glucose concentration were investigated for squalene production of the strain of Aurantiochytrium sp. 18W-13a, with a high content of squalene. Squalene production by this strain was optimum at 25°C, 25–50% seawater concentration and 2–6% glucose concentration. When this strain was grown in the optimum condition, the squalene content and production of approximately 171mg/g dry weight and 0.9g/L were much higher than that previously reported in thraustochytrids, plants and yeasts, respectively. Therefore, 18W-13a could be used as an alternative source of commercial squalene.
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Optimization of biomass and fatty acid production by Aurantiochytrium sp. strain 4W-1b Reviewed International journal
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
The biomass and lipid productions by a newly isolated Aurantiochytrium strain, 4W-1b, were investigated at different temperatures and glucose concentrations. The maximum biomass was produced at 15–25 °C. The biomass, lipid, and fatty acid productions were the maximum in a 6% glucose medium. The lipid and fatty acid productions were estimated to be approximately 11 g/L and 9 g/L, respectively, with the highest yields of docosahexaenoic acid (22:6; 1.5 g/L) and palmitic acid (16:0; 4.8 g/L). The 4W-1b strain is considered to have a high potential for uses in various industrial sectors, including fuel, health supplements, soap, and food oil companies.
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Thraustochytrid Aurantiochytrium sp. 18W-13a accumulates high amounts of squalene. Reviewed International journal
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
Here we report on the 18W-13a strain of Aurantiochytrium sp., which accumulates very high amounts of squalene. The squalene contents and production at 4 d of culture were 198 mg/g and 1.29±0.13 g/L, respectively, exceptionally high values compared to previous reports.
DOI： 10.1271/bbb.110430
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Detection of genes involved in fatty acid elongation and desaturation in thraustochytrid marine eukaryotes. Reviewed International journal
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
Heterotrophic marine protists known as thraustochytrids can synthesize polyunsaturated fatty acids (PUFAs) such as docosahexaenoic acid (DHA). The biosynthetic pathways of PUFAs in thraustochytrids are poorly understood, however. In this study, we attempted to reveal the enzymes involved in DHA synthesis in thraustochytrids. Nine thraustochytrid strains representing 3 genera (Aurantiochytrium, Schizochytrium, and Thraustochytrium) were used for PCR-based detection of the genes encoding Δ5-elongase and Δ4-desaturase and for fatty acid analysis. The degenerate primers were designed to amplify the Δ5-elongase and Δ4-desaturase genes, and the partial sequences of the enzymes were obtained from the genera Thraustochytrium and Schizochytrium. These fragments were identical to those of known Δ5-elongase and Δ4-desaturase. Neither Δ5-elongase nor Δ4-desaturase was detected in the strains belonging to the genus Aurantiochytrium, however, suggesting that this group likely synthesizes DHA not via the elongation/desaturation pathway but via an alternate pathway such as the polyketide synthase pathway. The fatty acid profiles of thraustochytrids were consistent with the presence of genes involved in PUFA biosynthesis in thraustochytrid genera. Thus, our findings suggest that two biosynthetic pathways for PUFAs exist in these organisms.
DOI： 10.5650/jos.60.475
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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
Thraustochytrids, marine protists known to accumulate polyunsaturated fatty acids (PUFAs) in lipid droplets, are considered an alternative to fish oils as a source of PUFAs. The major fatty acids produced in thraustochytrids are palmitic acid (C16:0), n − 6 docosapentaenoic acid (DPA) (C22:5 n − 6), and docosahexaenoic acid (DHA) (C22:6 n − 3), with eicosapentaenoic acid (EPA) (C20:5 n − 3) and arachidonic acid (AA) (C20:4 n − 6) as minor constituents. We attempted here to alter the fatty acid composition of thraustochytrids through the expression of a fatty acid Δ5 desaturase gene driven by the thraustochytrid ubiquitin promoter. The gene was functionally expressed in Aurantiochytrium limacinum mh0186, increasing the amount of EPA converted from eicosatetraenoic acid (ETA) (C20:4 n − 3) by the Δ5 desaturase. The levels of EPA and AA were also increased by 4.6- and 13.2-fold in the transgenic thraustochytrids compared to levels in the mock transfectants when ETA and dihomo-γ-linolenic acid (DGLA) (C20:3 n − 6) were added to the culture at 0.1 mM. Interestingly, the amount of EPA in the transgenic thraustochytrids increased in proportion to the amount of ETA added to the culture up to 0.4 mM. The rates of conversion and accumulation of EPA were much higher in the thraustochytrids than in baker's yeasts when the desaturase gene was expressed with the respective promoters. This report describes for the first time the finding that an increase of EPA could be accomplished by introducing the Δ5 desaturase gene into thraustochytrids and indicates that molecular breeding of thraustochytrids is a promising strategy for generating beneficial PUFAs.
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 International journal
Nagano, N., Matsui, S., Kuramura, T., Taoka, Y., Honda, D., and Hayashi, M.
Marine Biotechnology 13 133 - 136 2011
Joint Work
Cellulolytic ability was evaluated in 19 strains of thraustochytrids, representing nine genera, using carboxymethylcellulose (CMC) as a substrate. Extracellular cellulolytic enzyme activity was determined in the culture supernatants during cell growth. CMC hydrolysis was observed in 14 out of the 19 strains examined. These belonged to the genera Aplanochytrium, Botryochytrium, Oblongichytrium, Parietichytrium, Schizochytrium, Sicyoidochytrium, Thraustochytrium and Ulkenia. On the other hand, cellulolytic enzyme activity was not detected in any strains belonging to the genus Aurantiochytrium.
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Nagano, N., Taoka, Y., Honda, D., and Hayashi, M.
Journal of Oleo Science 58 ( 12 ) 623 - 628 2009.11
Joint Work
The effects of carbon sources, seawater concentration and seawater component in a culture medium were investigated to optimize culture conditions for growth by a marine thraustochytrid
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 International journal
Sekimoto, S., Klochkova, T. A., West, J. A., Beakes, G. W., and Honda, D.
Phycologia 48 ( 6 ) 460 - 472 2009.10
Joint Work
Authorship：Last author, Corresponding author
A holocarpic, oomycete endoparasite of the marine red alga Bostrychia moritziana collected in Madagascar and identified as Olpidiopsis sp. did not conform to morphological descriptions of any species of Olpidiopsis and had a host range that differed from that of known Olpidiopsis pathogens of red algae. We further tested the host range of this parasite and studied it by transmission electron microscopy and molecular means. It differs from other Olpidiopsis species, and we have named it O. bostrychiae. Molecular phylogenies inferred from SSU rRNA gene and COII amino acid sequences showed that O. bostrychiae branched before the main saprolegnialean and peronosporalean lineages within the monophyletic oomycetes. In the SSU rRNA gene tree, O. bostrychiae formed a clade with O. porphyrae, which infects Bangia and Porphyra spp. The two Olpidiopsis species were genetically and ultrastructurally distinct, supporting our decision to name an additional Olpidiopsis species that is parasitic on red algae.
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 International coauthorship International journal
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
The labyrinthulomycetes, also known as the ‘Labyrinthulomycota’ are saprotrophic or less frequently parasitic stramenopilan protists, usually in marine ecosystems. Their distinguishing feature is an ‘ectoplasmic net,’ an external cytoplasmic network secreted by a specialized organelle that attaches the cell to its substrate and secretes digestive enzymes for absorptive nutrition. In this study, one of our aims was to infer the phylogenetic position of the labyrinthulomycetes relative to the non-photosynthetic bicoeceans and oomycetes and the photosynthetic ochrophytes and thereby evaluate patterns of change from photosynthesis to saprotrophism among the stramenopiles. For the labyrinthulomycetes, we determined sequences of the actin, beta-tubulin, and elongation factor 1-alpha gene fragments and where necessary, ribosomal small subunit (SSU) genes. Multilocus analysis using standard tree construction techniques not only strongly supported the oomycetes as the sister group to the phototrophic stramenopiles, but also, for the first time with moderate statistical support, showed that the labyrinthulomycetes and the bicoecean as sister groups. The paraphyly of the non-photosynthetic groups was consistent with independent loss of photosynthesis in labyrinthulomycetes and oomycetes. We also wished to develop a phylogenetically based hypothesis for the origin of the gliding cell bodies and the ectoplasmic net found in some labyrinthulomycetes. The cells of species in Labyrinthula and Aplanochytrium share a specialized form of motility involving gliding on ectoplasmic tracks. Before our study, only ribosomal DNA genes had been determined for these genera and their phylogenetic position in the labyrinthulomycetes was equivocal. Multilocus phylogenies applying our newly determined protein-coding sequences divided the labyrinthulomycetes between sister clades ‘A’ and ‘B’ and showed that the monophyletic group containing all of the gliding species was nested among non-gliding species in clade B. This phylogeny suggested that species that glide via an ectoplasm evolved from species that had used the ectoplasm mainly for anchorage and assimilation rather than motility.
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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