研究業績

生物システム研究グループ

原著論文

2023

  1. Yasuzawa, Y., Shibuya, R., Senga, Y., Miyafusa, T., Honda, S.: Determination of the optimal connector length to enhance stability of backbone-circularized granulocyte colony-stimulating factor. FEBS Open Bio, 13:1910, 2023. DOI=10.1002/2211-5463.13692.
  2. Koto, A., Tamura, M., Wong, P.S., Aburatani, S., Privman, E., Stoffel, C., Crespi, A., McKenzie, S.K., Mendola, C.L, Kay, T., Keller, L.: Social isolation shortens lifespan through oxidative stress in ants. Nat. Commun., 14:5493, 2023. DOI=10.1038/s41467-023-41140-w.
  3. Sahara, T., Adachi, T., Nagamine, T., Fukano, T., Morita, N.: Draft genome sequence of a docosahexaenoic-acid-producing marine protist, thraustochytrid strain 12B. Microbiol. Resour. Announc. 12(9):e0027023, 2023. DOI=10.1128/MRA.00270-23.
  4. Okuda, T., Kato, K.: Serum components influence antibody reactivity to glycan and DNA antigens. Sci. Rep., 13:13644, 2023. DOI=0.1038/s41598-023-40707-3.
  5. Suenami, S., Koto, A., Miyazaki, R.: Basic Structures of Gut Bacterial Communities in Eusocial Insects. Insects, 14(5):444, 2023. DOI=10.3390/insects14050444.
  6. Yamaguchi, S., Fujioka, T., Yoshimi, A., Kumagai, T., Umemura, M., Abe, K., Machida, M., Kawai, K.: Discovery of a gene cluster for the biosynthesis of novel cyclic peptide compound, KK-1, in Curvularia clavata. Front. Fungal Biol., 3:1081179, 2023. DOI=10.3389/ffunb.2022.1081179.

2022

  1. Umemura, M., Tamano, K.: How to improve the production of peptidyl compounds in filamentous fungi. Front. Fungal Biol., 22(3)1085624, 2022. DOI=10.3389/ffunb.2022.1085624.
  2. Umemura, M., Kuriiwa, K., Dao, L.V.: Tandem repeats in precursor protein stabilize transcript levels and production levels of the fungal ribosomally synthesized and post-translationally modified peptide ustiloxin B. Fungal Genet. Biol., 160:103691, 2022. DOI=10.1016/j.fgb.2022.103691.
  3. Okuda, T., Kato, K.: Glycosphingolipids form characteristic-sized liposomes that correlate with their antibody-inducing activities in mice. Biochem. Biophys. Res. Commun., 634:48, 2022. DOI=10.1016/j.bbrc.2022.09.094.
  4. Okuda, T., Kitamura, M., Kato, K.: A zirconia-based column chromatography system optimized for the purification of IgM from hybridoma culture supernatants. Anal. Biochem., 657:114900, 2022. DOI=10.1016/j.ab.2022.114900.
  5. Suenaga, H., Matsuzawa, T., Sahara, T.: Discovery by metagenomics of a functional tandem repeat sequence that controls gene expression in bacteria, FEMS Microbiol. Ecol., 98:fiac037, 2022. DOI=10.1093/femsec/fiac037.

2021

  1. Takahashi, H., Umemura, M., Ninomiya, A., Kusuya, Y., Shimizu, M., Urayama, S.I., Watanabe, A., Kamei, K., Yaguchi, T., Hagiwara, D.: Interspecies Genomic Variation and Transcriptional Activeness of Secondary Metabolism-Related Genes in Aspergillus Section Fumigati. Front. Fungal Biol., 2:14, 2021. DOI=10.10/10.3389/ffunb.2021.656751.
  2. Takemura, M., Kubo, A., Watanabe, A., Sakuno, H., Minobe, Y., Sahara, T., Murata, M., Araki, M., Harada, H., Terada, Y., Yaoi, K., Ohdan, K., Misawa, N.: Pathway engineering for high-yield production of lutein in Escherichia coli. Synthetic Biol., 6:1, 2021 DOI=10.10/10.1093/synbio/ysab012.
  3. Takemura, M., Sahara, T., Misawa, N.: Violaxanthin: natural function and occurrence, biosynthesis, and heterologous production. Appl. Microbiol. Biotechnol., 105:6133, 2021 DOI=10.10/10.1007/s00253-021-11452-2.
  4. Shibuya, R., Miyafusa, T., Imamura, H., Ooishi, A., Honda, S.: Effect of backbone circularization on colloidal stability: Compaction of unfolded structures improves aggregation resistance of granulocyte colony-stimulating factor. Int. J. Pharm., 605:120774, 2021 DOI=10.1016/j.ijpharm.2021.120774.
  5. Shinkai, Y., Kuramochi, M., Miyafusa, T.: New Family Members of FG Repeat Proteins and Their Unexplored Roles During Phase Separation. Front. Cell Dev. Biol., 9:708702, 2021 DOI=10.3389/fcell.2021.708702.
  6. Miyafusa, T., Watanabe, H., Honda, S.,: Local disorder of the C-terminal segment of the heavy chain as a common sign of stressed antibodies evidenced with a peptide affinity probe specific to non-native IgG. Int. J. Biol. Macromol., 182:1697, 2021 DOI=10.1016/j.ijbiomac.2021.05.137.
  7. Okuda, T., Kato, K., Kitamura, M., Kasahara, S.: Purification of anti-glycoconjugate monoclonal antibodies using newly developed porous zirconia particles. Sci Rep 11: 3233, 2021. DOI=10.1038/s41598-021-82457-0.
  8. Shibao, H., Kutsukake, M., Fukatsu, T.: Temporal division of labor in an aphid social system. Sci Rep 11:1183, 2021. DOI=10.1038/s41598-021-81006-z.

2020

  1. Matsuzawa, T., Kameyama, A., Nakamichi, Y., Yaoi, K.: Identification and characterization of two xyloglucan-specific endo-1,4-glucanases in Aspergillus oryzae. Appl Microbiol Biotechnol, 104:8761-8773, 2020. DOI=10.1007/s00253-020-10883-7.
  2. Matsuzawa, T., Maehara, T., Kamisaka, Y., Ayabe-Chujo, Y., Takaku, H., Yaoi, K.: Identification and characterization of Pseudozyma antarctica Δ12 fatty acid desaturase and its utilization for the production of polyunsaturated fatty acids. J Biosci Bioeng 130:604-609, 2020. DOI=10.1016/j.jbiosc.2020.07.019.
  3. Kosakamoto, H.,Yamauchi, T., Akuzawa-Tokita, Y., Nishimura, K., Soga, T., Murakami, T., Mori, H., Yamamoto, K., Miyazaki, R., Koto, A., Miura, M., Obata, F.: Local necrotic cells trigger systemic immune activation via gut microbiome dysbiosis in Drosophila, Cell reports, 32, 107938, 2020. DOI=10.1016/j.celrep.2020.107938.
  4. Okuda, T.: Isolation and Characterization of Antibodies Induced by Immunization with TNF-α Inducible Globotetraosylceramide. Int J Mol Sci 21: 3632, 2020. DOI=10.3390/ijms21103632.
  5. Umemura, M., Kuriiwa, K., Dao, L.V., Okuda, T., Terai, G.: Promoter Tools for Further Development of Aspergillus oryzae as a platform for fungal secondary metabolite production. Fungal Biol Biotechnol. 7: 3, 2020. DOI=10.1186/s40694-020-00093-1.
  6. Koto, A., Nobu, M.K., Miyazaki, R.: Deep Sequencing Uncovers Caste-Associated Diversity of Symbionts in the Social Ant Camponotus japonicus. mBio. 2150-7511 ,2020. DOI=10.1128/mBio.00408-20.
  7. Matsuzawa, T., Kamisaka, Y., Maehara, T., Takaku, H., Yaoi, K.: Identification and characterization of two fatty acid elongases in Lipomyces starkeyi. Appl. Microbiol. Biotechnol. 104:2537–2544, 2020. DOI=10.1007/s00253-020-10401-9.
  8. Takaku, H., Miyajima, A., Kazama, H., Sato, R., Ara, S., Matsuzawa, T., Yaoi, K., Araki, H., Shida, Y., Ogasawara, W., Yamazaki, H.: A novel electroporation procedure for highly efficient transformation of Lipomyces starkeyi. J. Microbiol. Methods, 169:105816, 2020. DOI=10.1016/j.mimet.2019.105816.
  9. Matsuzawa, T., Kameyama, A., Yaoi, K.: Identification and characterization of a-xylosidase involved in xyloglucan degradation in Aspergillus oryzae. Appl. Microbiol. Biotechnol. 104:201–210, 2020. DOI=10.1007/s00253-019-10244-z.

2019

  1. Okuda, T., Shimizu, K., Hasaba, S., Date, M.,: Induction of specific adaptive immune responses by immunization with newly designed artificial glycosphingolipids. Sci Rep 9: 18803, 2019. DOI=10.1038/s41598-019-55088-9.
  2. Okuda, T.: A low-carbohydrate ketogenic diet induces the expression of very-low-density lipoprotein receptor in liver and affects its associated metabolic abnormalities. NPJ Sci Food. 3: 25, 2019. DOI=10.1038/s41538-019-0058-4.
  3. Okuda, T.: Data set for characterization of the glycosylation status of hepatic glycoproteins in mice fed a low-carbohydrate ketogenic diet. Data Brief 27: 104604, 2019. DOI=10.1016/j.dib.2019.104604.
  4. Okuda, T.: A low-carbohydrate ketogenic diet promotes ganglioside synthesis via the transcriptional regulation of ganglioside metabolism-related genes. Sci Rep 9: 7627, 2019. DOI=10.1038/s41598-019-43952-7.
  5. Matsuzawa, T., Watanabe, M., Kameda, T., Kameyama, A., Yaoi, K.: Cooperation between b-galactosidase and an isoprimeverose-producing oligoxyloglucan hydrolase is key for xyloglucan degradation in Aspergillus oryzae. FEBS J. 286:3182–3193, 2019. DOI=10.1111/febs.14848.
  6. Imai, M., Mihashi, A., Imai, T., Kimura, S., Matsuzawa, T., Yaoi, K., Shibata, N., Kakeshita, H., Igarashi, K., Kobayashi, Y., Sugiyama, J.: Selective fluorescence labeling: time-lapse enzyme visualization during sugarcane hydrolysis. Journal of Wood Science 65:17, 2019. DOI=10.1186/s10086-019-1798-0.
  7. Takemura, M., Kubo, A., Higuchi, Y., Maoka, T., Sahara, T., Yaoi, K., Ohdan, K., Umeno, D., Misawa, N.: Pathway engineering for efficient biosynthesis of violaxanthin in Escherichia coli. Appl. Microbiol. Biotechnol. 103: 9393-9399, 2019. DOI=10.1007/s00253-019-10182-w.
  8. Makino, M., Sahara, T., Morita, N., Ueno, H.: Carboxypeptidase Y activity and maintenance is modulated by a large helical structure. FEBS Open Bio 9: 1337-1343, 2019. DOI=10.1002/2211-5463.12686.
  9. Seike, T., Kobayashi, Y., Sahara, T., Ohgiya, S., Kamagata, Y., Fujimori, K.E.: Molecular evolutionary engineering to improve catalytic activity and performance of Saccharomyces cerevisiae xylose isomerase for micro-aerobic glucose/xylose co-fermentation. Biotechnology for Biofuels. 12:139, 2019. DOI=10.1186/s13068-019-1474-z.
  10. Kumagai, T., Tsukahara, M., Katayama, N., Yaoi, K., Aburatani, S., Ohdan, K., Fujimori, K.E.: Whole genome sequence of Monascus purpureus GB-01, an industrial strain for food colorant production. Microbiol. Resour. Announc. 8(24): e00196-19, 2019. DOI=10.1128/MRA.00196-19.
  11. Fujimori, K.E.*, Kobayashi, Y., Seike, T., Sahara, T., Ohgiya, S., Kamagata, Y.: Whole-Genome Sequence of an Isogenic Haploid Strain, Saccharomyces cerevisiae IR-2idA30(MATa), Established from the Industrial Diploid Strain IR-2. Microbiol. Resour. Announc. 2019 8 (17): e00018-19. DOI=10.1128/MRA.00018-19.
  12. Sameshima-Yamashita, Y., Watanabe, T., Tanaka, T., Tsuboi, S., Yarimizu, T., Morita, T., Koike, H., Suzuki, K., Kitamoto, H.: Construction of a Pseudozyma antarctica strain without foreign DNA sequences (self-cloning strain) for high yield production of a biodegradable plastic-degrading enzyme. Biosci. Biotechnol. Biochem. 3:1-10, 2019(Feb). DOI=10.1080/09168451.2019.1571898.

2018

  1. Matsuzawa T, Kameyama A, Yaoi K: A novel isoprimeverose-producing enzyme from Phaeoacremonium minimum is active at low concentrations of xyloglucan oligosaccharides. FEBS Open Bio 9: 92-100, 2018. DOI=10.1002/2211-5463.12549.
  2. Matsuzawa T*, Watanabe M*, Nakamichi Y, Fujimoto Z, Yaoi K (*contributed equally): Crystal structure and substrate recognition mechanism of Aspergillus oryzae isoprimeverose-roducing enzyme. J. Struct. Biol. 205: 84-90, 2018. DOI=10.1016/j.jsb.2018.11.005.
  3. Matsuzawa T, Maehara T, Kamisaka Y, Ara S, Takaku H, Yaoi K: Identification and characterization of Δ12 and Δ12/Δ15 bifunctional fatty acid desaturases in the oleaginous yeast Lipomyces starkeyi. Appl. Microbiol. Biotech. 102: 8817-8826, 2018. DOI=10.1007/s00253-018-9345-2.
  4. Kobayashi Y, Sahara T, Ohgiya S, Kamagata Y, Fujimori K E: Systematic optimization of gene expression of pentose phosphate pathway enhances ethanol production from a glucose/xylose mixed medium in a recombinant Saccharomyces cerevisiae. AMB Express 8(1), 2018. DOI=10.1186/s13568-018-0670-8.
  5. Okuda T: Data set for characterization of TNF-α-inducible glycosphingolipids in vascular endothelial cells. Data Brief 21: 29-35, 2018. DOI=10.1016/j.dib.2018.09.059.
  6. Okuda T: Data on immunoglobulin G antibodies induced by immunization of mice with globoside carrying very long-chain fatty acids. Data Brief 19: 256-260, 2018. DOI=10.1016/j.dib.2018.05.014.
  7. Okuda T, Fukui A: Generation of anti-oligosaccharide antibodies that recognize mammalian glycoproteins by immunization with a novel artificial glycosphingolipid. Biochem. Biophys. Res. Commun. 497: 983-989, 2018. DOI=10.1016/j.bbrc.2018.02.113.
  8. Saika A, Utashima Y, Koike H, Yamamoto S, Kishimoto T, Fukuoka T, Morita T: Identification of the gene PtMAT1 encoding acetyltransferase from the diastereomer type of mannosylerythritol lipid-B producer Pseudozyma tsukubaensis. J. Biosci. Bioeng. 126-6: 676-681, 2018. DOI=10.1016/j.jbiosc.2018.05.025.
  9. Inaba T, Sato Y, Koike H, Hori T, Kanno M, Kimura N, Kirimura K, Habe H: Draft Genome Sequence of Pseudomonas citronellolis LA18T, a Bacterium That Uses Levulinic Acid. Microbiol. Resour. Announc. 7(5): 1-2, 2018. DOI=10.1128/MRA.00906-18.
  10. Saika A, Utashima Y, Koike H, Yamamoto A, Kishimoto T, Fukuoka T, Morita T: Biosynthesis of mono-acylated mannosylerythritol lipid in an acyltransferase gene-disrupted mutant of Pseudozyma tsukubaensis. Appl. Microbiol. Biotechnol. 102(4): 1759-1767, 2018. DOI=10.1007/s00253-017-8698-2.

2017

  1. Adachi T, Sahara T, Okuyama H, Morita N: Glass Bead-based Genetic Transformation: An Efficient Method for Transformation of Thraustochytrid Microorganisms. J. Oleo Sci. 66: 791-795, 2017. DOI=10.5650/jos.ess17084.
  2. Tsujimoto Y, Saito R, Sahara T, Kimura N, Tsuruoka N, Shigeri Y, Watanabe K: Draft Genome Sequence of Caenibacillus caldisaponilyticus B157(T), a Thermophilic and Phospholipase-Producing Bacterium Isolated from Acidulocompost. Genome Announc.  5: e00089-17, 2017. DOI=10.1128/genomeA.00089-17.
  3. Okuda T: PUGNAc treatment provokes globotetraosylceramide accumulation in human umbilical vein endothelial cells. Biochem. Biophys. Res. Commun. 487: 76-82, 2017. DOI=10.1016/j.bbrc.2017.04.019.
  4. Saika A, Koike H, Yamamoto S, Kishimoto T, Morita T: Enhanced Production of a Diastereomer Type of Mannosylerythritol Lipid-B by the Basidiomycetous Yeast Pseudozyma tsukubaensis Expressing Lipase Genes from Pseudozyma antarctica. Appl. Microbiol. Biotechnol. 101(23-24): 8345-8352, 2017. DOI=10.1007/s00253-017-8589-6.
  5. Yarimizu T, Shimoi H, Sameshima‐Yamashita Y. Morita T, Koike H, Watanabe T, Kitamoto H: Targeted gene replacement at the URA3 locus of the basidiomycetous yeast Pseudozyma antarctica and its transformation using lithium acetate treatment. Yeast 34(12): 483-494, 2017. DOI=10.1002/yea.3251.
  6. Aoyagi T, Koike H, Morita T, Sato Y, Habe H, Hori, T: Draft genome sequence of Geobacter pelophilus Strain Dfr2, a ferric iron reducing bacterium. Genome Announcements. 5(24): e00537-17, 2017. DOI=10.1128/genomeA.00537-17.
  7. Tamano K, Miura A, Koike H, Kamisaka Y, Umemura M, Machida M: High-efficiency extracellular release of free fatty acids from Aspergillus oryzae using non-ionic surfactants. J. Biotechnol. 248: 9-14, 2017. DOI=10.1016/j.jbiotec.2017.03.002.
  8. Yagi H, Maehara T, TanakaT, Takehara R, Teramoto K, Yaoi K, Kaneko S: 4-O-Methyl modifications of glucuronic acids in xylans are indispensable for substrate discrimination by GH67 α-glucuronidase from Bacillus halodurans C-125. J. Appl. Glycosci. 64 :115-121, 2017. DOI=10.5458/jag.jag.JAG-2017_016.
  9. Maehara T, Yagi H, Sato T, Ohnishi-Kameyama M, Fujimoto Z, Kamino K, Kitamura K, John F, Yaoi K, Kaneko S: Characterization of a GH30 glucuronoxylan specific xylanase from Streptomyces turgidiscabies C56. Appl. Environ. Microbiol. 84: e01850-17, 2017. DOI=10.1128/AEM.01850-17.
  10. Ishi T, Matsuoka K, Ono H, Ohnishi-Kameyama M, Yaoi K, Nakano Y, Ohtani M, Demura T, Iwai H, Sato S: Characterization of xylan in the early stages of secondary cell wall formation in tobacco bright yellow-2 cells. Carbohydrate Polymers 176: 2017. DOI=10.1016/j.carbpol.2017.08.108.
  11. Matsuzawa T*, Watanabe M*, Yaoi K (*contributed equally): Improved thermostability of a metagenomic glucose-tolerant β-glycosidase based on its X-ray crystal structure. Appl. Microbiol. Biotechnol. 101: 8353-8363, 2017. DOI=10.1007/s00253-017-8525-9.
  12. Kameta N, Matsuzawa T, Yaoi K, Fukuda J, Masuda M: Glycolipid-based nanostructures with thermal-phase transition behavior functioning as solubilizers and refolding accelerators for protein aggregates. Soft Matter 13: 3084-3090, 2017. DOI=10.1039/C7SM00310B.
  13. Matsuzawa T, Kaneko S, Kishine N, Fujimoto Z, Yaoi K: Crystal structure of metagenomic β-xylosidase/α-L-arabinofuranosidase activated by calcium. J Biochem 162: 173-181, 2017. DOI=10.1093/jb/mvx012.
  14. Kobayashi Y, Sahara T, Suzuki T, Kamachi S, Matsushika A, Hoshino T, Ohgiya S, Kamagata Y, Fujimori KE: Genetic improvement of xylose metabolism by enhancing the expression of pentose phosphate pathway genes in Saccharomyces cerevisiae IR-2 for high-temperature ethanol production. J Ind Microbiol Biotechnol. 2017 Feb 8. DOI=10.1007/s10295-017-1912-5.
  15. Matsuzawa T, Yaoi K: Screening, identification, and characterization of a novel saccharide-stimulated β-glycosidase from a soil metagenomic library. Appl. Microbiol. Biotechnol. 101: 633-646, 2017. DOI=10.1007/s00253-016-7803-2.
  16. Okuda, T: Altered expression of O-GlcNAc-modified proteins in a mouse model whose glycemic status is controlled by a low carbohydrate ketogenic diet. Data in Brief. 10, 449-453, 2017. DOI=10.1007/s10719-013-9482-x.

2016

  1. Tani T, Taguchi H, Fujimori K E, Sahara T, Ohgiya S, Kamagata Y, Akamatsu T: Isolation and characterization of xylitol-assimilating mutants of recombinant Saccharomyces cerevisiae. J. Biosci. Bioeng. 122(4): 446-455, 2016. DOI=10.1016/j.jbiosc.2016.03.008.
  2. Kameta N, Matsuzawa T, Yaoi K, Masuda M: Short Polyethylene Glycol Chains Densely Bound to Soft Nanotube Channels for Inhibition of Protein Aggregation. RSC Advances 6: 36744-36750, 2016. DOI=10.1039/C6RA06793J.
  3. Saika A, Koike H, Fukuoka T, Yamamoto S, Kishimoto T, Morita T: A Gene Cluster for Biosynthesis of Mannosylerythritol Lipids Consisted of 4-O-β-D-Mannopyranosyl-(2R,3S)-erythritol as the Sugar Moiety in a Basidiomycetous Yeast Pseudozyma tsukubaensis. PLoS One，11: e0157858-, 2016. DOI=10.1371/journal.pone.0157858.
  4. Sato Y, Koike H, Kondoh S, Hori T, Kanno M, Kimura T, Morita T, Kirimura K, Habe H: Draft Genome Sequence of Burkholderia stabilis LA20W, a Trehalose Producer that Uses Levulinic Acid as a Substrate. Genome announcements，4: e00795-16, 2016. DOI=10.1128/genomeA.00795-16.
  5. Koitabashi M, Yamashita Y, Koike H, Sato T, Moriwaki J, Morita T, Watanabe A, Yoshida S, Kitamoto H: Biodegradable Plastic-degrading Activity of Various Species of Paraphoma. Journal of Oleo Science，65: 621-627, 2016. DOI=10.5650/jos.ess16067.
  6. Okuda, T., and Morita, N: A very low carbohydrate ketogenic diet increases hepatic glycosphingolipids related to regulation of insulin signalling. J. Funct. Foods. 21, 70-74, 2016. DOI=10.1016/j.jff.2015.11.040.
  7. Matsuzawa T, Kaneko S, Yaoi K: Improvement of thermostability and activity of Trichoderma reesei endo-xylanase Xyn III on insoluble substrates. Appl. Microbiol. Biotechnol. 100: 8043-8051, 2016. DOI=10.1007/s00253-016-7563-z.
  8. Matsuzawa T*, Jo T*, Uchiyama T, Manninen JA, Arakawa T, Miyazaki K, Fushinobu S, Yaoi K(*contributed equally): Crystal structure and identification of a key amino acid for glucose tolerance, substrate specificity, and transglycosylation activity of metagenomic β-glucosidase Td2F2. FEBS J. 283: 2340-2353, 2016. DOI=10.1111/febs.13743.
  9. Matsuzawa T, Kimura N, Suenaga H, Yaoi K: Screening, identification, and characterization of α-xylosidase from a soil metagenome. J. Biosci. Bioeng. 122: 393-399, 2016. DOI=10.1016/j.jbiosc.2016.03.012.
  10. Matsuzawa T, Mitsuishi Y, Kameyama A, Yaoi K: Identification of the gene encoding isoprimeverose-producing oligoxyloglucan hydrolase in Aspergillus oryzae. J. Biol. Chem. 291: 5080-5087, 2016. DOI=10.1074/jbc.M115.701474.
  11. Tsujimoto Y, Saito R, Furuya H, Ishihara D, Sahara T, Kimura N, Nishino T, Tsuruoka N, Shigeri Y, Watanabe K: Caenibacillus caldisaponilyticus gen. nov., sp. nov., a thermophilic, spore-forming and phospholipid-degrading bacterium isolated from acidulocompost. Int J Syst Evol Microbiol 66:2684–2690, 2016. DOI=10.1099/ijsem.0.001108.

2015

  1. Shida Y, Yamaguchi K, Nitta M, Nakamura A, Takahashi M, Kidokoro S, Mori K, Tashio K, Kuhara S, Matsuzawa T, Yaoi K, Sakamoto Y, Tanaka N, Morikawa Y, Ogasawara W: The impact of a single-nucleotide mutation of bgl2 on cellulose induction in a Trichoderma reesei mutant. Biotechnol. Biofuels 8: 230, 2015
  2. Mori A, Hara S, Sugahara T, Kojima T, Iwasaki Y, Kawarasaki Y, Sahara T, Ohgiya S, Nakano H: Signal peptide optimization tool for the secretion of recombinant protein from Saccharomyces cerevisiae. J Biosci Bioeng 120:518–525, 2015.
  3. Matsuzawa T, Kaneko S, Yaoi K: Screening, identification, and characterization of a GH43 family β-xylosidase/α-arabinofuranosidase from a compost microbial metagenome. Appl. Microbiol. Biotechnol. 99: 8943-8954, 2015
  4. Matsuzawa T, Koike H, Saika A, Fukuoka T, Sato S, Habe H, Kitamoto D, Morita T: Draft genome sequence of the yeast Starmerella bombicola NBRC10243, a producer of sophorolipids, glycolipid biosurfactants. Genome announcements, 3: e00176-15, 2015
  5. Uchiyama T, Yaoi K, Miyazaki K: Glucose-tolerant β-glucosidase retrieved from a Kusaya gravy metagenome. Front. Microbiol. 6: 548, 2015
  6. Suenaga H, Yamazoe A, Hosoyama A, Kimura N, Hirose J, Watanabe T, Fujihara H, Futagami T, Goto M, and Furukawa K: Draft genome sequence of the polychlorinated biphenyl-degrading bacterium Pseudomonas putida KF703 (NBRC 110666). Genome Announcement 3:e00142. 2015
  7. Suenaga H, Yamazoe A, Hosoyama A, Kimura N, Hirose J, Watanabe T, Fujihara H, Futagami T, Goto M, and Furukawa K: Draft genome sequence of the polychlorinated biphenyl-degrading bacterium Cupriavidus bacilensis KF708 (NBRC 110671). Genome Announcement 3:e00143. 2015
  8. Wongwarangkana C, Fujimori KE, Akiba M, Kinoshita S, Teruya M, Nezuo M, Tsukahara M, Watabe S and Asakawa S: Deep sequencing, profiling and detailed annotation of microRNAs in Takifugu rubripes. BMC Genomics 16:457, 2015
  9. Watanabe T, Suzuki K, Sato I, Morita T, Koike H, Shinozaki Y, Ueda H, Koitabashi M, Kitamoto H: Simultaneous bioethanol distillery wastewater treatment and xylanase production by the phyllosphere yeast Pseudozyma antarctica GB-4 (0). AMB Express 5: 121-121, 2015
  10. Fujii T, Koike H, Sawayama S, Yano S, Inoue H: Draft genome sequence of Talaromyces cellulolyticus Y-94, a source of lignocellulosic biomass-degrading enzymes. Genome announcements, 3: e00014-15, 2015
  11. Tamano K, Bruno KS, Koike H, Ishii T, Miura A, Umemura M, Baker SE, Machida M: Increased production of fatty acids by deletion of one of the six predicted acyl-CoA synthetases in Aspergillus oryzae. Appl. Microbiol. Biotech. 99: 3103-3113, 2015
  12. Tuomivaara ST, Yaoi K, O’Neill MA, York WS: Generation and structural validation of a library of diverse xyloglucan-derived oligosaccharides, including an update on xyloglucan nomenclature. Carbohydr. Res. 402: 56-66, 2015.

2014

  1. Makino M, Sahara T, Morita N, Ueno H: Amino acid substitution reveals the role of V-shape helix on construction of yeast carboxypeptidase Y. J. Biol. Macromol. 14: 27-41, 2014. DOI=10.14533/jbm.14.27.
  2. Sahara T, Fujimori KE, Nezuo M, Tsukahara M, Tochigi Y, Ohgiya S, Tang Y-Q, Kida K, Taguchi H, Akamatsu T, Kamagata Y: Draft Genome Sequence of Saccharomyces cerevisiae NAM34-4C, a Lactic Acid-Assimilating Industrial Yeast Strain. Genome Announc 2:e01145–13–e01145–13, 2014. DOI=10.1128/genomeA.01145-13.
  3. Sahara T, Fujimori KE, Nezuo M, Tsukahara M, Tochigi Y, Ohgiya S, Kamagata Y.: Draft Genome Sequence of Saccharomyces cerevisiae IR-2, a Useful Industrial Strain for Highly Efficient Production of Bioethanol. Genome Announc 2:e01160–13–e01160–13, 2014. DOI=10.1128/genomeA.01160-13.
  4. Suenaga H, Mizuta S, Miyazaki K, Yaoi K: Diversity of extradiol dioxygenases in aromatic-degrading microbial community explored using both culture-dependent and culture-independent approaches. FEMS Microbiol Ecol 90: 367-379, 2014. DOI=10.1111/1574-6941.12390.
  5. Matsuzawa T, Saito Y, Yaoi K: Key amino acid residues for the endo-processive activity of GH74 xyloglucanase. FEBS Lett. 588(9): 1731-1738, 2014. DOI=10.1016/j.febslet.2014.03.023.
  6. Morita T, Koike H, Hagiwara H, Ito E, Machida M, Sato S, Habe H, Kitamoto D: Genome and Transcriptome Analysis of the Basidiomycetous Yeast Pseudozyma antarctica Producing Extracellular Glycolipids. Mannosylerythritol Lipids. PLoS ONE 9:e86490, 2014. DOI=10.1371/journal.pone.0086490.
  7. Takeda I, Tamano K, Yamane N, Ishii T, Miura A, Umemura M, Terai G, Baker SE, Koike H, Machida M: Genome sequence of the mucoromycotina fungus Umbelopsis isabellina. an effective producer of lipids. Genome announcements 2: e00071-14, 2014. DOI=10.1128/genomeA.00071-14.
  8. Umemura M, Koike H, Nagano N, Ishii T, Kawano J, Yamane N, Kozone I, Horimoto K, Shin-ya K, Asai K, Yu J, Bennett JW, Machida M, MIDDAS-M: Motif-independent De novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data. PLoS ONE 8:e84082, 2014. DOI=10.1371/journal.pone.0084028.
  9. Umemura M, Nagano N, Koike H, Kawano J, Ishii T, Miyamura Y, Kikuchi M, Tamano K, Yu J, Shin-ya K, Machida M: Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus. Fungal Genet Biol. 68:23-30, 2014. DOI=10.1016/j.fgb.2014.04.011.
  10. Takeda I, Umemura M, Koike H, Asai K, Machida M: Motif-independent prediction of a secondary metabolism gene cluster using comparative genomics: Application to sequenced genomes of Aspergillus and ten other filamentous fungal species. DNA Research 21: dsu010, 2014. DOI=10.1093/dnares/dsu010.
  11. Saika A, Koike H, Hori T, Fukuoka T, Sato S, Habe H, Kitamoto D, Morita T: Draft genome sequence of the yeast Pseudozyma antarctica type strain JCM10317, a producer of the glycolipid biosurfactants, mannosylerythritol lipids. Genome announcements 2: e00878-14, 2014. DOI=10.1128/genomeA.00878-14.
  12. Koike H, Aerts A, LaButti K, Grigoriev IV, Baker SE: Comparative genomics analysis of Trichoderma reesei strains. Industrial Biotechnology 9: 352-367, 2014. DOI=10.1089/ind.2013.0015.

2013

  1. Okuda, T., Fukui, A., and Morita, N: Altered expression of O-GlcNAc-modified proteins in a mouse model whose glycemic status is controlled by a low carbohydrate ketogenic diet. Glycoconj. J. 30, 781-789, 2013. DOI=10.1007/s10719-013-9482-x.
  2. Yoshida K, Sakamoto S, Kawai T, Kobayashi Y, Sato K, Ichinose Y, Yaoi K, Akiyoshi-Endo M, Sato H, Takamizo T, Ohme-Takagi M, Mitsuda N: Engineering the Oryza sativa cell wall with rice NAC transcription factors regulating secondary wall formation. Frontiers in Plant Biotechnology 4：Article 383, 2013. DOI=10.3389/fpls.2013.00383.
  3. Sato S, Umemura M, Koike H, Habe H: Draft genome sequence of Gluconobacter frateurii NBRC 103465, a glyceric acid-producing strain. Genome Announcements 1:e00369-13, 2013. DOI=10.1128/genomeA.00369-13.
  4. Morita T, Koike H, Koyama Y, Hagiwara H, Ito E, Fukuoka T, Imura T, Machida M, Kitamoto D: Genome sequence of the basidiomycetous yeast Pseudozyma antarctica T-34, a producer of the glycolipid biosurfactants, mannosylerythritol lipids. Genome Announcements 1:e0006413, 2013. DOI=10.1128/genomeA.00064-13.
  5. Tamano K, Bruno KS, Karagiosis SA, Culley DE, Deng S, Collett JR, Umemura M, Koike H, Baker SE, Machida M: Increased production of fatty acids and triglycerides in Aspergillus oryzae by enhancing expressions of fatty acid synthesis-related genes. Appl Microbiol Biotech 97: 269-281, 2013. DOI=10.1007/s00253-012-4193-y.
  6. Umemura M, Koyama Y, Takeda I, Hagiwara H, Ikegami T, Koike H, Machida M: Fine De novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40. PLOS One 8: e63673, 2013. DOI=10.1371/journal.pone.0063673.
  7. Uchiyama T, Miyazaki K, Yaoi K: Characterization of a Novel β-Glucosidase from a Compost microbial metagenome with strong transglycosylation activity. J Biol Chem, 288: 18325-18334, 2013. DOI=10.1074/jbc.M113.471342.

2012

  1. Okuda, T., and Morita, N: A very low carbohydrate ketogenic diet prevents the progression of hepatic steatosis caused by hyperglycemia in a juvenile obese mouse model. Nutr. Diabetes 2, e50, 2012. DOI=10.1038/nutd.2012.24.
  2. Umemura M, Koike H, Yamane N, Koyama Y, Satou Y, Kikuzato I, Teruya M, Tsukahara M, Imada Y, Wachi Y, Miwa Y, Yano S, Tamano K, Kawarabayasi Y, Fujimori KE, Machida M, Hirano T.: Comparative genome analysis between Aspergillus oryzae strains reveals close relationship between sites of mutation localization and regions of highly divergent genes among Aspergillus species. DNA RESEARCH 19: 375-382, 2012. DOI=10.1093/dnares/dss019.
  3. Ichinose H, Araki Y, Michikawa M, Harazono K, Yaoi K, Karita S, Kaneko S: Characterization of an endo-processive type xyloglucanase having β-1,4-glucan binding module and an endo-type xyloglucanase from Streptomyces avermitilis. Appl Environ Microbiol 78: 7939-7945, 2012. DOI=10.1128/AEM.01762-12.
  4. Fujimori KE, Hazama K, Kawasaki T, Deguchi T, Yuba S: Intergenic region between TATA-box binding protein and proteasome subunit C3 genes of Medaka function as the bidirectional promoter in vitro and in vivo. Gene 511: 177-186, 2012. DOI=10.1016/j.gene.2012.09.077.
  5. Mie Y, Kowata K, Kojima N, Komatsu Y: Electrochemical properties of interstrand cross-linked DNA duplexes labeled with nile blue. Langmuir 28: 17211-17216, 2012. DOI=10.1021/la3036538.
  6. Deguchi T, Fujimori KE, Kawasaki T, Maruyama K, Yuba S: In vivo visualization of the lymphatic vessels in pFLT4-EGFP transgenic medaka. Genesis 50: 625-634, 2012. DOI=10.1002/dvg.22018.
  7. Yaoi K, Miyazaki K: Cloning and expression of isoprimeverose-producing oligoxyloglucan hydrolase from actinomycetes species, Oerskovia sp. Y1. J Appl Glycosci 59: 83-88, 2012. DOI=10.5458/jag.jag.JAG-2011_023.
  8. Ichikawa K, Kojima N, Hirano Y, Takebayashi T, Kowata K, Komatsu Y: Interstrand cross-link of DNA by covalently linking a pair of abasic sites. Chem Commun 48:2143-2145, 2012. DOI=10.1039/c2cc16785a.
  9. Mie Y, Kojima N, Kowata K, Komatsu Y: End-tether structure of DNA alters electron-transfer pathway of redox-labeled oligo-DNA duplex at electrode surface. Chem Lett 41:62-64, 2012. DOI=10.1246/cl.2012.62.

2011

  1. Marui J, Yamane N, Ohashi-Kunihiro S, Ando T, Terabayashi Y, Sano M, Ohashi S, Ohshima E, Tachibana K, Higa Y, Nishimura M, Koike H, Machida M: Kojic acid biosynthesis in Aspergillus oryzae is regulated by a Zn(II)2Cys6 transcriptional activator and induced by kojic acid at the transcriptional level. J Biosci Bioeng. 112:40-3, 2011. DOI=10.1016/j.jbiosc.2011.03.010.
  2. Terabayashi Y, Morita K, Park JY, Saito S, Shiina T, Inoko H, Ishiwata I, Fujimori KE, Hirano T: Construction of Japanese BAC library Yamato-2 (JY2): A set of 330K clone resources of damage-minimized DNA taken from a genetically established Japanese individual. Hum Cell. 24: 135-145, 2011. DOI=10.1007/s13577-011-0019-y.
  3. Fujii R, Minami A, Tsukagoshi T, Sato N, Sahara T, Ohgiya S, Gomi K, Oikawa H: Total biosynthesis of diterpene aphidicolin, a specific inhibitor of DNA polymerase alpha: Heterologous expression of four biosynthetic genes in Aspergillus oryzae. Biosci Biotechnol Biochem 75:1813-1817, 2011. DOI=10.1271/bbb.110366 .
  4. Kojima N, Komatsu Y: Development of novel chemical reagents for reliable genetic analyses. Synthesiology English Ed.4: 1-8, 2011. DOI=10.1021/acssynbio.0c00082.

2010

  1. Okuda, T., Nakakita, S. I., and Nakayama, K: Structural characterization and dynamics of globotetraosylceramide in vascular endothelial cells under TNF-alpha stimulation. Glycoconj. J. 27, 287-296, 2010. DOI=10.1007/s10719-009-9277-2.
  2. Marui J, Ohashi-Kunihiro S, Ando T, Nishimura M, Koike H, Machida M: Penicillin biosynthesis in Aspergillus oryzae and its overproduction by genetic engineering. J Biosci Bioeng. 110:8-11, 2010. DOI=10.1016/j.jbiosc.2010.01.001.
  3. Terabayashi Y, Sano M, Yamane N, Marui J, Tamano K, Sagara J, Dohmoto M, Oda K, Ohshima E, Tachibana K, Higa Y, Ohashi S, Koike H, Machida M: Identification and characterization of genes responsible for biosynthesis of kojic acid, an industrially important compound from Aspergillus oryzae. Fungal Genet Biol. 47:953-61, 2010. DOI=10.1016/j.fgb.2010.08.014.
  4. Tochigi Y, Sato N, Sahara T, Wu C, Saito S, Irie T, Fujibuchi W, Goda T, Yamaji R, Ogawa M, Ohmiya Y, Ohgiya S: A sensitive and convenient yeast reporter assay for high-throughput analysis by using a secretory luciferase from Cypridina noctiluca. Analy Chemistry 82:5768-5776, 2010. DOI=10.1021/ac100832b.
  5. Marui J, Yoshimi A, Hagiwara D, Fujii-Watanabe Y, Oda K, Koike H, Tamano K, Ishii T, Sano M, Machida M, Abe K: Use of the Aspergillus oryzae actin gene promoter in a novel reporter system for exploring antifungal compounds and their target genes. Appl Microbiol Biotechnol. 87:1829-40, 2010. DOI=10.1007/s00253-010-2627-y.
  6. Oda S, Mikami S, Urushihara U, Murata Y, Deguchi T, Kamei Y, Kitano T, Fujimori K, Yuba S, Todo T, Mitani H: Identification of a Functional Medaka Heat Shock Promoter and Characterization of Its Ability to Induce Exogenous Gene Expression in Medaka in vitro and in vivo. Zool Sci 27:410-415, 2010. DOI=10.2108/zsj.27.410.
  7. Kato Y, Ota K, Hidano Y, Azuma Y, Onaka T, Yaoi K, Mitsuishi Y: Further structural study of the xyloglucanase-derived eggplant xyloglucan oligo-saccharides. J Appl Glycosci 54: 265-268, 2010. DOI=10.5458/jag.57.265.
  8. Suenaga H, Nonaka K, Fujihara H, Goto M, Furukawa K: Hybrid pseudomonads engineered by two-step homologous recombination acquire novel degradation abilities toward aromatics and polychlorinated biphenyls. Appl Microbiol Biotechnol 88: 915-923, 2010. DOI=10.1007/s00253-010-2840-8.

2009

  1. Kawashima, N., Tsuji, D., Okuda, T., Itoh, K. and Nakayama, K: Mechanism of abnormal growth in astrocytes derived from a mouse model of GM2 gangliosidosis. J. Neurochem. 111, 1031-1041, 2009
  2. Anas, A., Okuda, T., Kawashima, N., Nakayama, K., Itoh, T., Ishikawa, M. and Biju, V: Clathrin-Mediated Endocytosis of Quantum DotPeptide Conjugates in Living Cells. ACS Nano. 3, 2419-2429, 2009
  3. Okuda, T., Furukawa, K. and Nakayama, K: A novel, promoter-based, target specific assay identifies 2-deoxy-d-glucose as an inhibitor of the globotriaosylceramide biosynthesis. FEBS J. 276, 5191-5202, 2009
  4. Fujimori KE: Characterization of the regulatory region of the dopa decarboxylase gene in Medaka: an in vivo green fluorescent protein reporter assay combined with a simple TA-cloning method. Mol Biotech 41:224-235 , 2009
  5. Itoh J, Suyama M, Imamura Y, Deguchi T, Fujimori K, Yuba S, Kawarahayasi Y, Kawasaki T: Functional and comparative genomics analyses of pmp22 in medaka fish. BMC Neurosci 10:60, 2009
  6. Kamei Y, Suzuki M, Watanabe K, Fujimori K, Kawasaki T, Deguchi T, Yoneda Y, Todo T, Takagi S, Funatsu T, Yuba S: Infrared laser-mediated gene induction in targeted single cells in vivo, Nature Methods 6:79-81, 2009
  7. Deguchi T, Fujimori K.E. Kawasaki T., Ohgushi H., Yuba S.: Molecular cloning and gene expression of the prox1a and prox1b genes in the medaka Oryzias latipes. Gene Exp Patterns 9:341-347, 2009
  8. Deguchi T, Fujimori KE, Takashi K, Ohgushi H: Expression patterns of the Egr1 and Egr3 genes during medaka embryonic development. Gene Exp Patterns 9:209-214, 2009
  9. Yaoi K, Kondo H, Hiyoshi A, Noro N, Sugimoto H, Tsuda S, Miyazaki K: The crystal structure of a xyloglucan-specific endo-β-1,4-glucanase from Geotrichum sp. M128 xyloglucanase reveals a key amino acid residue for substrate specificity. FEBS J 276: 5094-5100, 2009
  10. Kojima N, Takebayashi T, Mikami A, Ohtsuka E, Komatsu Y: Construction of highly reactive probes for abasic site detection by introduction of an aromatic and a guanidine residue into an aminooxy group. J Am Chem Soc 131:13208-13209, 2009
  11. Kojima N, Takebayashi T, Mikami A, Ohtsuka E, Komatsu Y: Efficient synthesis of oligonucleotide conjugates on solid-support using an (aminoethoxycarbonyl)aminohexyl group for 5′-terminal modification. Bioorg Med Chem Lett19:2144-2147, 2009
  12. Kojima N, Takebayashi T, Mikami A, Ohtsuka E, Komatsu Y: Development of novel chemical probes to detect abasic sites in DNA. Nucleic Acids Symp Ser 53:45-46, 2009
  13. Suenaga H, Mizuta S, Miyazaki K: The molecular basis for adaptive evolution in novel extradiol dioxygenases retrieved from the metagenome. FEMS Microbiol Ecol 69: 472-480, 2009
  14. Suenaga H, Koyama Y, Miyakoshi M, Miyazaki R, Yano H, Sota M, Ohtsubo Y, Tsuda M, Miyazaki M: Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis. ISME J 3: 1335-1348, 2009

2008

  1. Okuda, T. and Nakayama, K: Identification and characterization of the human Gb3/CD77 synthase gene promoter. Glycobiology 18, 1028-1035, 2008
  2. Tamano K, Sano M, Yamane N, Terabayashi Y, Toda T, Sunagawa M, Koike H, Hatamoto O, Umitsuki G, Takahashi T, Koyama Y, Asai R, Abe K, Machida M.: Transcriptional regulation of genes on the non-syntenic blocks of Aspergillus oryzae and its functional relationship to solid-state cultivation. Fungal Genet Biol. 45:139-51, 2008
  3. Kawasaki T, Saito K, Deguchi T, Fujimori KE, Tadokoro M, Yuba S, Ohgushi H, Kawarabayasi Y: Pharmacological characterization of isoproterenol-treated medaka fish. Pharmacol Res 58:348-355, 2008
  4. Fujimori KE, Kawasaki T, Deguchi T, Yuba S: Characterization of a nervous system-specific promoter for growth-associated protein 43 in Medaka (Oryzias latipes). Brain Res 1245:1-15, 2008
  5. MinSun K, Okuyama M, Yaoi K, Mitsuishi Y, Kim YM, Mori H, Kimura A: Glycoside hydrolase family 31 Escherichia coli α-xylosidase. Biocat Biotransform 26: 96-103, 2008
  6. Yamamoto S, Sahara T, Sato D, Kawasaki K, Ohgiya S, Inoue A, Ojima T: Catalytically important amino acid residues of abalone alginate lyase HdAly assessed by site-directed mutagenesis. Enzyme and Microbial Biotechnology 43:396-402, 2008
  7. Komatsu Y, Kojima N, Sugino M, Mikami A, Nonaka K, Fujinawa Y, Sugimoto T, Sato K, Matsubara K, Ohtsuka E: Novel amino linkers enabling efficient labeling and convenient purification of amino-modified oligonucleotides. Bioor Med Chem 16:941-949, 2008
  8. Kojima N, Takebayashi T, Mikami A, Sugino M, Ohtsuka E, Komatsu Y: Comparison of the chemical properties of a novel amino-linker with various amino modifications. Nucleic Acids Symp Ser52:463-464, 2008
  9. Komatsu Y, Kojima N, Takebayashi T, Mikami A, Sugino M, Ohtsuka E: Construction of an aminooxy derivative for RNA and DNA labeling. Nucleic Acids Symp Ser 52:393-394, 2008
  10. Mori T, Suenaga H, Miyazaki K: Metagenomic Approach to the Identification of UDP-Glucose 4-Epimerase as a Menadione Resistant Protein. Biosci Biotechnol Biochem 72: 1611-1614, 2008
  11. Mori T, Mizuta S, Suenaga H, Miyazaki K: Metagenomic screening for bleomycin resistance genes. Appl Environ Microbiol 74: 6803-6805. 2008

2007

  1. Furukawa, K., Tajima, O., Okuda, T., Tokuda, N., and Furukawa, K: Knockout mice and glycolipids. COMPREHENSIVE GLYCOSCIENCE 4, 149-157, 2007.
  2. Okamura H, Yokoyama K, Koike H, Yamada M, Shimowasa A, Kabasawa M, Kawashima T, Suzuki M: A structural dode for discriminating between transcription signals revealed by the Feast/Famine regulatory protein DM1 in complex with ligands. Structure 15:1325-38, 2007
  3. Yokoyama K, Ishijima SA, Koike H, Kurihara C, Shimowasa A, Kabasawa M, Kawashima T, Suzuki M: Feast/Famine regulation by transcription factor FL11 for the survival of the hperthermophilic archaeon Pyrococcus OT3.  Structure 15:1542-54, 2007
  4. MinSunK, Okuyama M, Yaoi K, Mitsuishi Y, Kim YM, Mori H, Kimura A: Aglycone specificity of Escherichia coli α-xylosidase investigated by transxylosylation. FEBS J 274: 6074-6084，2007
  5. Ishida T, Yaoi K, Hiyoshi A, Igarashi K, Samejima M: Substrate recognition by glycoside hydrolase family 74 xyloglucanase from the basidiomycete Phanerochaete chrysosporium. FEBS J 274: 5727-5736，2007
  6. Yaoi K, Kondo H, Hiyoshi A, Noro N, Sugimoto H, Tsuda S, Mitsuishi Y, Miyazaki K: The structural basis for the exo-mode of action in GH74 oligoxyloglucan reducing end-specific cellobiohydrolase. J Mol Biol 370: 53-62, 2007
  7. Ishikawa H, Hoshino Y, Motoki Y, Kawahara T, Kitajima M, Kitami M, Watanabe A, Bravo A, Soberon M, Honda A, Yaoi K, Sato R: A system for the directed evolution of the insecticidal protein from Bacillus thuringiensis. Mol Biotechnol 36: 90-101，2007
  8. Yaoi K, Hiyoshi A, Mitsuishi Y: Screening, Purification, and Characterization of a Prokaryotic Isoprimeverose-producing Oligoxyloglucan Hydrolase from Oerskovia sp. Y1. J Appl Glycosci 54: 91-94, 2007
  9. Suenaga H, Ohnuki T, Miyazaki K: Functional Screening of metagenomic library for genes involved in microbial degradation of aromatic compounds. Environ Microbiol 9: 2289-2297, 2007

総説

  1. 沓掛磨也子, 植松圭吾, 深津武馬: ゴールで生活するアブラムシの安全快適な住まいづくりと社会生活, 植物科学最前線 12: 80-88, 2021. DOI=10.24480/bsj-review.12b2.00203.
  2. Matsuzawa T, Watanabe A, Shintani T, Gomi K, Yaoi K: Enzymatic degradation of xyloglucans by Aspergillus species: a comparative view of this genus. Appl Microbiol Biotechnol 105:2701-2711, 2021. DOI=10.1007/s00253-021-11236-8.
  3. Okuda T: Application of the antibody-inducing activity of glycosphingolipids to human diseases. Int J Mol Sci 22: 3776, 2021. DOI=10.3390/ijms22073776.
  4. 加藤且也, 北村昌大, 永田 夫久江, 李誠鎬, 奥田徹哉, 平野篤, 笠原真二郎: 抗体医薬製造のコスト低減に向けて─多孔質ジルコニアによる簡便な抗体精製法の開発─. セラミックス 56: 244-247, 2021.
  5. Takaku H, Matsuzawa T, Yaoi K, Yamazaki H: Lipid metabolism of the oleaginous yeast Lipomyces starkeyi. Appl Microbiol Biotechnol 104:6141-6148, 2020. DOI=10.1007/s00253-020-10695-9.
  6. Okuda T: Dietary Control of Ganglioside Expression in Mammalian Tissues. Int J Mol Sci 21: 177, 2020
  7. Matsuzawa T: The metagenome approach: a new resource for glycosidase. Trends Glycosci. Glycotechnol., 31, 15-20, 2019
  8. Saika A, Koike H, Fukuoka T, Morita T: Tailor-made mannosylerythritol lipids: current state and perspectives. Appl. Microbiol. Biotechnol. 102(16): 6877-6884, 2018
  9. Watanabe M*, Matsuzawa T*, Yaoi K(*equal contribution): Rational protein design for thermostabilization of glycoside hydrolases based on structural analysis. Appl. Microbiol. Biotechnol., 102, 8677-8684, 2018
  10. Okuda T: Design of Carrier Molecules Suitable for Inducing Immunity to Oligosaccharide Antigens: Application to Anti-Glycoprotein Monoclonal Antibodies. Trends Glycosci. Glycotechnol., 30(175), E113-E116, 2018
  11. 奥田徹哉：オリゴ糖の免疫原性増強に適したキャリア分子の開発と糖タンパク質認識抗体獲得への応用、Trends Glycosci. Glycotechnol., 30(175), J87-J90, 2018
  12. 松沢智彦： 培養法とメタゲノム方によるユニークな新規糖質加水分解酵素の単離と解析、応用糖質科学（日本応用糖質科学会）, 8, 206-210, 2018
  13. 松沢智彦、木村信忠、末永光： メタゲノムを利用した有用酵素の探索、応用糖質科学（日本応用糖質科学会）, 8, 164-167, 2018
  14. 矢追克郎： メタゲノムについて、応用糖質科学、日本応用糖質科学会、2018年第8巻第1号, pp.76-76
  15. 雜賀 あずさ、小池 英明、福岡 徳馬、森田 友岳：Tailor-made mannosylerythritol lipids: current state and perspectives. Appl. Microbiol. Biotechnol. 102(16): 6877-6884, 2018
  16. 佐藤 由也、小池 英明：メタトランスクリプトーム解析：RNA-seqで環境を診る. 生物工学会誌. 96: 403-407, 2018
  17. Matsuzawa T, Yaoi K: GH74 xyloglucanases: Structures and modes of activity. Trends in Glycoscience and Glycotechnology, 28:E63-E70, 2016
  18. Umemura M, Koike H, Machida M: Motif-independent de novo detection of secondary metabolite gene clusters–toward identification from filamentous fungi. Frontiers in microbiology 6: 371, 2015
  19. 末永光：メタゲノム手法は微生物培養法を凌駕するのか？（未開拓遺伝子資源アクセスツールとしてのパフォーマンス比較）、化学と生物（日本農芸化学会誌）、53：488-490、2015
  20. 末永光、小山芳典：たかがアセンブリ？―次世代シーケンス解析はじめの一歩―、生物工学会誌、92：28、2014
  21. 矢追克郎: キシログルカンとそのオリゴ糖、応用糖質科学（日本応用糖質科学会誌）2: 185-190、2012
  22. 小池 英明：糸状菌ゲノム解析への招待（２）、日本菌学会会報　53： 43-46、2012
  23. 小池英明、町田雅之：ゲノム科学に基づくコウジ酸生合成遺伝子の解明、バイオサイエンスとインダストリー 70-3:206-208、2012
  24. Suenaga H: Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities. Environ. Microbiol. 14: 13-22, 2012
  25. 扇谷悟、佐原健彦、栃木裕貴、佐藤なつ子、呉純、近江谷克裕：（2011）：産業技術総合研究所における酵母を用いた研究の事例　－発現系・レポーターアッセイの実用化，組換え体の安全管理－　生物工学会誌 89, 539-543. 2011.
  26. 小池 英明：糸状菌ゲノム解析への招待（１）、日本菌学会会報，52，75-81、2011
  27. 末永光、宮崎健太郎：メタゲノム解析により明らかにされた環境中の芳香族化合物分解遺伝子の姿、化学と生物（日本農芸化学会誌）、48：100-106、 2010
  28. 伊藤公夫、末永光、宮崎健太郎、中村和憲：メタゲノム解析を利用した安水含有フェノール分解関連酵素の解明、用水と廃水、51：65-70、2009
  29. 藤森 一浩、平野 隆：次世代シーケンサー～その技術と拓く未来～、応用物理学会誌，78-12，1103-111, 2009
  30. 西村麻里江、町田 雅之、小池 英明：糸状菌ゲノム解析のインパクト、化学と生物，46-1， 32-40、2008
  31. 末永光、宮崎健太郎：酵素スクリーニングの新技術―メタゲノム解析の意義と課題―、生化学（日本生化学会誌）、80：666-669、2008
  32. 佐原健彦、扇谷悟：出芽酵母における低温条件を利用した蛋白質生産　バイオサイエンスとインダストリー 65, 130-131. 2007.
  33. 奥田徹哉、徳田典代、古川圭子、古川鋼一：細菌毒素と糖脂質受容体：O157感染を中心に. 実験医学増刊号 25, 949-953, 2007

著書

  1. スマートセルインダストリー、シームシー出版、2018/06/20
  2. 植物細胞壁実験法、キシログルカン分解酵素の活性測定、弘前大学出版会、2016/02/24
  3. Suenaga H, and Miyazaki K: Extradiol dioxygenases retrieved from the metagenome. Encyclopedia of Metagenomics. SpringerReference: Springer-Verlag GmbH, 2014
  4. 小池 英明、町田 雅之：菌類の事典，「基礎編13.1：ゲノム」「基礎編13.3.1：核内遺伝子」「基礎編13.5.10：二次代謝産物合成にかかわる遺伝子」，朝倉書店、2013
  5. Kojima N, Komatsu Y: Synthesis and application of highly reactive amino linkers for functional oligonucleotides. Current Protocols in Nucleic Acid Chemistry, Unit 4.48. 1-23, Egli M, Herdewijn P, Matsuda A, Sanghvi YS eds., John Wiley & Sons, Ltd., 2012
  6. 奥田徹哉、近江谷克裕：抗体の標識／修飾 – 酵素標識 – 　 新機能抗体開発ハンドブック(浜窪隆雄監修)　（株）エヌ・ティー・エス、205-208, 2012
  7. 小池 英明、町田 雅之：発酵・醸造食品の最新技術と機能性Ⅱ，第20章 コウジ酸の生合成遺伝子,麹菌培養条件に応答した遺伝子発現機構，シーエムシー出版、2011
  8. 古川鋼一、近藤裕史、奥田徹哉、古川圭子：グロボ系糖脂質欠損マウス　生物機能モデルと新しいリソース・リサーチツール　Seriesモデル動物利用マニュアル（小幡裕一、城石俊彦編集）　（株）エル・アイ・シー、311-313, 2011
  9. Kojima N, Komatsu Y: Hydroxylamine, oxime and hydroxamic acid derivatives of nucleic acids. The chemistry of hydroxylamines, oximes and hydroxamic acids, Vol. 2, Chap. 13. Rappoport, Z, Liebman JF eds., John Wiley & Sons, Ltd., 807-851, 2010
  10. 藤森 一浩、河原林 裕：もっと知りたいPCR実験（塩基配列決定とPCR）, 講談社サイエンティフィク, 2010
  11. 末永光、宮崎健太郎：芳香族化合物分解酵素、酵素利用技術体系, エヌ・ティー・エス, 2010
  12. Suenaga H, Miyazaki K: Exploration of a microbial community for novel genetic resources using activity-based screening of a metagenomic library. Metagenomics and its Applications in Agriculture, Biomedicine and Environmental studies. Nova Science Publishers, Inc., 2010
  13. Suenaga H, Kanagawa T, Miyazaki K: A culture-independent novel approach to the monitoring of the activity and stability of activated sludge in wastewater treatment. Sludge: Types, Treatment Processes and Disposal. Nova Science Publishers, Inc., 2009

特許

国内

  1. 特許6697780号:ストレス応答プロモーター(藤森 一浩、小林 洋介、佐原 健彦、扇谷 悟、鎌形 洋一)2020/4/30登録
  2. 特願2018-148011:キシロースを優先的に利用するためのキシロース輸送タンパク質変異体とその利用(藤森 一浩、佐原 健彦、扇谷 悟、鎌形 洋一)2018/8/6出願
  3. 特願2018-212755：変異酵母及びそれを使用したタンパク質の製造方法（森田友岳、小池英明、大前奈月、北本 宏子、鎗水透、山下結香）2018年11月13日出願
  4. 特願2018-052952（特願2017-054264 2017/03/21）：シュードザイマ・アンタクティカの新規菌株（森田友岳、小池英明、北本 宏子、鈴木 健、鎗水 透、山下 結香、渡部 貴志）2018年3月20日出願
  5. 特許6486440号（登録）：真菌由来のリボソームペプチドを製造する方法（長野希美、梅村舞子、小池英明、新家一男、町田雅之、熊谷 俊高）2017年10月10日出願
  6. 特許6172687号：シアリル化糖鎖を認識するモノクローナル抗体（奥田徹哉）2017年7月14日登録
  7. 特許6143240号：糖鎖抗原の免疫誘導剤（奥田徹哉、清水弘樹）2017年5月19日登録
  8. 特願2017-006497（優先出願：特願2016-076125）：生成物阻害耐性および基質阻害耐性を有するβ－グルコシダーゼ、それをコードする遺伝子（松沢智彦、渡邊真宏、矢追克郎）2017年1月18日出願
  9. 特願2017-008703：ＭＥＬ－Ｄの製造方法，（森田友岳、雜賀あずさ、福岡徳馬、小池英明、北本大、山本周平、岸本高英）2017/01/20出願
  10. 特願2016-076125：生成物阻害耐性および基質阻害耐性を有するβ－グルコシダーゼ、それをコードする遺伝子（松沢智彦、矢追克郎）2016年4月15日出願
  11. 特願2016-191438：モノアシル型ＭＥＬ（森田友岳、雜賀あずさ、福岡徳馬、小池英明、北本大、山本周平、岸本高英）2016年9月29日出願
  12. 特願2016-140286（優先権出願、特願2015-142214）：タンパク質発現用塩基配列及びそれを用いるタンパク質の製造方法（町田雅之、小池英明、國永万保子、萩原央子、光澤 茂信、新川 智、田中 麻衣子）2016年7月15日出願
  13. 特願2016-131142：含油廃水処理方法およびそれを用いた処理装置（佐藤由也、小池英明、堀知行、稲葉知大、尾形敦、羽部浩）2016年6月30日出願
  14. 特許5946149号：二次代謝系遺伝子を含む遺伝子クラスタの予測方法、予測プログラム及び予測装置（町田雅之、梅村舞子、小池英明、竹田至）2016年6月10日登録
  15. 特願2016-112087：バイオサーファクタント産生組み換え微生物（森田友岳、雜賀あずさ、小池英明、福岡徳馬、北本大、山本周平、岸本高英）2016年6月3日出願
  16. 特許6483916号：変異型キシロース代謝酵素とその利用（清家泰介、藤森一浩、小林洋介、佐原健彦、扇谷悟、鎌形洋一）2019年2月22日登録
  17. 特願2015-092216：耐熱性を有するキシラナーゼ（矢追克郎、松沢智彦）2015年4月28日出願
  18. 特許6156770号：キシロースの発酵能が強化された酵母とその利用（扇谷 悟、鎌形 洋一、藤森 一浩、佐原 健彦、赤松 隆、田口久貴）2017年6月16日登録
  19. 特許5598875号：排水中のカテコールの分解方法（末永光、宮崎健太郎、中村和憲、伊藤公夫）2014年8月登録
  20. 特許5578598号：新規な芳香環水酸化酵素及びその遺伝子（末永光、宮崎健太郎）2014年07日登録
  21. 特願2015-514756：糖鎖抗原の免疫誘導剤（奥田徹哉、清水弘樹）2014年5月2日出願
  22. 特願2015-514757：シアリル化糖鎖を認識するモノクローナル抗体（奥田徹哉）2014年5月2日出願
  23. 特許5548999号：カテコール分解酵素および排水中のカテコールの分解方法（末永光、宮崎健太郎、中村和憲、伊藤公夫）2014年5月登録
  24. 特許5549000号：カテコール分解酵素および排水中のカテコールの分解方法（末永光、宮崎健太郎、中村和憲、伊藤公夫）2014年5月登録
  25. 特許5392681号：高濃度のグルコース耐性を有するβ－グルコシダーゼ（宮崎健太郎、矢追克郎、内山拓）2013年10月25日登録
  26. 特許5219017号：カテコール分解酵素（末永光、宮崎健太郎、中村和憲、伊藤公夫）2013年3月登録
  27. 特許5196448号：アミノオキシ基を含有する反応性化合物（小松康雄、小島直、野中謙）2013年2月15日登録
  28. 特許5131828号：新規ブレオマイシン耐性遺伝子（宮崎健太郎、末永光、小山芳典、森智夫）2012年11月登録
  29. 特許5110580号：リンパ管可視化トランスジェニックメダカ及び該メダカを用いたリンパ管新生阻害薬のスクリーニング法（出口 友則、藤森 一浩、川﨑 隆史、弓場 俊輔）2012年10月19日登録
  30. 特願2013-211811：獣毛繊維の識別用プライマーと識別方法（小池英明、山根倫子、町田雅之、吉岡陽一郎、佐野元昭）2012年9月24日出願
  31. 特許5083788号：オリゴヌクレオチドプローブ（小松康雄、小島直、野中謙、藤縄由美、橋田順也、武藤勇）2012年9月14日登録
  32. 特許5008067号：新規なイソプリメベロース生成加水分解酵素をコードする遺伝子、ならびに該酵素の製造方法（矢追克郎、三石安）2012年6月8日登録
  33. 特願2011-284851：組換え微生物（劉 生浩、五十嵐 一暁、矢追克郎、宮崎健太郎）2011年12月27日出願
  34. 特許4788942号：特定生物種検出のためのデオキシリボザイム（末永光、金川貴博）2011年07月登録
  35. 特開2011-007644：血管内皮炎症を検出するための方法及びキット（奥田徹哉）2011年1月13日公開
  36. 特許5780560号：遺伝子クラスタ及び遺伝子の探索、同定法およびそのための装置（町田雅之、小池英明、梅村舞子、浅井潔、堀本勝久、光山統泰）2015年7月24日登録
  37. 特願2010-078134：グルコース存在下で活性を増加するβ－グルコシダーゼ（宮崎健太郎、矢追克郎、内山拓）2010年3月30日出願
  38. 特許4336820号：オリゴヌクレオチドプローブ（小松康雄、小島 直、佐藤浩輔、野中 謙、藤縄由美）2009年7月10日登録
  39. 特許4332630号：酵母由来プロモーターならびにこれを用いたベクターおよび発現系（佐原健彦、扇谷悟、合田孝子、川崎公誠）2009年7月3日登録
  40. 特許5729702号：コウジ酸の産生に必須の遺伝子を利用してコウジ酸の産生量を向上する方法（町田雅之、小池英明、寺林靖宣、山根倫子、丸井淳一朗、大箸信一、佐野元昭、相良純一、織田健、北川治恵、比嘉良喬、立花國治、大島栄治）2015年4月17日登録
  41. 特許4958019号：ミトコンドリアＤＮＡ可変領域塩基配列による水産魚介類の標識および識別のための方法（平野隆、町田雅之、小池英明、添田 栄一）2012年3月30日登録
  42. 特許4122428号：新規なキシログルカン分解酵素、それをコードする遺伝子、ならびに該酵素の製造方法（矢追克郎、三石安）2008年5月16日登録
  43. 特許4096089号：骨格筋不死化細胞に由来する知覚神経軸索伸長因子（藤森 一浩、波佐間 久美子、田口 隆久）2008年03月21日登録
  44. 特許3837497号：新規なキシログルカンオリゴ糖分解酵素、それをコードする遺伝子、ならびに該酵素の製造方法（矢追克郎、三石安）2006年8月11日登録

国外

  1. 特許EP2993182B1（欧州）IMMUNITY INDUCER FOR SACCHARIDE ANTIGENS（奥田徹哉、清水弘樹） 2020年10月14日登録
  2. ストレス応答プロモーター(藤森 一浩、小林 洋介、佐原 健彦、扇谷 悟、鎌形 洋一) PCT/JP2017/030430、2017/8/24出願
  3. キシロースを優先的に利用するためのキシロース輸送タンパク質変異体とその利用(藤森 一浩、佐原 健彦、扇谷 悟、鎌形 洋一) PCT/JP2019/031003、2019/8/6出願
  4. 登録査定（米国）:変異型キシロース代謝酵素とその利用(清家 泰介、藤森 一浩、小林 洋介、佐原 健彦、扇谷 悟、鎌形 洋一)＊登録待ち
  5. 変異型キシロース代謝酵素とその利用(清家 泰介、藤森 一浩、小林 洋介、佐原 健彦、扇谷 悟、鎌形 洋一) PCT/JP2017/012104、2017/3/24出願
  6. 特開168763（タイ）:キシロースの発酵能が強化された酵母とその利用(扇谷 悟、鎌形 洋一、藤森 一浩、佐原 健彦) 2017/10/5公開
  7. 特許IDP000059924号（インドネシア）:キシロースの発酵能が強化された酵母とその利用(扇谷 悟、鎌形 洋一、藤森 一浩、佐原 健彦) 2019/6/20登録
  8. 特許EP2993184B1（欧州）MONOCLONAL ANTIBODY RECOGNIZING SIALYLATED SUGAR CHAINS （奥田徹哉） 2019年3月13日 登録
  9. 特許US10307471B2（米国） IMMUNITY INDUCER FOR SACCHARIDE ANTIGENS（奥田徹哉、清水弘樹） 2019年6月4日登録
  10. 特許10006056号（米国）：キシロースの発酵能が強化された酵母とその利用（扇谷 悟、鎌形 洋一、藤森 一浩、佐原 健彦、赤松 隆、田口久貴）2018年6月26日成立
  11. 特許9796785B2号（米国）：MONOCLONAL ANTIBODY RECOGNIZING SIALYLATED SUGAR CHAINS（奥田徹哉）2017年10月24日 登録
  12. バイオサーファクタント産生組み換え微生物（森田友岳、雜賀あずさ、小池英明、福岡徳馬、北本大、山本周平、岸本高英）PCT/JP2017/018154（WIPO）2017/05/15出願
  13. マンノース移転酵素遺伝子、組換えベクター、形質転換体、１－Ｏ－β－マンノシルエリスリトールリピッドの製造方法（森田友岳、羽部浩、北本大、小池英明、福岡徳馬、山本周平、岸本高英）PCT/JP2016/061760（WIPO）、2016年4月12日PCT出願
  14. IMMUNITY INDUCER FOR SACCHARIDE ANTIGENS（奥田徹哉、清水弘樹）14/888353 (US), 14791926.0 (EP) 2014年5月2日出願
  15. MONOCLONAL ANTIBODY RECOGNIZING SIALYLATED SUGAR CHAINS（奥田 徹哉）14/888147 (US), 14792262.9 (EP) 2014年5月2日出願
  16. アミノ化オリゴヌクレオチド用固相担体（小松康雄、小島直） PCT/JP2012/069381 (WIPO)、2013年02月21日
  17. 遺伝子クラスタ及び遺伝子の探索、同定法およびそのための装置（町田雅之、小池英明、梅村舞子、浅井潔、堀本勝久、光山統泰）PCT/JP2011/071731（WIPO）、2011年09月22日
  18. 抗菌剤の標的遺伝子の選定とその機能推定方法（町田雅之、玉野孝一、小池英明、石井智子、安藤朋広、阿部 敬悦、丸井 淳一朗、佐野 元昭、織田 健）PCT/JP2009/006455（WIPO）、2009年11月28日
  19. 特許7491857号（米国）：オリゴヌクレオチドプローブ（小松康雄、小島 直、佐藤浩輔、野中 謙、藤縄由美）2009年2月17日成立
  20. 特許7371847号（米国）：酵母由来プロモーターならびにこれを用いたベクターおよび発現系（佐原健彦、扇谷悟、合田孝子、川崎公誠）2008年5月13日成立