Bio-System Research Group
publications

    Original Papers

    2021

    1. 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.
    2. 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 LV, 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 japonicusmBio. 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. 2020, 104:2537–2544. 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 2020, 169:105816. 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. 2020, 104:201–210. 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. 2019, 286:3182–3193. 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 2019, 65:17. 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. 2019, 12:139. 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. 2019, 8 (24): e00196-19. 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
  15. 2008

  16. Okuda, T. and Nakayama, K: Identification and characterization of the human Gb3/CD77 synthase gene promoter. Glycobiology 18, 1028-1035, 2008
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. Mori T, Mizuta S, Suenaga H, Miyazaki K: Metagenomic screening for bleomycin resistance genes. Appl Environ Microbiol 74: 6803-6805. 2008
  27. 2007

  28. Furukawa, K., Tajima, O., Okuda, T., Tokuda, N., and Furukawa, K: Knockout mice and glycolipids. COMPREHENSIVE GLYCOSCIENCE 4, 149-157, 2007.
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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

    Review

  1. 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.
  2. Okuda T: Application of the antibody-inducing activity of glycosphingolipids to human diseases. Int J Mol Sci 22: 3776, 2021. DOI=10.3390/ijms22073776.
  3. 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.
  4. Okuda T: Dietary Control of Ganglioside Expression in Mammalian Tissues. Int J Mol Sci 21: 177, 2020
  5. Matsuzawa T: The metagenome approach: a new resource for glycosidase. Trends Glycosci. Glycotechnol., 31, 15-20, 2019
  6. Saika A, Koike H, Fukuoka T, Morita T: Tailor-made mannosylerythritol lipids: current state and perspectives. Appl. Microbiol. Biotechnol. 102(16): 6877-6884, 2018
  7. 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
  8. 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
  9. Matsuzawa T, Yaoi K: GH74 xyloglucanases: Structures and modes of activity. Trends in Glycoscience and Glycotechnology, 28:E63-E70.
  10. 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
  11. Suenaga H: Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities. Environ. Microbiol. 14: 13-22, 2012

Publications

  1. Suenaga H, and Miyazaki K: Extradiol dioxygenases retrieved from the metagenome. Encyclopedia of Metagenomics. SpringerReference: Springer-Verlag GmbH, 2014
  2. 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
  3. 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
  4. 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
  5. 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

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Bioproduction Research Institute

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