Details of the Researcher

PHOTO

Yutaka Tamaru
Section
Green Goals Initiative
Job title
Professor
Degree

  • Ph. D. (Mie University)

Research History 8

  • 2024/10 - Present
    Tohoku University　Graduate School of Engineering Department of Biomolecular Engineering　Professor

  • 2024/06 - Present
    Tohoku University　Green Cross-tech Research Center　Professor

  • 2024/04 - Present
    Tohoku University　Graduate School of Engineering Department of Applied Chemistry　Professor

  • 2013/07 - 2024/03
    Mie University　Graduate School of Bioresources　Professor

  • 2002/11 - 2013/06
    三重大学生物資源学部 助教授/准教授

  • 2000/07 - 2002/10
    Mie University　Faculty of Bioresources

  • 1997/04 - 2000/06
    カリフォルニア大学デービス校分子細胞生物学 リサーチ・アソシエイト

  • 2024/04 -
    Emeritus Professor

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Education 1

  • Mie University

    - 1997

Committee Memberships 4

  • 日本生物工学会北日本支部　代議員

    2024/05 - Present

  • バイオインダストリー協会　グリーン・イノベーション・フォーラム委員

    2018 - Present

  • 日本生化学会　代議員

    2019/09 - 2023/09

  • 日本生物工学会　理事・中部支部長

    2021/05 - 2023/05

Professional Memberships 7

  • 日本ゲノム編集学会

  • 日本生化学会

  • 日本薬理学会

  • 日本分子生物学会

  • アメリカ微生物学会

  • 日本生物工学会

  • 日本農芸化学会

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Research Interests 8

  • Synthetic Biology

  • Biochemistry

  • 比較機能ゲノミクス

  • システムバイオロジー

  • Biotechnology

  • Molecular Biology

  • Applied Bacteriology

  • The Utilization for Aquatic Bioresources

Research Areas 5

  • Energy / Earth resource engineering, energy science /

  • Life sciences / Marine/Aquatic life sciences /

  • Life sciences / Applied microbiology /

  • Life sciences / Molecular biology /

  • Manufacturing technology (mechanical, electrical/electronic, chemical engineering) / Applied biofunctional and bioprocess engineering /

Awards 1

  1. Emeritus Professor

    2024/04

Papers 164

  1. Proteomic Characterization of the Clostridium cellulovorans Cellulosome and Noncellulosomal Enzymes with Sorghum Bagasse

    Mohamed Y. Eljonid, Fumiyoshi Okazaki, Eiji Hishinuma, Naomi Matsukawa, Sahar Hamido, Yutaka Tamaru

    International Journal of Molecular Sciences　2025/12/03

    DOI： 10.3390/ijms262311728 　

  2. β-1,3-Xylanase BcXyn26A from Bacteroides cellulosilyticus exhibits a unique exo-mode of action that liberates β-1,3-xylobiose

    Sanae Hori, Kotone Yamamoto, Toshiyoshi Araki, Yutaka Tamaru, Katsutoshi Hori, Satoshi Fukuzaki, Takahiko Aoki, Fumiyoshi Okazaki

    Biochemical and Biophysical Research Communications　2025/11

    DOI： 10.1016/j.bbrc.2025.152810 　

  3. Cyclical short-term fasting and refeeding effects on immunological alteration of the disk abalone, Haliotis discus discus

    Dien Arista Anggorowati, Liqing Zang, Yutaka Tamaru, Takahiko Aoki, Fumiyoshi Okazaki

    AQUACULTURE, FISH AND FISHERIES　5　(3)　2025/06

    DOI： 10.1002/aff2.70061 　

    ISSN： 2693-8847

  4. Recent research advances on non-linear phenomena in various biosystems

    Yutaka Tamaru, Shuji Nakanishi, Kenya Tanaka, Mitsuo Umetsu, Hikaru Nakazawa, Aruto Sugiyama, Tomoyuki Ito, Naofumi Shimokawa, Masahiro Takagi

    Journal of Bioscience and Bioengineering　2023/08

    DOI： 10.1016/j.jbiosc.2023.03.012 　

  5. Comparison of Different Carbon Sources on Biomethane Production with Clostridium cellulovorans and Methanogens

    Haruki Sawada, Hisao Tomita, Fumiyoshi Okazaki, Yutaka Tamaru

    Applied Microbiology　2023/05/25

    DOI： 10.3390/applmicrobiol3020035 　

  6. Recent research advances on non-linear phenomena in various biosystems

    Tamaru, Y., Nakanishi, S., Tanaka, K., Umetsu, M., Nakazawa, H., Sugiyama, A., Ito, T., Shimokawa, N., Takagi, M.

    Journal of Bioscience and Bioengineering　2023

    DOI： 10.1016/j.jbiosc.2023.03.012 　

    ISSN： 1347-4421 1389-1723

  7. Investigation into the combustion kinetics and spontaneous ignition of sweet sorghum as energy resource

    Numan Luthfi, Tappei Ohkoshi, Yutaka Tamaru, Takashi Fukushima, Kenji Takisawa

    Bioresources and Bioprocessing　9　(1)　2022/12

    DOI： 10.1186/s40643-022-00536-0 　

    eISSN： 2197-4365

  8. Perturbation by Antimicrobial Bacteria of the Epidermal Bacterial Flora of Rainbow Trout in Flow-Through Aquaculture. International-journal

    Hajime Nakatani, Naoki Yamada, Naoki Hashimoto, Fumiyoshi Okazaki, Tomoko Arakawa, Yutaka Tamaru, Katsutoshi Hori

    Biology　11　(8)　2022/08/22

    DOI： 10.3390/biology11081249 　

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    The bacterial flora of the epidermal mucus of fish is closely associated with the host's health and susceptibility to pathogenic infections. In this study, we analyzed the epidermal mucus bacteria of rainbow trout (Oncorhynchus mykiss) reared in flow-through aquaculture under environmental perturbations. Over ~2 years, the bacteria present in the skin mucus and water were analyzed based on the 16S rDNA sequences. The composition of the mucus bacterial community showed significant monthly fluctuations, with frequent changes in the dominant bacterial species. Analysis of the beta- and alpha-diversity of the mucus bacterial flora showed the fluctuations of the composition of the flora were caused by the genera Pseudomonas, Yersinia, and Flavobacterium, and some species of Pseudomonas and Yersinia in the mucus were identified as antimicrobial bacteria. Examination of the antimicrobial bacteria in the lab aquarium showed that the natural presence of antimicrobial bacteria in the mucus and water, or the purposeful addition of them to the rearing water, caused a transition in the mucus bacteria community composition. These results demonstrate that specific antimicrobial bacteria in the water or in epidermal mucus comprise one of the causes of changes in fish epidermal mucus microflora.

  9. Enzymatic Characterization of Unused Biomass Degradation Using the Clostridium cellulovorans Cellulosome

    Eljonaid, M.Y., Tomita, H., Okazaki, F., Tamaru, Y.

    Microorganisms　10　(12)　2022

    DOI： 10.3390/microorganisms10122514 　

    ISSN： 2076-2607

  10. Investigation into the combustion kinetics and spontaneous ignition of sweet sorghum as energy resource

    Luthfi, N., Ohkoshi, T., Tamaru, Y., Fukushima, T., Takisawa, K.

    Bioresources and Bioprocessing　9　(1)　2022

    DOI： 10.1186/s40643-022-00536-0 　

    ISSN： 2197-4365

  11. Direct IBE fermentation from mandarin orange wastes by combination of Clostridium cellulovorans and Clostridium beijerinckii

    Hisao Tomita, Fumiyoshi Okazaki, Yutaka Tamaru

    AMB Express　9　(1)　2019/12/01

    DOI： 10.1186/s13568-018-0728-7 　

    eISSN： 2191-0855

  12. The Second-Generation Biomethane from Mandarin Orange Peel under Cocultivation with Methanogens and the Armed Clostridium cellulovorans Invited Peer-reviewed

    Hisao Tomita, Yutaka Tamaru

    Fermentation　5　(4)　95　2019/11/04

    DOI： 10.3390/fermentation5040095 　

  13. Biomethane production from sugar beet pulp under cocultivation with Clostridium cellulovorans and methanogens Peer-reviewed

    Hisao Tomita, Fumiyoshi Okazaki, Yutaka Tamaru

    AMB EXPRESS　9　2019/02

    DOI： 10.1186/s13568-019-0752-2 　

    ISSN： 2191-0855

  14. The Second-Generation Biomethane from Mandarin Orange Peel under Cocultivation with Methanogens and the Armed Clostridium cellulovorans

    Hisao Tomita, Yutaka Tamaru

    Fermentation　5　(4)　2019

    DOI： 10.3390/fermentation5040095 　

    eISSN： 2311-5637

  15. Synergistic properties of cellulases from Clostridium cellulovorans in the presence of cellobiose

    Kosuke Yamamoto, Yutaka Tamaru

    AMB Express　6　(1)　1-6　2016/12/01

    DOI： 10.1186/s13568-015-0169-5 　

    eISSN： 2191-0855

  16. Temporal fluctuation in the abundance of alginate-degrading bacteria in the gut of abalone Haliotis gigantea over 1 year

    Reiji Tanaka, Toshiyuki Shibata, Hideo Miyake, Tetsushi Mori, Yutaka Tamaru, Mitsuyoshi Ueda, Peter Bossier

    Aquaculture Research　47　(9)　2899-2908　2016/09/01

    DOI： 10.1111/are.12740 　

    ISSN： 1355-557X

    eISSN： 1365-2109

  17. Temporal fluctuation in the abundance of alginate-degrading bacteria in the gut of abalone Haliotis gigantea over 1year Peer-reviewed

    Reiji Tanaka, Toshiyuki Shibata, Hideo Miyake, Tetsushi Mori, Yutaka Tamaru, Mitsuyoshi Ueda, Peter Bossier

    AQUACULTURE RESEARCH　47　(9)　2899-2908　2016/09

    DOI： 10.1111/are.12740 　

    ISSN： 1355-557X

    eISSN： 1365-2109

  18. Important Roles of the Cellulosome on Degradation of Plant Biomass

    Kosuke Yamamoto, Yutaka Tamaru

    New and Future Developments in Microbial Biotechnology and Bioengineering: Microbial Cellulase System Properties and Applications　3-8　2016/08/02

    DOI： 10.1016/B978-0-444-63507-5.00001-0 　

  19. Bacterial strategies for plant cell wall degradation and their genomic information

    Yutaka Tamaru, Roy H. Doi

    Handbook of Carbohydrate-Modifying Biocatalysts　2　897-925　2016/07/11

    DOI： 10.4032/9789814669795 　

  20. Direct visualization of replication dynamics in early zebrafish embryos. International-journal

    Kenji Kuriya, Eriko Higashiyama, Eriko Avşar-Ban, Nanami Okochi, Kaede Hattori, Shin Ogata, Shin-Ichiro Takebayashi, Masato Ogata, Yutaka Tamaru, Katsuzumi Okumura

    Bioscience, biotechnology, and biochemistry　80　(5)　945-8　2016/05

    DOI： 10.1080/09168451.2016.1141039 　

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    We analyzed DNA replication in early zebrafish embryos. The replicating DNA of whole embryos was labeled with the thymidine analog 5-ethynyl-2'-deoxyuridine (EdU), and spatial regulation of replication sites was visualized in single embryo-derived cells. The results unveiled uncharacterized replication dynamics during zebrafish early embryogenesis.

  21. Synergistic properties of cellulases from Clostridium cellulovorans in the presence of cellobiose. International-journal

    Kosuke Yamamoto, Yutaka Tamaru

    AMB Express　6　(1)　1-1　2016/03

    DOI： 10.1186/s13568-015-0169-5 　

    More details Close

    An anaerobic mesophile, Clostridium cellulovorans, produces a multienzyme complex called the cellulosome and actively degrades polysaccharides in the plant cell wall. C. cellulovorans also changes cellulosomal subunits to form highly active combinations dependent on the carbon substrate. A previous study reported on the synergistic effects of exoglucanase S (ExgS) and endoglucanase H (EngH) that are classified into the glycosyl hydrolase (GH) families 48, and 9, respectively. In this study, we investigated synergistic effects of ExgS and EngK, a GH9 cellulase different from EngH. In addition, since EngK was known to produce cellobiose as its main product, the inhibition on cellulase activity of EngK with cellobiose was examined. As a result, the effect of cellobiose inhibition on EngK coexistent with ExgS was found to be much lower than that with EngH. Thus, although EngH and EngK are in the same GH9 family, enzymatic activity in the presence of cellobiose was significantly different.

  22. Conservation of the Nrf2-Mediated Gene Regulation of Proteasome Subunits and Glucose Metabolism in Zebrafish

    Yutaka Tamaru

    Oxidative Medicine and Cellular Longevity　2016

    DOI： 10.1155/2016/5720574 　

  23. Direct visualization of replication dynamics in early zebrafish embryos

    Yutaka Tamaru

    Bioscience, Biotechnology, and Biochemistry　2016

    DOI： 10.1080/09168451.2016.1141039 　

  24. Temporal fluctuation in the abundance of alginate-degrading bacteria in the gut of abalone Haliotis gigantea over 1year

    Yutaka Tamaru

    Aquaculture Research　2016

    DOI： 10.1111/ARE.12740 　

  25. Synergistic properties of cellulases from Clostridium cellulovorans in the presence of cellobiose

    Yamamoto, K., Tamaru, Y.

    AMB Express　6　(1)　2016

    DOI： 10.1186/s13568-015-0169-5 　

    ISSN： 2191-0855

  26. Direct visualization of replication dynamics in early zebrafish embryos

    Kuriya, K., Higashiyama, E., Av?ar-Ban, E., Okochi, N., Hattori, K., Ogata, S., Takebayashi, S.-I., Ogata, M., Tamaru, Y., Okumura, K.

    Bioscience, Biotechnology and Biochemistry　80　(5)　2016

    DOI： 10.1080/09168451.2016.1141039 　

    ISSN： 1347-6947 0916-8451

  27. Temporal fluctuation in the abundance of alginate-degrading bacteria in the gut of abalone Haliotis gigantea over 1 year

    Tanaka, R., Shibata, T., Miyake, H., Mori, T., Tamaru, Y., Ueda, M., Bossier, P.

    Aquaculture Research　47　(9)　2016

    DOI： 10.1111/are.12740 　

    ISSN： 1365-2109 1355-557X

  28. Conservation of the Nrf2‐Mediated Gene Regulation of Proteasome Subunits and Glucose Metabolism in Zebrafish

    Vu Thanh Nguyen, Yuji Fuse, Junya Tamaoki, Shin-ichi Akiyama, Masafumi Muratani, Yutaka Tamaru, Makoto Kobayashi

    Oxidative Medicine and Cellular Longevity　2016　2016/01

    DOI： 10.1155/2016/5720574 　

    ISSN： 1942-0994 1942-0900

  29. Direct visualization of replication dynamics in early zebrafish embryos

    Kenji Kuriya, Eriko Higashiyama, Eriko Avşar-Ban, Nanami Okochi, Kaede Hattori, Shin Ogata, Shin Ichiro Takebayashi, Masato Ogata, Yutaka Tamaru, Katsuzumi Okumura

    Bioscience, Biotechnology and Biochemistry　80　(5)　945-948　2016

    DOI： 10.1080/09168451.2016.1141039 　

    ISSN： 0916-8451

    eISSN： 1347-6947

  30. Conservation of the Nrf2-Mediated Gene Regulation of Proteasome Subunits and Glucose Metabolism in Zebrafish

    Vu Thanh Nguyen, Yuji Fuse, Junya Tamaoki, Shin Ichi Akiyama, Masafumi Muratani, Yutaka Tamaru, Makoto Kobayashi

    Oxidative Medicine and Cellular Longevity　2016　2016

    DOI： 10.1155/2016/5720574 　

    ISSN： 1942-0900

    eISSN： 1942-0994

  31. Important Roles of the Cellulosome on Degradation of Plant Biomass

    Yutaka Tamaru

    New and Future Developments in Microbial Biotechnology and Bioengineering: Microbial Cellulase System Properties and Applications　2016

    DOI： 10.1016/B978-0-444-63507-5.00001-0 　

  32. Important Roles of the Cellulosome on Degradation of Plant Biomass

    Yamamoto, K., Tamaru, Y.

    New and Future Developments in Microbial Biotechnology and Bioengineering: Microbial Cellulase System Properties and Applications　2016

    DOI： 10.1016/B978-0-444-63507-5.00001-0 　

  33. Bacterial strategies for plant cell wall degradation and their genomic information

    Tamaru, Y., Doi, R.H.

    Handbook of Carbohydrate-Modifying Biocatalysts　2　2016

    DOI： 10.4032/9789814669795 　

  34. Conservation of the Nrf2-Mediated Gene Regulation of Proteasome Subunits and Glucose Metabolism in Zebrafish. International-journal

    Vu Thanh Nguyen, Yuji Fuse, Junya Tamaoki, Shin-Ichi Akiyama, Masafumi Muratani, Yutaka Tamaru, Makoto Kobayashi

    Oxidative medicine and cellular longevity　2016　5720574-5720574　2016

    DOI： 10.1155/2016/5720574 　

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    The Keap1-Nrf2 system is an evolutionarily conserved defense mechanism against oxidative and xenobiotic stress. Besides the exogenous stress response, Nrf2 has been found to regulate numerous cellular functions, including protein turnover and glucose metabolism; however, the evolutionary origins of these functions remain unknown. In the present study, we searched for novel target genes associated with the zebrafish Nrf2 to answer this question. A microarray analysis of zebrafish embryos that overexpressed Nrf2 revealed that 115 candidate genes were targets of Nrf2, including genes encoding proteasome subunits and enzymes involved in glucose metabolism. A real-time quantitative PCR suggested that the expression of 3 proteasome subunits (psma3, psma5, and psmb7) and 2 enzymes involved in glucose metabolism (pgd and fbp1a) were regulated by zebrafish Nrf2. We thus next examined the upregulation of these genes by an Nrf2 activator, diethyl maleate, using Nrf2 mutant zebrafish larvae. The results of real-time quantitative PCR and whole-mount in situ hybridization showed that all of these 5 genes were upregulated by diethyl maleate treatment in an Nrf2-dependent manner, especially in the liver. These findings implied that the Nrf2-mediated regulation of the proteasome subunits and glucose metabolism is evolutionarily conserved among vertebrates.

  35. Direct visualization of DNA replication dynamics in zebrafish cells

    Kenji Kuriya, Eriko Higashiyama, Eriko Avşar-Ban, Yutaka Tamaru, Shin Ogata, Shin Ichiro Takebayashi, Masato Ogata, Katsuzumi Okumura

    Zebrafish　12　(6)　432-439　2015/12

    DOI： 10.1089/zeb.2015.1151 　

    ISSN： 1545-8547

  36. Formosa haliotis sp. Nov., a brown-alga-degrading bacterium isolated from the gut of the abalone haliotis gigantea

    Reiji Tanaka, Ilse Cleenwerck, Yukino Mizutani, Shunpei Iehata, Toshiyuki Shibata, Hideo Miyake, Tetsushi Mori, Yutaka Tamaru, Mitsuyoshi Ueda, Peter Bossier, Peter Vandamme

    International Journal of Systematic and Evolutionary Microbiology　65　(12)　4388-4393　2015/12

    DOI： 10.1099/ijsem.0.000586 　

    ISSN： 1466-5026

  37. Direct Visualization of DNA Replication Dynamics in Zebrafish Cells. International-journal

    Kenji Kuriya, Eriko Higashiyama, Eriko Avşar-Ban, Yutaka Tamaru, Shin Ogata, Shin-ichiro Takebayashi, Masato Ogata, Katsuzumi Okumura

    Zebrafish　12　(6)　432-9　2015/12

    DOI： 10.1089/zeb.2015.1151 　

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    Spatiotemporal regulation of DNA replication in the S-phase nucleus has been extensively studied in mammalian cells because it is tightly coupled with the regulation of other nuclear processes such as transcription. However, little is known about the replication dynamics in nonmammalian cells. Here, we analyzed the DNA replication processes of zebrafish (Danio rerio) cells through the direct visualization of replicating DNA in the nucleus and on DNA fiber molecules isolated from the nucleus. We found that zebrafish chromosomal DNA at the nuclear interior was replicated first, followed by replication of DNA at the nuclear periphery, which is reminiscent of the spatiotemporal regulation of mammalian DNA replication. However, the relative duration of interior DNA replication in zebrafish cells was longer compared to mammalian cells, possibly reflecting zebrafish-specific genomic organization. The rate of replication fork progression and ori-to-ori distance measured by the DNA combing technique were ∼ 1.4 kb/min and 100 kb, respectively, which are comparable to those in mammalian cells. To our knowledge, this is a first report that measures replication dynamics in zebrafish cells.

  38. Formosa haliotis sp. nov., a brown-alga-degrading bacterium isolated from the gut of the abalone Haliotis gigantea. International-journal Peer-reviewed

    Reiji Tanaka, Ilse Cleenwerck, Yukino Mizutani, Shunpei Iehata, Toshiyuki Shibata, Hideo Miyake, Tetsushi Mori, Yutaka Tamaru, Mitsuyoshi Ueda, Peter Bossier, Peter Vandamme

    International journal of systematic and evolutionary microbiology　65　(12)　4388-4393　2015/12

    DOI： 10.1099/ijsem.0.000586 　

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    Four brown-alga-degrading, Gram-stain-negative, aerobic, non-flagellated, gliding and rod-shaped bacteria, designated LMG 28520T, LMG 28521, LMG 28522 and LMG 28523, were isolated from the gut of the abalone Haliotis gigantea obtained in Japan. The four isolates had identical random amplified polymorphic DNA patterns and grew optimally at 25 °C, at pH 6.0-9.0 and in the presence of 1.0-4.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences placed the isolates in the genus Formosa with Formosa algae and Formosa arctica as closest neighbours. LMG 28520T and LMG 28522 showed 100 % DNA-DNA relatedness to each other, 16-17 % towards F. algae LMG 28216T and 17-20 % towards F. arctica LMG 28318T; they could be differentiated phenotypically from these established species. The predominant fatty acids of isolates LMG 28520T and LMG 28522 were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 1 G and iso-C15 : 0. Isolate LMG 28520T contained menaquinone-6 (MK-6) as the major respiratory quinone and phosphatidylethanolamine, two unknown aminolipids and an unknown lipid as the major polar lipids. The DNA G+C content was 34.4 mol% for LMG 28520T and 35.5 mol% for LMG 28522. On the basis of their phylogenetic and genetic distinctiveness, and differential phenotypic properties, the four isolates are considered to represent a novel species of the genus Formosa, for which the name Formosa haliotis sp. nov. is proposed. The type strain is LMG 28520T ( = NBRC 111189T).

  39. Formosa haliotis sp nov., a brown-alga-degrading bacterium isolated from the gut of the abalone Haliotis gigantea Peer-reviewed

    Reiji Tanaka, Ilse Cleenwerck, Yukino Mizutani, Shunpei Iehata, Toshiyuki Shibata, Hideo Miyake, Tetsushi Mori, Yutaka Tamaru, Mitsuyoshi Ueda, Peter Bossier, Peter Vandamme

    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY　65　4388-4393　2015/12

    DOI： 10.1099/ijsem.0.000586 　

    ISSN： 1466-5026

    eISSN： 1466-5034

  40. Formosa haliotis sp nov., a brown-alga-degrading bacterium isolated from the gut of the abalone Haliotis gigantea

    Yutaka Tamaru

    International Journal of Systematic and Evolutionary Microbiology　2015

    DOI： 10.1099/IJSEM.0.000586 　

  41. Direct Visualization of DNA Replication Dynamics in Zebrafish Cells

    Yutaka Tamaru

    Zebrafish　2015

    DOI： 10.1089/ZEB.2015.1151 　

  42. Formosa haliotis sp. Nov., a brown-alga-degrading bacterium isolated from the gut of the abalone haliotis gigantea

    Tanaka, R., Cleenwerck, I., Mizutani, Y., Iehata, S., Shibata, T., Miyake, H., Mori, T., Tamaru, Y., Ueda, M., Bossier, P., V, amme, P.

    International Journal of Systematic and Evolutionary Microbiology　65　(12)　2015

    DOI： 10.1099/ijsem.0.000586 　

    ISSN： 1466-5026

  43. Direct visualization of DNA replication dynamics in zebrafish cells

    Kuriya, K., Higashiyama, E., Av?ar-Ban, E., Tamaru, Y., Ogata, S., Takebayashi, S.-I., Ogata, M., Okumura, K.

    Zebrafish　12　(6)　2015

    DOI： 10.1089/zeb.2015.1151 　

    ISSN： 1545-8547

  44. A noncellulosomal mannanase26E contains a CBM59 in clostridium cellulovorans

    Yamamoto, K., Tamaru, Y.

    BioMed Research International　2014　2014

    DOI： 10.1155/2014/438787 　

    ISSN： 2314-6141 2314-6133

  45. A noncellulosomal mannanase26E contains a CBM59 in clostridium cellulovorans

    Kosuke Yamamoto, Yutaka Tamaru

    BioMed Research International　2014　2014

    DOI： 10.1155/2014/438787 　

    ISSN： 2314-6133

    eISSN： 2314-6141

  46. A noncellulosomal mannanase26E contains a CBM59 in Clostridium cellulovorans. International-journal

    Kosuke Yamamoto, Yutaka Tamaru

    BioMed research international　2014　438787-438787　2014

    DOI： 10.1155/2014/438787 　

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    A multicomponent enzyme-complex prevents efficient degradation of the plant cell wall for biorefinery. In this study, the method of identifying glycoside hydrolases (GHs) to degrade hemicelluloses was demonstrated. The competence of C. cellulovorans, which changes to be suitable for degradation of each carbon source, was used for the method. C. cellulovorans was cultivated into locust bean gum (LBG) that is composed of galactomannan. The proteins produced by C. cellulovorans were separated into either fractions binding to crystalline cellulose or not. Proteins obtained from each fraction were further separated by SDS-PAGE and were stained with Coomassie Brilliant Blue and were detected for mannanase activity. The proteins having the enzymatic activity for LBG were cut out and were identified by mass spectrometry. As a result, four protein bands were classified into glycosyl hydrolase family 26 (GH26) mannanases. One of the identified mannanases, Man26E, contains a carbohydrate-binding module (CBM) family 59, which binds to xylan, mannan, and Avicel. Although mannose and galactose are the same as a hexose, the expression patterns of the proteins from C. cellulovorans were quite different. More interestingly, zymogram for mannanase activity showed that Man26E was detected in only LBG medium.

  47. Biochemical characterization of a thermostable β-1,3-xylanase from the hyperthermophilic eubacterium, Thermotoga neapolitana strain DSM 4359 Peer-reviewed

    Fumiyoshi Okazaki, Nanami Nakashima, Chiaki Ogino, Yutaka Tamaru, Akihiko Kondo

    Applied Microbiology and Biotechnology　97　(15)　6749-6757　2013/08

    DOI： 10.1007/s00253-012-4555-5 　

    ISSN： 0175-7598

    eISSN： 1432-0614

  48. Display of Clostridium cellulovorans xylose isomerase on the cell surface of Saccharomyces cerevisiae and its direct application to xylose fermentation

    Miki Ota, Hiroshi Sakuragi, Hironobu Morisaka, Kouichi Kuroda, Hideo Miyake, Yutaka Tamaru, Mitsuyoshi Ueda

    Biotechnology Progress　29　(2)　346-351　2013/04

    DOI： 10.1002/btpr.1700 　

    ISSN： 8756-7938

    eISSN： 1520-6033

  49. Fixation of CO2 in Clostridium cellulovorans analyzed by 13C-isotopomer-based target metabolomics

    Shinohara, M., Sakuragi, H., Morisaka, H., Miyake, H., Tamaru, Y., Fukusaki, E., Kuroda, K., Ueda, M.

    AMB Express　3　2013

    DOI： 10.1186/2191-0855-3-61 　

    ISSN： 2191-0855

  50. Display of Clostridium cellulovorans xylose isomerase on the cell surface of Saccharomyces cerevisiae and its direct application to xylose fermentation

    Ota, M., Sakuragi, H., Morisaka, H., Kuroda, K., Miyake, H., Tamaru, Y., Ueda, M.

    Biotechnology Progress　29　(2)　2013

    DOI： 10.1002/btpr.1700 　

    ISSN： 8756-7938 1520-6033

  51. Biochemical characterization of a thermostable β-1,3-xylanase from the hyperthermophilic eubacterium, Thermotoga neapolitana strain DSM 4359

    Okazaki, F., Nakashima, N., Ogino, C., Tamaru, Y., Kondo, A.

    Applied Microbiology and Biotechnology　97　(15)　2013

    DOI： 10.1007/s00253-012-4555-5 　

    ISSN： 0175-7598 1432-0614

  52. Fixation of CO<inf>2</inf> in Clostridium cellulovorans analyzed by 13C-isotopomer-based target metabolomics

    Masahiro Shinohara, Hiroshi Sakuragi, Hironobu Morisaka, Hideo Miyake, Yutaka Tamaru, Eiichiro Fukusaki, Kouichi Kuroda, Mitsuyoshi Ueda

    AMB Express　3　1-6　2013

    DOI： 10.1186/2191-0855-3-61 　

    eISSN： 2191-0855

  53. Display of Clostridium cellulovorans xylose isomerase on the cell surface of Saccharomyces cerevisiae and its direct application to xylose fermentation. International-journal

    Miki Ota, Hiroshi Sakuragi, Hironobu Morisaka, Kouichi Kuroda, Hideo Miyake, Yutaka Tamaru, Mitsuyoshi Ueda

    Biotechnology progress　29　(2)　346-51　2013

    DOI： 10.1002/btpr.1700 　

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    Xylose isomerase (XI) is a key enzyme in the conversion of D-xylose, which is a major component of lignocellulosic biomass, to D-xylulose. Genomic analysis of the bacterium Clostridium cellulovorans revealed the presence of XI-related genes. In this study, XI derived from C. cellulovorans was produced and displayed using the yeast cell-surface display system, and the xylose assimilation and fermentation properties of this XI-displaying yeast were examined. XI-displaying yeast grew well in medium containing xylose as the sole carbon source and directly produced ethanol from xylose under anaerobic conditions.

  54. Fixation of CO2 in Clostridium cellulovorans analyzed by 13C-isotopomer-based target metabolomics Peer-reviewed

    Masahiro Shinohara, Hiroshi Sakuragi, Hironobu Morisaka, Hideo Miyake, Yutaka Tamaru, Eiichiro Fukusaki, Kouichi Kuroda, Mitsuyoshi Ueda

    AMB Express　3　1-6　2013

    Publisher: Springer Verlag

    DOI： 10.1186/2191-0855-3-61 　

    ISSN： 2191-0855

  55. Functional and heterologous expression of human protein O-linked mannose β-1,2-N-acetylglucosaminyltransferase 1 in zebrafish

    Eriko Avşar-Ban, Hisayoshi Ishikawa, Shin'ichi Akiyama, Hiroshi Manya, Tamao Endo, Yutaka Tamaru

    Journal of Bioscience and Bioengineering　114　(2)　237-239　2012/08

    DOI： 10.1016/j.jbiosc.2012.03.013 　

    ISSN： 1389-1723

    eISSN： 1347-4421

  56. Functional and heterologous expression of human protein O-linked mannose β-1,2-N-acetylglucosaminyltransferase 1 in zebrafish.

    Eriko Avşar-Ban, Hisayoshi Ishikawa, Shin'ichi Akiyama, Hiroshi Manya, Tamao Endo, Yutaka Tamaru

    Journal of bioscience and bioengineering　114　(2)　237-9　2012/08

    DOI： 10.1016/j.jbiosc.2012.03.013 　

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    Although membrane-associated proteins are related to many diseases and are important targets for drug discovery, their expression is often difficult in bacterial hosts such as Escherichia coli. To overcome this limitation, here, we focused on a novel host-vector system in zebrafish for the expression of human protein O-linked mannose β-1,2-N-acetylglucosaminyltransferase 1 (hPOMGnT1) which is related to muscle-eye-brain disease. For the expression of hPOMGnT1, the vector pZex-EGFP-pXI-hPOMGnT1 was constructed and injected into fertilized eggs. Using this system, we demonstrated that recombinant hPOMGnT1 was successfully expressed in the whole bodies of zebrafish embryos.

  57. BACTERIAL STRATEGIES FOR PLANT CELL DEGRADATION AND THEIR GENOMIC INFORMATION

    Yutaka Tamaru

    Carbohydrate-modifying Biocatalysts　2012

    DOI： 10.4032/9789814303484 　

  58. Functional and heterologous expression of human protein O-linked mannose β-1,2-N-acetylglucosaminyltransferase 1 in zebrafish

    Av?ar-Ban, E., Ishikawa, H., Akiyama, S., Manya, H., Endo, T., Tamaru, Y.

    Journal of Bioscience and Bioengineering　114　(2)　2012

    DOI： 10.1016/j.jbiosc.2012.03.013 　

    ISSN： 1389-1723 1347-4421

  59. Profile of native cellulosomal proteins of Clostridium cellulovorans adapted to various carbon sources

    Yutaka Tamaru

    AMB Express　2012

    DOI： 10.1186/2191-0855-2-37 　

  60. Profile of native cellulosomal proteins of Clostridium cellulovorans adapted to various carbon sources

    Morisaka, H., Matsui, K., Tatsukami, Y., Kuroda, K., Miyake, H., Tamaru, Y., Ueda, M.

    AMB Express　2　(1)　2012

    DOI： 10.1186/2191-0855-2-37 　

    ISSN： 2191-0855

  61. Profile of native cellulosomal proteins of Clostridium cellulovorans adapted to various carbon sources

    Hironobu Morisaka, Kazuma Matsui, Yohei Tatsukami, Kouichi Kuroda, Hideo Miyake, Yutaka Tamaru, Mitsuyoshi Ueda

    AMB Express　2　(1)　2012

    DOI： 10.1186/2191-0855-2-37 　

    eISSN： 2191-0855

  62. Profile of native cellulosomal proteins of Clostridium cellulovorans adapted to various carbon sources Peer-reviewed

    Hironobu Morisaka, Kazuma Matsui, Yohei Tatsukami, Kouichi Kuroda, Hideo Miyake, Yutaka Tamaru, Mitsuyoshi Ueda

    AMB Express　2　(1)　1-7　2012

    DOI： 10.1186/2191-0855-2-37 　

    ISSN： 2191-0855

  63. Bacterial strategies for plant cell degradation and their genomic information

    Yutaka Tamaru, Roy H. Doid

    Carbohydrate-Modifying Biocatalysts　761-789　2011/11/30

    DOI： 10.4032/9789814303484 　

  64. Tissue-restricted expression of Nrf2 and its target genes in zebrafish with gene-specific variations in the induction profiles

    Hitomi Nakajima, Yaeko Nakajima-Takagi, Tadayuki Tsujita, Shin Ichi Akiyama, Takeshi Wakasa, Katsuki Mukaigasa, Hiroshi Kaneko, Yutaka Tamaru, Masayuki Yamamoto, Makoto Kobayashi

    PLoS ONE　6　(10)　2011/10/25

    DOI： 10.1371/journal.pone.0026884 　

    eISSN： 1932-6203

  65. Putative role of cellulosomal protease inhibitors in Clostridium cellulovorans based on gene expression and measurement of activities Peer-reviewed

    Hirokazu Meguro, Hironobu Morisaka, Kouichi Kuroda, Hideo Miyake, Yutaka Tamaru, Mitsuyoshi Ueda

    Journal of Bacteriology　193　(19)　5527-5530　2011/10

    DOI： 10.1128/JB.05022-11 　

    ISSN： 0021-9193

  66. セルロソーム生産菌 Clostridium cellulovorans 743B の全ゲノム解析 Peer-reviewed

    三宅, 英雄, 田丸, 浩

    三重大学大学院生物資源学研究科紀要　37　1-9　2011/02/01

    Publisher: 三重大学大学院生物資源学研究科

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    application/pdf Among Clostridia, an extracellular enzyme complex called the cellulosomes produced by Clostridium species are particularly designed for efficient degradation of plant cell wall polysaccharides. Clostridium cellulovorans 743B, an anaerobic and mesophilic bacterium, produces the cellulosomes on the cell surface and free extracellular enzymes called noncellulosomes. Recently, we have reported the whole genome sequence of C. cellulovorans comprising 4,220 predicted genes in 5.10Mbp. As a result, the genome size of C. cellulovorans was about 1Mbp larger than that of other cellulosome-producing clostridia, mesophilic C. cellulolyticum and thermophilic C. thermocellum. A total of 57 cellulosomal genes were found in the C. cellulovorans genome, in addition to two novel genes encoding scaffolding proteins CbpB and CbpC. C. cellulovorans genome included not only cellulosomal genes but also a large number of genes encoding noncellulosomal enzymes, the genome expansion of C. cellulovorans included genes more related to degradation of polysaccharides, such as hemicelluloses and pectins, than to cellulose. Clostridia の中にはセルロソームと呼ばれる細胞外に酵素複合体を形成する Clostridium 属が存在し、それらは植物細胞壁を効率よく分解する。Clostridium cellulovorans 743B は, 嫌気性中温菌であり, 細胞表層にセルロソームと細胞外にフリーな酵素であるノンセルロソームを生産する。近年, 我々は, C. cellulovorans の全ゲノム配列を決定し, 予想される遺伝子は 4,220 あり, そのゲノムサイズは 5.1Mbp であった。中温菌である C. cellulolyticum や高温菌である C. thermocellum と比較すると C. cellulovorans は約 1Mbp ゲノムサイズが大きいことが分かった。C. cellulovorans のゲノム中にセルロソーマルな遺伝子は合計 57 個あり, 新たに 2 つの骨格タンパク質をコードする遺伝子である CbpB と CbpC が見つかった。C. cellulovorans のゲノムは, セルロソーマルな遺伝子だけでなく, 多数のノンセルロソーマルな酵素をコードする遺伝子が含まれており, セルロースを分解する酵素よりもヘミセルロースやペクチンを分解する酵素の方が多く含まれていた。

  67. セルロソーム生産菌Clostridium cellulovorans 743Bの全ゲノム解析

    三宅, 英雄, 田丸, 浩

    三重大学大学院生物資源学研究科紀要 = The bulletin of the Graduate School of Bioresources Mie University　(37)　1-9　2011/02

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    Clostridiaの中にはセルロソームと呼ばれる細胞外に酵素複合体を形成するClostridium属が存在し, それらは植物細胞壁を効率よく分解する。Clostridium cellulovorans 743Bは、嫌気性中温菌であり，細胞表層にセルロソームと細胞外にフリーな酵素であるノンセルロソームを生産する。近年，我々は，C. cellulovoransの全ゲノム配列を決定し，予想される遺伝子は4,220あり，そのゲノムサイズは5.1Mbpであった。中温菌であるC.cellulolyticumや高温菌であるC.thermocellum と比較するとC.cellulovorans は約1Mbpゲノムサイズが大きいことが分かった。C.cellulovoransのゲノム中にセルロソーマルな遺伝子は合計57個あり，新たに2つの骨格タンパク質をコードする遺伝子であるCbpBとCbpCが見つかった。C.cellulovoransのゲノムは，セルロソーマルな遺伝子だけでなく，多数のノンセルロソーマルな酵素をコードする遺伝子が含まれており，セルロースを分解する酵素よりもへミセルロースやペクチンを分解する酵素の方が多く含まれていた。

  68. Tissue-restricted expression of Nrf2 and its target genes in zebrafish with gene-specific variations in the induction profiles

    Nakajima, H., Nakajima-Takagi, Y., Tsujita, T., Akiyama, S.-I., Wakasa, T., Mukaigasa, K., Kaneko, H., Tamaru, Y., Yamamoto, M., Kobayashi, M.

    PLoS ONE　6　(10)　2011

    DOI： 10.1371/journal.pone.0026884 　

    ISSN： 1932-6203

  69. Putative Role of Cellulosomal Protease Inhibitors in Clostridium cellulovorans Based on Gene Expression and Measurement of Activities

    Yutaka Tamaru

    Journal of Bacteriology　2011

    DOI： 10.1128/JB.05022-11 　

  70. Comparison of the mesophilic cellulosome-producing Clostridium cellulovorans genome with other cellulosome-related clostridial genomes

    Yutaka Tamaru

    Microbial Biotechnology　2011

    DOI： 10.1111/J.1751-7915.2010.00210.X 　

  71. Putative role of cellulosomal protease inhibitors in Clostridium cellulovorans based on gene expression and measurement of activities

    Meguro, H., Morisaka, H., Kuroda, K., Miyake, H., Tamaru, Y., Ueda, M.

    Journal of Bacteriology　193　(19)　2011

    DOI： 10.1128/JB.05022-11 　

    ISSN： 0021-9193 1098-5530

  72. Comparison of the mesophilic cellulosome-producing Clostridium cellulovorans genome with other cellulosome-related clostridial genomes

    Tamaru, Y., Miyake, H., Kuroda, K., Nakanishi, A., Matsushima, C., Doi, R.H., Ueda, M.

    Microbial Biotechnology　4　(1)　2011

    DOI： 10.1111/j.1751-7915.2010.00210.x 　

    ISSN： 1751-7907 1751-7915

  73. Comparison of the mesophilic cellulosome-producing Clostridium cellulovorans genome with other cellulosome-related clostridial genomes

    Yutaka Tamaru, Hideo Miyake, Kouichi Kuroda, Akihito Nakanishi, Chiyuki Matsushima, Roy H. Doi, Mitsuyoshi Ueda

    Microbial Biotechnology　4　(1)　64-73　2011/01

    DOI： 10.1111/j.1751-7915.2010.00210.x 　

    ISSN： 1751-7907

    eISSN： 1751-7915

  74. Bacterial strategies for plant cell degradation and their genomic information

    Tamaru, Y., Doid, R.H.

    Carbohydrate-Modifying Biocatalysts　2011

    DOI： 10.4032/9789814303484 　

  75. Tissue-restricted expression of Nrf2 and its target genes in zebrafish with gene-specific variations in the induction profiles. International-journal

    Hitomi Nakajima, Yaeko Nakajima-Takagi, Tadayuki Tsujita, Shin-Ichi Akiyama, Takeshi Wakasa, Katsuki Mukaigasa, Hiroshi Kaneko, Yutaka Tamaru, Masayuki Yamamoto, Makoto Kobayashi

    PloS one　6　(10)　e26884　2011

    DOI： 10.1371/journal.pone.0026884 　

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    The Keap1-Nrf2 system serves as a defense mechanism against oxidative stress and electrophilic toxicants by inducing more than one hundred cytoprotective proteins, including antioxidants and phase 2 detoxifying enzymes. Since induction profiles of Nrf2 target genes have been studied exclusively in cultured cells, and not in animal models, their tissue-specificity has not been well characterized. In this paper, we examined and compared the tissue-specific expression of several Nrf2 target genes in zebrafish larvae by whole-mount in situ hybridization (WISH). Seven zebrafish genes (gstp1, mgst3b, prdx1, frrs1c, fthl, gclc and hmox1a) suitable for WISH analysis were selected from candidates for Nrf2 targets identified by microarray analysis. Tissue-restricted induction was observed in the nose, gill, and/or liver for all seven genes in response to Nrf2-activating compounds, diethylmaleate (DEM) and sulforaphane. The Nrf2 gene itself was dominantly expressed in these three tissues, implying that tissue-restricted induction of Nrf2 target genes is defined by tissue-specific expression of Nrf2. Interestingly, the induction of frrs1c and gclc in liver and nose, respectively, was quite low and that of hmox1a was restricted in the liver. These results indicate the existence of gene-specific variations in the tissue specificity, which can be controlled by factors other than Nrf2.

  76. Comparison of the mesophilic cellulosome-producing Clostridium cellulovorans genome with other cellulosome-related clostridial genomes Peer-reviewed

    Yutaka Tamaru, Hideo Miyake, Kouichi Kuroda, Akihito Nakanishi, Chiyuki Matsushima, Roy H. Doi, Mitsuyoshi Ueda

    Microbial Biotechnology　4　(1)　64-73　2011/01

    DOI： 10.1111/j.1751-7915.2010.00210.x 　

    ISSN： 1751-7907

  77. 次世代バイオ燃料開発に向けたセルロソーム生産菌ゲノム解読

    田丸, 浩, 山本, 康介, 川出, 雄二郎, 三宅, 英雄

    三重大学社会連携研究センター研究報告　18　135-138　2010/12/01

    Publisher: 三重大学社会連携研究センター

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    application/pdf

  78. Crystal structure of zinc-finger domain of Nanos and its functional implications

    Hiroshi Hashimoto, Kodai Hara, Asami Hishiki, Shigeta Kawaguchi, Naoki Shichijo, Keishi Nakamura, Satoru Unzai, Yutaka Tamaru, Toshiyuki Shimizu, Mamoru Sato

    EMBO Reports　11　(11)　848-853　2010/11

    DOI： 10.1038/embor.2010.155 　

    ISSN： 1469-221X

    eISSN： 1469-3178

  79. Crystal structure of zinc-finger domain of Nanos and its functional implications. International-journal

    Hiroshi Hashimoto, Kodai Hara, Asami Hishiki, Shigeta Kawaguchi, Naoki Shichijo, Keishi Nakamura, Satoru Unzai, Yutaka Tamaru, Toshiyuki Shimizu, Mamoru Sato

    EMBO reports　11　(11)　848-53　2010/11

    DOI： 10.1038/embor.2010.155 　

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    Nanos is an RNA-binding protein that is involved in the development and maintenance of germ cells. In combination with Pumilio, Nanos binds to the 3' untranslated region of a messenger RNA and represses its translation. Nanos has two conserved Cys-Cys-His-Cys zinc-finger motifs that are indispensable for its function. In this study, we have determined the crystal structure of the zinc-finger domain of zebrafish Nanos, for the first time revealing that Nanos adopts a novel zinc-finger structure. In addition, Nanos has a conserved basic surface that is directly involved in RNA binding. Our results provide the structural basis for further studies to clarify Nanos function.

  80. Protein O-mannosylation is necessary for normal embryonic development in zebrafish

    Eriko Avşar-Ban, Hisayoshi Ishikawa, Hiroshi Manya, Masatoki Watanabe, Shinichi Akiyama, Hideo Miyake, Tamao Endo, Yutaka Tamaru

    Glycobiology　20　(9)　1089-1102　2010/09

    DOI： 10.1093/glycob/cwq069 　

    ISSN： 0959-6658

    eISSN： 1460-2423

  81. Protein O-mannosylation is necessary for normal embryonic development in zebrafish Peer-reviewed

    Eriko Avsar-Ban, Hisayoshi Ishikawa, Hiroshi Manya, Masatoki Watanabe, Shinichi Akiyama, Hideo Miyake, Tamao Endo, Yutaka Tamaru

    GLYCOBIOLOGY　20　(9)　1089-1102　2010/09

    DOI： 10.1093/glycob/cwq069 　

    ISSN： 0959-6658

    eISSN： 1460-2423

  82. Genome sequence of the cellulosome-producing mesophilic organism Clostridium cellulovorans 743B

    Yutaka Tamaru, Hideo Miyake, Kouichi Kuroda, Akihito Nakanishi, Yujiro Kawade, Kousuke Yamamoto, Masaaki Uemura, Yasuhiro Fujita, Roy H. Doi, Mitsuyoshi Ueda

    Journal of Bacteriology　192　(3)　901-902　2010/02

    DOI： 10.1128/JB.01450-09 　

    ISSN： 0021-9193

  83. Genome sequence of the cellulosome-producing mesophilic organism Clostridium cellulovorans 743B Peer-reviewed

    Yutaka Tamaru, Hideo Miyake, Kouichi Kuroda, Akihito Nakanishi, Yujiro Kawade, Kousuke Yamamoto, Masaaki Uemura, Yasuhiro Fujita, Roy H. Doi, Mitsuyoshi Ueda

    Journal of Bacteriology　192　(3)　901-902　2010/02

    DOI： 10.1128/JB.01450-09 　

    ISSN： 0021-9193

  84. ソフトバイオマス完全糖化を目指したデザイナブルセルロソームの構築

    88　(7)　336-339　2010

    Publisher:

    ISSN： 0919-3758

  85. Crystal structure of zinc-finger domain of Nanos and its functional implications

    Yutaka Tamaru

    EMBO Reports　2010

    DOI： 10.1038/EMBOR.2010.155 　

  86. Comparative genomics of the mesophilic cellulosome-producing Clostridium cellulovorans and its application to biofuel production via consolidated bioprocessing

    Yutaka Tamaru

    Environmental Technology　2010

    DOI： 10.1080/09593330.2010.490856 　

  87. Genome Sequence of the Cellulosome-Producing Mesophilic Organism Clostridium cellulovorans 743B

    Yutaka Tamaru

    Journal of Bacteriology　2010

    DOI： 10.1128/JB.01450-09 　

  88. Comparative genomics of the mesophilic cellulosome-producing Clostridium cellulovorans and its application to biofuel production via consolidated bioprocessing

    Tamaru, Y., Miyake, H., Kuroda, K., Ueda, M., Doi, R.H.

    Environmental Technology　31　(8-9)　2010

    DOI： 10.1080/09593330.2010.490856 　

    ISSN： 1479-487X 0959-3330

  89. Crystal structure of zinc-finger domain of Nanos and its functional implications

    Hashimoto, H., Hara, K., Hishiki, A., Kawaguchi, S., Shichijo, N., Nakamura, K., Unzai, S., Tamaru, Y., Shimizu, T., Sato, M.

    EMBO Reports　11　(11)　2010

    DOI： 10.1038/embor.2010.155 　

    ISSN： 1469-221X 1469-3178

  90. Protein O-mannosylation is necessary for normal embryonic development in zebrafish

    Av?ar-Ban, E., Ishikawa, H., Manya, H., Watanabe, M., Akiyama, S., Miyake, H., Endo, T., Tamaru, Y.

    Glycobiology　20　(9)　2010

    DOI： 10.1093/glycob/cwq069 　

    ISSN： 0959-6658 1460-2423

  91. Genome sequence of the cellulosome-producing mesophilic organism Clostridium cellulovorans 743B

    Tamaru, Y., Miyake, H., Kuroda, K., Nakanishi, A., Kawade, Y., Yamamoto, K., Uemura, M., Fujita, Y., Doi, R.H., Ueda, M.

    Journal of Bacteriology　192　(3)　2010

    DOI： 10.1128/JB.01450-09 　

    ISSN： 0021-9193

  92. Comparative genomics of the mesophilic cellulosome-producing Clostridium cellulovorans and its application to biofuel production via consolidated bioprocessing Peer-reviewed

    Yutaka Tamaru, Hideo Miyake, Kouichi Kuroda, Mitsuyoshi Ueda, Roy H. Doi

    Environmental Technology　31　(8-9)　889-903　2010

    DOI： 10.1080/09593330.2010.490856 　

    ISSN： 0959-3330

  93. Research and development of combinatorial bioengineering using zebrafish and its application on drug discovery

    Yutaka Tamaru

    Yakugaku Zasshi　129　(11)　1285-1293　2009/11

    DOI： 10.1248/yakushi.129.1285 　

    ISSN： 0031-6903

    eISSN： 1347-5231

  94. [Research and development of combinatorial bioengineering using zebrafish and its application on drug discovery].

    Yutaka Tamaru

    Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan　129　(11)　1285-93　2009/11

    ISSN： 0031-6903

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    The main challenge of the post-genomic era is to functionally characterize genes identified by the genome sequencing projects. Model organisms, including zebrafish (Danio rerio), are indispensable for this demanding task. Zebrafish has recently been successfully incorporated into large-scale genetic screens due to the optical clarity of the embryos and their accessibility to various experimental techniques throughout development. The attractiveness of the zebrafish as a model organism is enhanced by the biological availability of continuously improving genomic tools and methodologies for functional characterization of the genes. In addition, transparent zebrafish embryos are well suited to manipulations involving DNA or mRNA injection, cell labeling, and transplantation. Once the scheduled zebrafish genome project is complete, targeted genetic manipulations in zebrafish would be able to become even more desirable. In my laboratory, we propose that the "embryoarray technology" supports to characterize especially unknown proteins using zebrafish embryos which offer a platform for assessing the biological effects by not only chemical compounds including medical drugs, siRNAs (small interfering RNAs) and micro RNAs, but foreign genes that are never existing in zebrafish. Thus, zebrafish offers a high-quality, high-throughput bioassay tool for determining the biological effect of small molecules as well as for dissecting biological pathways. In this review, I would like to introduce a couple of recent data that we have constructed the gene expression system in zebrafish and have succeeded to produce several membrane-associated proteins. Furthermore, several tools with zebrafish embryos are available to examine the interactions between protein-protein using fully automatic high-throughput microinjection system.

  95. Purification, crystallization and initial X-ray diffraction study of the zinc-finger domain of zebrafish Nanos Peer-reviewed

    Hiroshi Hashimoto, Shigeta Kawaguchi, Kodai Hara, Keishi Nakamura, Toshiyuki Shimizu, Yutaka Tamaru, Mamoru Sato

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　65　(Pt 9)　959-961　2009/09

    DOI： 10.1107/S1744309109032163 　

    ISSN： 1744-3091

  96. Purification, crystallization and initial X-ray diffraction study of the zinc-finger domain of zebrafish Nanos

    Hiroshi Hashimoto, Shigeta Kawaguchi, Kodai Hara, Keishi Nakamura, Toshiyuki Shimizu, Yutaka Tamaru, Mamoru Sato

    Acta Crystallographica Section F: Structural Biology and Crystallization Communications　65　(9)　959-961　2009/08/20

    DOI： 10.1107/S1744309109032163 　

    ISSN： 1744-3091

    eISSN： 1744-3091

  97. A novel application of metabolomics in vertebrate development

    Shunsuke Hayashi, Shinichi Akiyama, Yutaka Tamaru, Yasuaki Takeda, Toshinobu Fujiwara, Kunio Inoue, Akio Kobayashi, Shingo Maegawa, Eiichiro Fukusaki

    Biochemical and Biophysical Research Communications　386　(1)　268-272　2009/08/14

    DOI： 10.1016/j.bbrc.2009.06.041 　

    ISSN： 0006-291X

    eISSN： 1090-2104

  98. A novel application of metabolomics in vertebrate development. International-journal

    Shunsuke Hayashi, Shinichi Akiyama, Yutaka Tamaru, Yasuaki Takeda, Toshinobu Fujiwara, Kunio Inoue, Akio Kobayashi, Shingo Maegawa, Eiichiro Fukusaki

    Biochemical and biophysical research communications　386　(1)　268-72　2009/08/14

    DOI： 10.1016/j.bbrc.2009.06.041 　

    More details Close

    Many studies have demonstrated the functions of individual genes associated with embryogenesis and have determined the genome sequences of several organisms. Despite the availability of enormous amount of genetic information, dynamic changes that occur during embryogenesis have not yet been completely understood. In order to understand the dynamic processes involved in embryogenesis, we employed the metabolomic approach. The results of our study indicated that there is a close correlation between metabolomes and developmental stages. Our method enables the identification of embryonic stages using metabolomes as "fingerprints." In this manner, we could successfully predict embryonic development on the basis of metabolomic fingerprints. This is the first report describing a model for predicting vertebrate development by using metabolomics.

  99. Research and development of combinatorial bioengineering using zebrafish and its application on drug discovery

    Tamaru, Y.

    Yakugaku Zasshi　129　(11)　2009

    DOI： 10.1248/yakushi.129.1285 　

    ISSN： 0031-6903 1347-5231

  100. A novel application of metabolomics in vertebrate development

    Hayashi, S., Akiyama, S., Tamaru, Y., Takeda, Y., Fujiwara, T., Inoue, K., Kobayashi, A., Maegawa, S., Fukusaki, E.

    Biochemical and Biophysical Research Communications　386　(1)　2009

    DOI： 10.1016/j.bbrc.2009.06.041 　

    ISSN： 0006-291X 1090-2104

  101. Cloning and characterization of a β-1,4-mannanase 5C possessing a family 27 carbohydrate-binding module from a marine bacterium, Vibrio sp. strain MA-138

    Tanaka, M., Umemoto, Y., Okamura, H., Nakano, D., Tamaru, Y., Araki, T.

    Bioscience, Biotechnology and Biochemistry　73　(1)　2009

    DOI： 10.1271/bbb.80521 　

    ISSN： 0916-8451 1347-6947

  102. Purification, crystallization and initial X-ray diffraction study of the zinc-finger domain of zebrafish Nanos

    Hashimoto, H., Kawaguchi, S., Hara, K., Nakamura, K., Shimizu, T., Tamaru, Y., Sato, M.

    Acta Crystallographica Section F: Structural Biology and Crystallization Communications　65　(9)　2009

    DOI： 10.1107/S1744309109032163 　

    ISSN： 1744-3091

  103. Cloning and characterization of a β-1,4-mannanase 5C possessing a family 27 carbohydrate-binding module from a marine bacterium, Vibrio sp. strain MA-138

    Megumi Tanaka, Yoshiaki Umemoto, Hidenori Okamura, Daiichirou Nakano, Yutaka Tamaru, Toshiyoshi Araki

    Bioscience, Biotechnology and Biochemistry　73　(1)　109-116　2009

    DOI： 10.1271/bbb.80521 　

    ISSN： 0916-8451

    eISSN： 1347-6947

  104. Cloning and characterization of a beta-1,4-mannanase 5C possessing a family 27 carbohydrate-binding module from a marine bacterium, Vibrio sp. strain MA-138. International-journal

    Megumi Tanaka, Yoshiaki Umemoto, Hidenori Okamura, Daiichirou Nakano, Yutaka Tamaru, Toshiyoshi Araki

    Bioscience, biotechnology, and biochemistry　73　(1)　109-16　2009/01

    eISSN： 1347-6947

    More details Close

    The beta-1,4-mannanase 5C gene (man5C) of Vibrio sp. strain MA-138 was cloned and expressed in Escherichia coli. The man5C gene consisted of 2,010 bp nucleotides encoding a protein of 669 amino acids with a predicted molecular weight of 76,309. beta-1,4-Mannanase (Man5C) is a modular enzyme composed of a catalytic module belonging to glycoside hydrolase family 5, a linker region, and a putative carbohydrate-binding module (CBM) belonging to family 27. Recombinant Man5C exhibited maximal activity at 50 degrees C at pH 7.0, and it had a K(m) of 0.6 mg ml(-1) and a V(max) of 556.2 micromol min(-1) mumol(-1) for glucomannan. Binding studies revealed that the C-terminal putative CBM27 had the ability to bind soluble beta-mannans and contributed to increasing the rate of depolymerization by binding to the polymeric substrate. Man5C of Vibrio sp. MA-138 is the first non-extremophile enzyme to be identified as a beta-mannanase possessing CBM27.

  105. Femtosecond pulsed laser as a microscalpel for microdissection and isolation of specific sections from biological samples

    Masaaki Sakakura, Shinichiro Kajiyama, Masafumi Tsutsumi, Jinhai Si, Eiichiro Fukusaki, Yutaka Tamaru, Shin Ichi Akiyama, Kiyotaka Miura, Kazuyuki Hirao, Mitsuyoshi Ueda

    Japanese Journal of Applied Physics, Part 1: Regular Papers and Short Notes and Review Papers　46　(9 A)　5859-5864　2007/09/07

    DOI： 10.1143/JJAP.46.5859 　

    ISSN： 0021-4922

    eISSN： 1347-4065

  106. Construction of an expression vector containing a β-actin promoter region for gene transfer by microinjection in red sea bream Pagrus major

    Keitaro Kato, Masayoshi Takagi, Yutaka Tamaru, Shin Ichi Akiyama, Takafumi Konishi, Osamu Murata, Hidemi Kumai

    Fisheries Science　73　(2)　440-445　2007/04

    DOI： 10.1111/j.1444-2906.2007.01352.x 　

    ISSN： 0919-9268

    eISSN： 1444-2906

  107. A unique β-agarase, AgaA, from a marine bacterium, Vibrio sp. strain PO-303

    Jinhua Dong, Yutaka Tamaru, Toshiyoshi Araki

    Applied Microbiology and Biotechnology　74　(6)　1248-1255　2007/04

    DOI： 10.1007/s00253-006-0781-z 　

    ISSN： 0175-7598

  108. Construction of an expression vector containing a beta-actin promoter region for gene transfer by microinjection in red sea bream Pagrus major

    Keitaro Kato, Masayoshi Takagi, Yutaka Tamaru, Shin-Ichi Akiyama, Takafumi Konishi, Osamu Murata, Hidemi Kumai

    FISHERIES SCIENCE　73　(2)　440-445　2007/04

    DOI： 10.1111/j.1444-2906.2007.01352.x 　

    ISSN： 0919-9268

  109. Molecular cloning, expression, and characterization of a β-agarase gene, agaD, from a marine bacterium, Vibrio sp. strain PO-303

    Dong, J., Tamaru, Y., Araki, T.

    Bioscience, Biotechnology and Biochemistry　71　(1)　2007

    DOI： 10.1271/bbb.60304 　

    ISSN： 0916-8451 1347-6947

  110. A unique β-agarase, AgaA, from a marine bacterium, Vibrio sp. strain PO-303

    Dong, J., Tamaru, Y., Araki, T.

    Applied Microbiology and Biotechnology　74　(6)　2007

    DOI： 10.1007/s00253-006-0781-z 　

    ISSN： 0175-7598

  111. Construction of an expression vector containing a β-actin promoter region for gene transfer by microinjection in red sea bream Pagrus major

    Kato, K., Takagi, M., Tamaru, Y., Akiyama, S.-I., Konishi, T., Murata, O., Kumai, H.

    Fisheries Science　73　(2)　2007

    DOI： 10.1111/j.1444-2906.2007.01352.x 　

    ISSN： 0919-9268 1444-2906

  112. Molecular cloning, expression, and characterization of a β-agarase gene, agaD, from a marine bacterium, Vibrio sp. strain PO-303

    Jinhua Dong, Yutaka Tamaru, Toshiyoshi Araki

    Bioscience, Biotechnology and Biochemistry　71　(1)　38-46　2007

    DOI： 10.1271/bbb.60304 　

    ISSN： 0916-8451

    eISSN： 1347-6947

  113. Femtosecond pulsed laser as a microscalpel for microdissection and isolation of specific sections from biological samples

    Sakakura, M., Kajiyama, S., Tsutsumi, M., Si, J., Fukusaki, E., Tamaru, Y., Akiyama, S.-I., Miura, K., Hirao, K., Ueda, M.

    Japanese Journal of Applied Physics, Part 1: Regular Papers and Short Notes and Review Papers　46　(9 A)　2007

    DOI： 10.1143/JJAP.46.5859 　

    ISSN： 0021-4922 1347-4065

  114. Cloning of the novel gene encoding β-agarase C from a marine bacterium, Vibrio sp. strain PO-303, and characterization of the gene product

    Jinhua Dong, Shinnosuke Hashikawa, Takafumi Konishi, Yutaka Tamaru, Toshiyoshi Araki

    Applied and Environmental Microbiology　72　(9)　6399-6401　2006/09

    DOI： 10.1128/AEM.00935-06 　

    ISSN： 0099-2240

  115. Application of the arming system for the expression of the 380R antigen from red sea bream iridovirus (RSIV) on the surface of yeast cells: A first step for the development of an oral vaccine

    Yutaka Tamaru, Masanori Ohtsuka, Keitaro Kato, Sadao Manabe, Kouichi Kuroda, Mitsuaki Sanada, Mitsuyoshi Ueda

    BIOTECHNOLOGY PROGRESS　22　(4)　949-953　2006/08

    DOI： 10.1021/bp060130x 　

    ISSN： 8756-7938

    eISSN： 1520-6033

  116. Enhancing the tolerance of zebrafish (Danio rerio) to heavy metal toxicity by the expression of plant phytochelatin synthase. International-journal

    Takafumi Konishi, Sachiko Matsumoto, Yusuke Tsuruwaka, Kentaro Shiraki, Kazumasa Hirata, Yutaka Tamaru, Masahiro Takagi

    Journal of biotechnology　122　(3)　316-25　2006/04/10

    DOI： 10.1016/j.jbiotec.2005.12.013 　

    ISSN： 0168-1656

  117. Cloning of the novel gene encoding β-agarase C from a marine bacterium, Vibrio sp. strain PO-303, and characterization of the gene product

    Dong, J., Hashikawa, S., Konishi, T., Tamaru, Y., Araki, T.

    Applied and Environmental Microbiology　72　(9)　2006

    DOI： 10.1128/AEM.00935-06 　

    ISSN： 0099-2240

  118. Enhancing the tolerance of zebrafish (Danio rerio) to heavy metal toxicity by the expression of plant phytochelatin synthase

    Konishi, T., Matsumoto, S., Tsuruwaka, Y., Shiraki, K., Hirata, K., Tamaru, Y., Takagi, M.

    Journal of Biotechnology　122　(3)　2006

    DOI： 10.1016/j.jbiotec.2005.12.013 　

    ISSN： 0168-1656

  119. The first thermodynamic characterization of β-1,3-Xylanase from a marine bacterium

    Fumiyoshi Okazaki, Kentaro Shiraki, Yutaka Tamaru, Toshiyoshi Araki, Masahiro Takagi

    Protein Journal　24　(7-8)　413-421　2005/11

    DOI： 10.1007/s10930-005-7637-8 　

    ISSN： 1572-3887

    eISSN： 1875-8355

  120. The first thermodynamic characterization of b-1,3-xylanase from a marine bacterium. International-journal

    Fumiyoshi Okazaki, Kentaro Shiraki, Yutaka Tamaru, Toshiyoshi Araki, Masahiro Takagi

    Protein J.　24　(7-8)　413-421　2005/11/01

    DOI： 10.1007/s10930-005-7637-8 　

    ISSN： 1572-3887

  121. The first crystal structure of a family 31 carbohydrate-binding module with affinity to β-1,3-xylan

    Hiroshi Hashimoto, Youichi Tamai, Fumiyoshi Okazaki, Yutaka Tamaru, Toshiyuki Shimizu, Toshiyoshi Araki, Mamoru Sato

    FEBS Letters　579　(20)　4324-4328　2005/08/15

    DOI： 10.1016/j.febslet.2005.06.062 　

    ISSN： 0014-5793

  122. The first crystal structure of a family 31 carbohydrate-binding module with affinity to beta-1,3-xylan. International-journal Peer-reviewed

    Hiroshi Hashimoto, Youichi Tamai, Fumiyoshi Okazaki, Yutaka Tamaru, Toshiyuki Shimizu, Toshiyoshi Araki, Mamoru Sato

    FEBS letters　579　(20)　4324-8　2005/08/15

    ISSN： 0014-5793

    More details Close

    Here, we present the crystal structure of the family 31 carbohydrate-binding module (CBM) of beta-1,3-xylanase from Alcaligenes sp. strain XY-234 (AlcCBM31) determined at a resolution of 1.25A. The AlcCBM31 shows affinity with only beta-1,3-xylan. The AlcCBM31 molecule makes a beta-sandwich structure composed of eight beta-strands with a typical immunoglobulin fold and contains two intra-molecular disulfide bonds. The folding topology of AlcCBM31 differs from that of the large majority of other CBMs, in which eight beta-strands comprise a beta-sandwich structure with a typical jelly-roll fold. AlcCBM31 shows structural similarity with CBM structures of family 34 and family 9, which also adopt structures based on immunoglobulin folds.

  123. A new class of glutathione S-transferase from the hepatopancreas of the red sea bream Pagrus major

    Takafumi Konishi, Keitaro Kato, Toshiyoshi Araki, Kentaro Shiraki, Masahiro Takagi, Yutaka Tamaru

    Biochemical Journal　388　(1)　299-307　2005/05/15

    DOI： 10.1042/BJ20041578 　

    ISSN： 0264-6021

  124. A new class of glutathione S-transferase from the hepatopancreas of the red sea bream Pagrus major

    Takafumi Konishi, Keitaro Kato, Toshiyoshi Araki, Kentaro Shiraki, Masahiro Takagi, Yutaka Tamaru

    Biochemical Journal　388　(1)　299-307　2005/05/15

    DOI： 10.1042/BJ20041578 　

    ISSN： 0264-6021

  125. Molecular cloning and characterization of α-class glutathione S-transferase genes from the hepatopancreas of red sea bream, Pagrus major

    Takafumi Konishi, Keitaro Kato, Toshiyoshi Araki, Kentaro Shiraki, Masahiro Takagi, Yutaka Tamaru

    Comparative Biochemistry and Physiology - C Toxicology and Pharmacology　140　(3-4)　309-320　2005/03

    DOI： 10.1016/j.cca.2005.02.012 　

    ISSN： 1532-0456

  126. The first thermodynamic characterization of β-1,3-Xylanase from a marine bacterium

    Okazaki, F., Shiraki, K., Tamaru, Y., Araki, T., Takagi, M.

    Protein Journal　24　(7-8)　2005

    DOI： 10.1007/s10930-005-7637-8 　

    ISSN： 1875-8355 1572-3887

  127. The first crystal structure of a family 31 carbohydrate-binding module with affinity to β-1,3-xylan

    Hashimoto, H., Tamai, Y., Okazaki, F., Tamaru, Y., Shimizu, T., Araki, T., Sato, M.

    FEBS Letters　579　(20)　2005

    DOI： 10.1016/j.febslet.2005.06.062 　

    ISSN： 0014-5793

  128. Molecular cloning and characterization of α-class glutathione S-transferase genes from the hepatopancreas of red sea bream, Pagrus major

    Konishi, T., Kato, K., Araki, T., Shiraki, K., Takagi, M., Tamaru, Y.

    Comparative Biochemistry and Physiology - C Toxicology and Pharmacology　140　(3-4)　2005

    DOI： 10.1016/j.cca.2005.02.012 　

    ISSN： 1532-0456

  129. A new class of glutathione S-transferase from the hepatopancreas of the red sea bream Pagrus major

    Konishi, T., Kato, K., Araki, T., Shiraki, K., Takagi, M., Tamaru, Y.

    Biochemical Journal　388　(1)　2005

    DOI： 10.1042/BJ20041578 　

    ISSN： 0264-6021

  130. Molecular cloning and characterization of α-class glutathione S-transferase genes from the hepatopancreas of red sea bream, Pagrus major

    Takafumi Konishi, Keitaro Kato, Toshiyoshi Araki, Kentaro Shiraki, Masahiro Takagi, Yutaka Tamaru

    Comparative Biochemistry and Physiology - C Toxicology and Pharmacology　140　(3-4)　309-320　2005

    DOI： 10.1016/j.cca.2005.02.012 　

    ISSN： 1532-0456

  131. Cellulosomes from mesophilic bacteria

    Doi, R.H., Kosugi, A., Murashima, K., Tamaru, Y., Han, S.O.

    Journal of Bacteriology　185　(20)　2003

    DOI： 10.1128/JB.185.20.5907-5914.2003 　

    ISSN： 0021-9193

  132. Cell-surface-anchoring role of N-terminal surface layer homology domains of Clostridium cellulovorans EngE. International-journal

    Akihiko Kosugi, Koichiro Murashima, Yutaka Tamaru, Roy H Doi

    Journal of bacteriology　184　(4)　884-8　2002/02

    ISSN： 0021-9193

    More details Close

    engE, coding for endoglucanase E, one of the three major subunits of the Clostridium cellulovorans cellulosome, has been cloned and sequenced (Y. Tamaru and R. H. Doi, J. Bacteriol. 181:3270-3276, 1999). The N-terminal-half region of EngE possesses three repeated surface layer homology (SLH) domains, which are homologous to those of some bacterial S-layer proteins. Also, the C-terminal-half region consists of a catalytic domain of glycosyl hydrolase family 5 and a duplicated sequence (dockerin) for binding EngE to scaffolding protein CbpA. Our hypothesis is that the SLH domains serve in the role of anchoring to the cell surface. This model was investigated by using recombinant EngEs (rEngE) with and without SLH domains that were synthesized in Escherichia coli and cell wall preparations from C. cellulovorans. When rEngE and SLH polypeptides of EngE were incubated with cell wall fragments prepared by sodium dodecyl sulfate treatment, these proteins bound strongly to the cell wall. However, rEngEs without SLH domains lost their ability to bind to cell walls. When rEngE was incubated with mini-CbpA, consisting of two cohesin domains, and cell wall fragments, the mini-CbpA was able to bind to the cell wall with rEngE. However, the binding of mini-CbpA was dramatically inhibited by addition of a chelating reagent, such as EDTA, which prevents cohesin-dockerin interactions. These results suggest not only that the SLH domains of EngE can bind to the cell surface but also that EngE plays an anchoring role for cellulosomes through the interaction of its dockerin domain with a CbpA cohesin.

  133. Novel carbohydrate-binding module of β-1,3-xylanase from a marine bacterium, Alcaligenes sp. strain XY-234

    Okazaki, F., Tamaru, Y., Hashikawa, S., Li, Y.-T., Araki, T.

    Journal of Bacteriology　184　(9)　2002

    DOI： 10.1128/JB.184.9.2399-2403.2002 　

    ISSN： 0021-9193

  134. Cell-surface-anchoring role of N-terminal surface layer homology domains of Clostridium cellulovorans EngE

    Kosugi, A., Murashima, K., Tamaru, Y., Doi, R.H.

    Journal of Bacteriology　184　(4)　2002

    DOI： 10.1128/jb.184.4.884-888.2002 　

    ISSN： 0021-9193

  135. Heterologous production of Clostridium cellulovorans engB, using protease-deficient Bacillus subtilis, and preparation of active recombinant cellulosomes

    Murashima, K., Chen, C.-L., Kosugi, A., Tamaru, Y., Doi, R.H., Wong, S.

    Journal of Bacteriology　184　(1)　2002

    DOI： 10.1128/JB.184.1.76-81.2002 　

    ISSN： 0021-9193

  136. Formation of protoplasts from cultured tobacco cells and Arabidopsis thaliana by the action of cellulosomes and pectate lyase from Clostridium cellulovorans

    Tamaru, Y., Ui, S., Murashima, K., Kosugi, A., Chan, H., Doi, R.H., Liu, B.

    Applied and Environmental Microbiology　68　(5)　2002

    DOI： 10.1128/AEM.68.5.2614-2618.2002 　

    ISSN： 0099-2240

  137. Heterologous production of Clostridium cellulovorans engB, using protease-deficient Bacillus subtilis, and preparation of active recombinant cellulosomes

    K. Murashima, C. L. Chen, A. Kosugi, Y. Tamaru, R. H. Doi, S. Wong

    Journal of Bacteriology　184　(1)　76-81　2002

    DOI： 10.1128/JB.184.1.76-81.2002 　

    ISSN： 0021-9193

  138. Cell-surface-anchoring role of N-terminal surface layer homology domains of Clostridium cellulovorans EngE

    Akihiko Kosugi, Koichiro Murashima, Yutaka Tamaru, Roy H. Doi

    Journal of Bacteriology　184　(4)　884-888　2002

    DOI： 10.1128/jb.184.4.884-888.2002 　

    ISSN： 0021-9193

  139. Novel carbohydrate-binding module of β-1,3-xylanase from a marine bacterium, Alcaligenes sp. strain XY-234

    Fumiyoshi Okazaki, Yutaka Tamaru, Shinnosuke Hashikawa, Yu Teh Li, Toshiyoshi Araki

    Journal of Bacteriology　184　(9)　2399-2403　2002

    DOI： 10.1128/JB.184.9.2399-2403.2002 　

    ISSN： 0021-9193

  140. Formation of protoplasts from cultured tobacco cells and Arabidopsis thaliana by the action of cellulosomes and pectate lyase from Clostridium cellulovorans

    Yutaka Tamaru, Sadaharu Ui, Koichiro Murashima, Akihiko Kosugi, Helen Chan, Roy H. Doi, Bo Liu

    Applied and Environmental Microbiology　68　(5)　2614-2618　2002

    DOI： 10.1128/AEM.68.5.2614-2618.2002 　

    ISSN： 0099-2240

  141. Heterologous production of Clostridium cellulovorans engB, using protease-deficient Bacillus subtilis, and preparation of active recombinant cellulosomes. International-journal

    Koichiro Murashima, Chyi-Liang Chen, Akihiko Kosugi, Yutaka Tamaru, Roy H Doi, Sui-Lam Wong

    Journal of bacteriology　184　(1)　76-81　2002/01

    ISSN： 0021-9193

    More details Close

    In cellulosomes produced by Clostridium spp., the high-affinity interaction between the dockerin domain and the cohesin domain is responsible for the assembly of enzymatic subunits into the complex. Thus, heterologous expression of full-length enzymatic subunits containing the dockerin domains and of the scaffolding unit is essential for the in vitro assembly of a "designer" cellulosome, or a recombinant cellulosome with a specific function. We report the preparation of Clostridium cellulovorans recombinant cellulosomes containing the enzymatic subunit EngB and the scaffolding unit, mini-CbpA, containing a cellulose binding domain, a putative cell wall binding domain, and two cohesin units. The full-length EngB containing the dockerin domain was expressed by Bacillus subtilis WB800, which is deficient in eight extracellular proteases, to prevent the proteolytic cleavage of the enzymatic subunit between the catalytic and dockerin domains that was observed in previous attempts to express EngB with Escherichia coli. The assembly of recombinant EngB with the mini-CbpA was confirmed by immunostaining, a cellulose binding experiment, and native polyacrylamide gel electrophoresis analysis.

  142. Pectate lyase A, an enzymatic subunit of the Clostridium cellulovorans cellulosome

    Yutaka Tamaru, Roy H. Doi

    Proceedings of the National Academy of Sciences of the United States of America　98　(7)　4125-4129　2001/03/27

    DOI： 10.1073/pnas.071045598 　

    ISSN： 0027-8424

  143. Suppressive Effects of Green Tea Polyphenols on Microbial Growth and Volatile Basic Nitrogen Content in Round Form Yellowtail (Seriola quinqueradiata) Meat during Ice Storage

    Noriyuki ISHIHARA, Toshiyoshi ARAKI, Yutaka TAMARU, Misa INOUE, Akifumi NISHIMURA, Nobuyuki AOI, Djong-Chi CHU, Lekh Raj JUNEJA, Tatsuo MORISHITA

    food preservation science　27　(5)　269-276　2001

    Publisher: Japan Association of Food Preservation Scientists

    DOI： 10.5891/jafps.27.269 　

    ISSN： 1344-1213

    eISSN： 2186-1277

  144. Pectate lyase A, an enzymatic subunit of the Clostridium cellulovorans cellulosome

    Tamaru, Y., Doi, R.H.

    Proceedings of the National Academy of Sciences of the United States of America　98　(7)　2001

    DOI： 10.1073/pnas.071045598 　

    ISSN： 0027-8424

  145. The clostridium cellulovorans cellulosome: An enzyme complex with plant cell wall degrading activity

    Doi, R.H., Tamaru, Y.

    Chemical Records　1　(1)　2001

    DOI： 10.1002/1528-0691(2001)1:1<24::aid-tcr5>3.0.co;2-w 　

    ISSN： 1527-8999

  146. The clostridium cellulovorans cellulosome: An enzyme complex with plant cell wall degrading activity

    Roy H. Doi, Yutaka Tamaru

    Chemical Records　1　(1)　24-32　2001

    DOI： 10.1002/1528-0691(2001)1:1<24::aid-tcr5>3.0.co;2-w 　

    ISSN： 1527-8999

  147. The engL gene cluster of Clostridium cellulovorans contains a gene for cellulosomal ManA

    Tamaru, Y., Doi, R.H.

    Journal of Bacteriology　182　(1)　2000

    DOI： 10.1128/JB.182.1.244-247.2000 　

    ISSN： 0021-9193

  148. A large gene cluster for the Clostridium cellulovorans cellulosome

    Tamaru, Y., Karita, S., Ibrahim, A., Chan, H., Doi, R.H.

    Journal of Bacteriology　182　(20)　2000

    DOI： 10.1128/JB.182.20.5906-5910.2000 　

    ISSN： 0021-9193

  149. A large gene cluster for the Clostridium cellulovorans cellulosome

    Y. Tamaru, S. Karita, A. Ibrahim, H. Chan, R. H. Doi

    Journal of Bacteriology　182　(20)　5906-5910　2000

    DOI： 10.1128/JB.182.20.5906-5910.2000 　

    ISSN： 0021-9193

  150. The engL gene cluster of Clostridium cellulovorans contains a gene for cellulosomal ManA

    Yutaka Tamaru, Roy H. Doi

    Journal of Bacteriology　182　(1)　244-247　2000/01

    DOI： 10.1128/JB.182.1.244-247.2000 　

    ISSN： 0021-9193

  151. Three surface layer homology domains at the N terminus of the Clostridium cellulovorans major cellulosomal subunit engE

    Yutaka Tamaru, Doi Roy H

    Journal of Bacteriology　181　(10)　3270-3276　1999/05

    DOI： 10.1128/jb.181.10.3270-3276.1999 　

    ISSN： 0021-9193

  152. Three surface layer homology domains at the N terminus of the Clostridium cellulovorans major cellulosomal subunit engE

    Tamaru, Y., Roy H, D.

    Journal of Bacteriology　181　(10)　1999

    DOI： 10.1128/jb.181.10.3270-3276.1999 　

    ISSN： 0021-9193

  153. Cellulosome and noncellulosomal cellulases of Clostridium cellulovorans

    Doi, R.H., Park, J.-S., Liu, C.-C., Malburg Jr., L.M., Tamaru, Y., Ichiishi, A., Ibrahim, A.

    Extremophiles　2　(2)　1998

    DOI： 10.1007/s007920050042 　

    ISSN： 1431-0651

  154. Cloning, DNA sequencing, and expression of the β-1,4-mannanase gene from a marine bacterium, Vibrio sp. strain MA-138

    Tamaru, Y., Araki, T., Morishita, T., Kimura, T., Sakka, K., Ohmiya, K.

    Journal of Fermentation and Bioengineering　83　(2)　1997

    DOI： 10.1016/S0922-338X(97)83584-2 　

    ISSN： 0922-338X

  155. Cloning, DNA sequencing, and expression of the β-1,4-mannanase gene from a marine bacterium, Vibrio sp. strain MA-138

    Yutaka Tamaru, Toshiyoshi Araki, Tatsuo Morishita, Tetsuya Kimura, Kazuo Sakka, Kunio Ohmiya

    Journal of Fermentation and Bioengineering　83　(2)　201-205　1997

    DOI： 10.1016/S0922-338X(97)83584-2 　

    ISSN： 0922-338X

  156. Purification and characterization of an extracellular β-1,4-mannanase from a marine bacterium, Vibrio sp. strain MA-138

    Tamaru, Y., Araki, T., Amagoi, H., Mori, H., Morishita, T.

    Applied and Environmental Microbiology　61　(12)　1995

    DOI： 10.1128/aem.61.12.4454-4458.1995 　

    ISSN： 0099-2240

  157. Purification and characterization of an extracellular β-1,4-mannanase from a marine bacterium, Vibrio sp. strain MA-138

    Y. Tamaru, T. Araki, H. Amagoi, H. Mori, T. Morishita

    Applied and Environmental Microbiology　61　(12)　4454-4458　1995

    DOI： 10.1128/aem.61.12.4454-4458.1995 　

    ISSN： 0099-2240

  158. ISOLATION AND REGENERATION OF HAPLOID PROTOPLASTS FROM BANGIA ATROPURPUREA (RHODOPHYTA) WITH MARINE BACTERIAL ENZYMES

    Toshiyoshi Araki, Michio Hayakawa, Yutaka Tamaru, Keiji Yoshimatsu, Tatsuo Morishita

    Journal of Phycology　30　(6)　1040-1046　1994/12

    DOI： 10.1111/j.0022-3646.1994.01040.x 　

    ISSN： 0022-3646

    eISSN： 1529-8817

  159. ISOLATION AND REGENERATION OF HAPLOID PROTOPLASTS FROM BANGIA ATROPURPUREA (RHODOPHYTA) WITH MARINE BACTERIAL ENZYMES

    Araki, T., Hayakawa, M., Tamaru, Y., Yoshimatsu, K., Morishita, T.

    Journal of Phycology　30　(6)　1994

    DOI： 10.1111/j.0022-3646.1994.01040.x 　

    ISSN： 1529-8817 0022-3646

  160. β-1,4-mannanases from marine bacteria, Vibrio spp. MA-129 and MA-138

    Araki, T., Tamaru, Y., Morishita, T.

    Journal of General and Applied Microbiology　38　(4)　1992

    DOI： 10.2323/jgam.38.343 　

    ISSN： 0022-1260

  161. β-1,4-mannanases from marine bacteria, Vibrio spp. MA-129 and MA-138

    T. Araki, Y. Tamaru, T. Morishita

    Journal of General and Applied Microbiology　38　(4)　343-351　1992

    DOI： 10.2323/jgam.38.343 　

    ISSN： 0022-1260

  162. Comparison of Different Carbon Sources on Biomethane Pro-Duction With Clostridium cellulovorans and Methanogens

    Yutaka Tamaru

    DOI： 10.20944/preprints202305.0930.v1 　

  163. Effects of Different Carbon Sources on Biomethane Production with <em>Clostridium Cellulovorans</em> and Methanogens

    Yutaka Tamaru

    DOI： 10.20944/preprints202302.0185.v3 　

  164. Effects of Different Carbon Sources on Biomethane Production with <em>Clostridium Cellulovorans</em> and Methanogens

    Yutaka Tamaru

    DOI： 10.20944/preprints202302.0185.v1 　

Show all ︎Show first 5

Misc. 74

  1. Recent research advances on non-linear phenomena in various biosystems

    Yutaka Tamaru, Shuji Nakanishi, Kenya Tanaka, Mitsuo Umetsu, Hikaru Nakazawa, Aruto Sugiyama, Tomoyuki Ito, Naofumi Shimokawa, Masahiro Takagi

    Journal of Bioscience and Bioengineering　136　(2)　75-86　2023/08

    DOI： 10.1016/j.jbiosc.2023.03.012 　

    ISSN： 1389-1723

    eISSN： 1347-4421

  2. Probiotic feed development in fish farming

    山田紗里奈, 岡崎文美, 梅川碧里, 中谷肇, 堀克敏, 田丸浩

    日本生物工学会大会講演要旨集　73rd　2021

  3. Analysis of microbiome in paddy soil by NGS and identification of nanowire bacteria

    日本農芸化学会大会講演要旨集(Web)　2021　2021

    ISSN： 2186-7976

  4. 飼育環境によるニジマス表皮細菌叢の変遷

    中谷肇, 山田尚毅, 荒川友子, 橋本直樹, 小幡宏志郎, 岡崎文美, 田丸浩, 堀克敏

    日本水産学会大会講演要旨集(CD-ROM)　2021　2021

  5. 水田土壌細菌叢のNGS解析と発電菌の同定

    林真由, 岡崎文美, 田丸浩

    日本分子生物学会年会プログラム・要旨集(Web)　43rd　2020

  6. 好冷性海洋細菌が産生するβ-1,3-キシラナーゼの機能解析

    谷口瑞季, 工藤基徳, 荻野千秋, 近藤昭彦, 田丸浩, 青木恭彦, 岡崎文美

    日本農芸化学会中部支部例会講演要旨集(Web)　187th　2020

  7. Clostridium cellulovoransとClostridium beijerinckiiによる温州みかん残渣からのIBE発酵

    富田寿男, 岡崎文美, 岡崎文美, 岡崎文美, 田丸浩, 田丸浩, 田丸浩

    日本生物工学会大会講演要旨集　71st　2019

  8. Clostridium cellulovoransおよびメタン生成菌の共培養によるシュガービートパルプからのバイオメタンガス生産

    富田寿男, 岡崎文美, 岡崎文美, 岡崎文美, 田丸浩, 田丸浩, 田丸浩

    日本生物工学会大会講演要旨集　71st　2019

  9. 好冷性海洋細菌Psychroflexus torquis由来β-1,3-キシラナーゼの酵素化学的諸性質

    谷口瑞季, 工藤基徳, 荻野千秋, 近藤昭彦, 田丸浩, 青木恭彦, 岡崎文美

    日本生物工学会大会講演要旨集　71st　2019

  10. リポソームを用いたキンギョ免疫法によるscFv断片の取得

    岡崎文美, 岡崎文美, 岡崎文美, 栗山風貴子, 安達優華, 田丸浩, 田丸浩, 田丸浩

    日本生物工学会大会講演要旨集　71st　2019

  11. キンギョゲノムを基にした水泡液中の遺伝子発現と抗体遺伝子の多様性解析

    岡崎文美, 岡崎文美, 岡崎文美, 田丸浩, 田丸浩, 田丸浩

    日本分子生物学会年会プログラム・要旨集(Web)　42nd　2019

  12. キンギョ由来抗体遺伝子の多様性解析と抗原特異的scFv断片の取得

    岡崎文美, 岡崎文美, 岡崎文美, 栗山風貴子, 百瀬直樹, 額田夏生, 田丸浩, 田丸浩, 田丸浩

    日本生化学会大会(Web)　92nd　2019

  13. Clostridium cellulovoransによる多様なセルロース系バイオマスを活用したバイオリファイナリー構築

    富田寿男, 岡崎文美, 田丸浩

    日本農芸化学会大会講演要旨集(Web)　2018　2018

    ISSN： 2186-7976

  14. キンギョ由来抗体遺伝子の多様性解析と抗原特異的scFv断片の取得

    岡崎文美, 岡崎文美, 岡崎文美, 額田夏生, 百瀬直樹, 田丸浩, 田丸浩, 田丸浩

    日本生物工学会大会講演要旨集　70th　2018

  15. Clostridium cellulovoransおよびClostridium beijerinckii共培養によるシュガービートパルプからの酪酸生産

    富田寿男, 川出雄二郎, 岡崎文美, LOPEZ-CONTRERAS Ana M., 田丸浩, 田丸浩, 田丸浩

    日本農芸化学会大会講演要旨集(Web)　2017　2017

    ISSN： 2186-7976

  16. キンギョ抗体遺伝子の多様性解析と抗原特異的scFv断片の取得

    岡崎文美, 岡崎文美, 額田夏生, 百瀬直樹, 田丸浩, 田丸浩, 田丸浩

    日本生化学会大会(Web)　90th　2017

  17. バイオインターフェイス(前編)生命現象から見たバイオインターフェイス セルロソーム生産菌によるバイオインターフェイスとバイオリファイナリーへの応用

    岡崎文美, 田丸浩

    生物工学会誌　94　(11)　2016

    ISSN： 0919-3758

  18. Clostridium cellulovoransおよびClostridium beijerinckiiの共培養系によるシュガービートパルプからの有用物質生産

    川出雄二郎, 富田寿男, 岡崎文美, LOPEZ-CONTRERAS Ana M., 田丸浩, 田丸浩, 田丸浩

    日本生物工学会大会講演要旨集　68th　2016

  19. 2P-165 Componential analysis of Sargassaceae from Vietnam for biorefinery

    Makino,Saki, Duy Vo,Triet, Terada,Ryuta, Kawaguchi,Shigeo, Tanaka,Reiji, Miyake,Hideo, Tamaru,Yutaka, Mori,Tetsushi, Yoshikawa,Hiroyuki, Kuroda,Kouichi, Ueda,Mitsuyoshi, Shibata,Toshiyuki

    67　216　2015/09/25

    Publisher: 日本生物工学会

  20. 3P-098 Analysis on composition and antioxidative properties of phlorotannins isolated from Eisenia and Ecklonia species

    Sugiura,Shingo, Nagayama,Kohki, Tanaka,Reiji, Miyake,Hideo, Tamaru,Yutaka, Kawaguchi,Shigeo, Kuroda,Kouichi, Ueda,Mitsuyoshi, Shibata,Toshiyuki

    67　295　2015/09/25

    Publisher: 日本生物工学会

  21. 3P-186 Study on the construction of cellulosome form Clostridium cellulovorans

    Nagaya,Chiaki, Ishikawa,Gaku, Tanaka,Reiji, Shibata,Toshiyuki, Kuroda,Kouichi, Ueda,Mitsuyoshi, Tamaru,Yutaka, Miyake,Hideo

    67　317　2015/09/25

    Publisher: 日本生物工学会

  22. 3P-187 Expression of the mini-cellulosome of Clostridium cellulovorans in butanol producing Clostridium beijerinckii : The effect of scaffold protein and cellulosomal enzyme

    Hiramatsu,Aiko, Kuroda,Kouichi, Ueda,Mitsuyoshi, Tamaru,Yutaka, Miyake,Hideo

    67　317　2015/09/25

    Publisher: 日本生物工学会

  23. 2P-135 Quantitative analysis of carbohydrates in Eisenia species

    Shibata,Toshiyuki, Tanaka,Reiji, Miyake,Hideo, Tamaru,Yutaka, Mori,Tetsushi, Yoshikawa,Hiroyuki, Kawaguchi,Shigeo, Kuroda,Kouichi, Ueda,Mitsuyoshi

    66　140　2014/08/05

    Publisher: 日本生物工学会

  24. 3P-180 Genome-wide dynamic transcriptional profiling in Clostridium cellulovorans using RNA-Seq

    Ishikawa,Takashi, Takashima,Kazuya, Okada,Masako, Tanaka,Reiji, Shibata,Toshiyuki, Kuroda,Kouichi, Ueda,Mitsuyoshi, Tamaru,Yutaka, Miyake,Hideo

    66　239　2014/08/05

    Publisher: 日本生物工学会

  25. 3P-182 Study of the interaction between cellulosomal enzymes and scaffolding proteins from Clostridium cellulovorans

    Ishikawa,Gaku, Nagaya,Chiaki, Esaka,Kohei, Tanaka,Reiji, Shibata,Toshiyuki, Kuroda,Kouichi, Ueda,Mitsuyoshi, Tamaru,Yutaka, Miyake,Hideo

    66　240　2014/08/05

    Publisher: 日本生物工学会

  26. 3P-181 Regulatory mechanisms for expression of cellulosomal and non-cellulosomal genes in Clostridium cellulovorans

    Takashima,Kazuya, Ishikawa,Takashi, Tanaka,Reiji, Shibata,Toshiyuki, Kuroda,Kouichi, Ueda,Mitsuyoshi, Tamaru,Yutaka, Miyake,Hideo

    66　240　2014/08/05

    Publisher: 日本生物工学会

  27. 3P-183 Analysis of cohesin-dockerin interaction in Clostridium cellulovorans

    Nagaya,Chiaki, Ishikawa,Gaku, Tanaka,Reiji, Shibata,Toshiyuki, Kuroda,Kouichi, Ueda,Mitsuyoshi, Tamaru,Yutaka, Miyake,Hideo

    66　240　2014/08/05

    Publisher: 日本生物工学会

  28. 3P-184 Expression of the cellulosomal gene cluster of Clostridium cellulovorans in butanol producing Clostridium beijerinckii

    Hiramatsu,Aiko, Kuroda,Kouichi, Ueda,Mitsuyoshi, Tamaru,Yutaka, Miyake,Hideo

    66　240　2014/08/05

    Publisher: 日本生物工学会

  29. 1P-197 Quantitative analysis of saccharides in brown algal biomass

    Shibata,Toshiyuki, Matsuoka,Izumi, Tanaka,Reiji, Miyake,Hideo, Tamaru,Yutaka, Mori,Tetsushi, Yoshikawa,Hiroyuki, Kawaguchi,Shigeo, Kuroda,Kouichi, Ueda,Mitsuyoshi

    65　67　2013/08/25

    Publisher: 日本生物工学会

  30. 2P-134 Cloning, expression and characterization of cellulosomal mannanase from Clostridium cellulovorans and the its interaction with novel scaffolding protein CbpB

    Ishikawa,Gaku, Nakajima,Daichi, Hara,Hiromi, Tanaka,Reiji, Shibata,Toshiyuki, Kuroda,Kouichi, Ueda,Mitsuyoshi, Tamaru,Yutaka, Miyake,Hideo

    65　138　2013/08/25

    Publisher: 日本生物工学会

  31. 2P-135 RNA-Seq transcriptome analysis focused on the cellulosomal and noncellulosomal genes of Clostridium cellulovorans

    Miyake,Hideo, Takashima,Kazuya, Ishikawa,Takashi, Shibata,Toshiyuki, Tanaka,Reiji, Kuroda,Kouichi, Ueda,Mitsuyoshi, Tamaru,Yutaka

    65　138　2013/08/25

    Publisher: 日本生物工学会

  32. 3P-016 Proteomic analysis of enzymes produced by Clostridium cellulovorans in response to various biomasses

    Esaka,Kohei, Matsui,Kazuma, Morisaka,Hironobu, Kuroda,Kouichi, Miyake,Hideo, Tamaru,Yutaka, Ueda,Mitsuyoshi

    65　192　2013/08/25

    Publisher: 日本生物工学会

  33. 2P-186 Performance Characteristic of High-Throughput Injection System for Zebrafish Fertilized Eggs

    Avsar,Eriko, Miyake,Hideo, Obata,Masaru, Hashimoto,Kousei, Hashimoto,Masatoshi, Tamaru,Yutaka

    65　151　2013/08/25

    Publisher: 日本生物工学会

  34. 4Hp01 Spectrum analysis of phlorotannins isolated from brown alga Eisenia bicyclis

    Fuji,Youhei, Shibata,Toshiyuki, Tanaka,Reiji, Miyake,Hideo, Kawaguchi,Shigeo, Tamaru,Yutaka, Kuroda,Kouichi, Ueda,Mitsuyoshi

    64　232　2012/09/25

    Publisher: 日本生物工学会

  35. 4Cp26 Function analysis of a novel cellulosomal scaffolding protein CbpB from Clostridium cellulovorans 743B

    Miyake,Hideo, Nakajima,Daichi, Nagano,Akihiko, Morisaka,Hironobu, Kuroda,Kouichi, Ueda,Mitsuyoshi, Tamaru,Yutaka

    64　201　2012/09/25

    Publisher: 日本生物工学会

  36. Yeast cell surface display of xylose isomerase from C. cellulovorans toward efficient xylose fermentation

    Kouichi Kuroda, Miki Ota, Hironobu Morisaka, Hideo Miyake, Yutaka Tamaru, Mitsuyoshi Ueda

    NEW BIOTECHNOLOGY　29　S48-S48　2012/09

    DOI： 10.1016/j.nbt.2012.08.132 　

    ISSN： 1871-6784

    eISSN： 1876-4347

  37. Focused proteome analysis of cellulosome of Clostridium cellulovorans

    Kazuma Matsui, Hironobu Morisaka, Kouichi Kuroda, Yutaka Tamaru, Hideo Miyake, Mitsuyoshi Ueda

    NEW BIOTECHNOLOGY　29　S49-S49　2012/09

    DOI： 10.1016/j.nbt.2012.08.136 　

    ISSN： 1871-6784

    eISSN： 1876-4347

  38. Putative role of cellulosomal protease inhibitors in Clostridium cellulovorans based on gene expression and measurement of activities

    Hirokazu Meguro, Hironobu Morisaka, Kouichi Kuroda, Hideo Miyake, Yutaka Tamaru, Mitsuyoshi Ueda

    Journal of Bacteriology　193　(19)　5527-5530　2011/10

    DOI： 10.1128/JB.05022-11 　

    ISSN： 0021-9193

    eISSN： 1098-5530

  39. 2Ea04 Cloning and protein expression of the cellulosomal scaffolding protein CbpB from Clostridium cellulovorans 743B

    Nakajima,Daichi, Yamamoto,Kousuke, Morisaka,Hironobu, Kuroda,Kouichi, Ueda,Mitsuyoshi, Tamaru,Yutaka, Miyake,Hideo

    63　141　2011/08/25

    Publisher: 日本生物工学会

  40. 1Ap01 Xylose fermentation by yeast displaying xylose isomerase

    Ota,Miki, Sakuragi,Hiroshi, Kuroda,Kouichi, Miyake,Hideo, Tamaru,Yutaka, Ueda,Mitsuyoshi

    63　21　2011/08/25

    Publisher: 日本生物工学会

  41. Investigation the Role of Protein O-Mannosylation during Development

    Tamao Endo, Eriko Avsar-Ban, Hiroshi Manya, Yutaka Tamaru

    GLYCOBIOLOGY　20　(11)　1485-1485　2010/11

    ISSN： 0959-6658

  42. 2P-1045 Development of high-throughput protein production system using zebrafish

    MIYAKE,Hideo, NAKATANI,Hajime, OBATA,Masaru, HASHIMOTO,Masatoshi, TAMARU,Yutaka

    平成22年度　20　2010/09/25

    Publisher: 日本生物工学会

  43. 3P-2034 Function and its role of cellulosomal peptidase inhibitors from Clostridium cellulovorans

    MEGURO,Hirokazu, KURODA,Kouichi, MIYAKE,Hideo, TAMARU,Yutaka, UEDA,Mitsuyoshi

    平成22年度　152　2010/09/25

    Publisher: 日本生物工学会

  44. 2P-2074 Analysis of whole genome in Clostridium cellulovorans and its feature of the genes encoding carbohydrate-related enzymes

    TAMARU,Yutaka, MIYAKE,Hideo, KURODA,Kouichi, DOI,Roy H., UEDA,Mitsuyoshi

    平成22年度　125　2010/09/25

    Publisher: 日本生物工学会

  45. Comparative genomics of the mesophilic cellulosome-producing Clostridium cellulovorans and its application to biofuel production via consolidated bioprocessing

    Yutaka Tamaru, Hideo Miyake, Kouichi Kuroda, Mitsuyoshi Ueda, Roy H. Doi

    Environmental Technology　31　(8-9)　889-903　2010/07

    DOI： 10.1080/09593330.2010.490856 　

    ISSN： 0959-3330

    eISSN： 1479-487X

  46. 平成21年度VBLプロジェクト実施報告書 ゼブラフィッシュによる次世代型ポストゲノム研究開発

    田丸 浩, 三宅 英雄, 中谷 肇

    Research activities reports　9　58-63　2010/03

    Publisher: Tsu : Mie University Venture Business Laboratory

  47. 平成20年度VBLプロジェクト実施報告書 ゼブラフィッシュによる次世代型ポストゲノム研究開発

    田丸 浩, 三宅 英雄, 中谷 肇

    Research activities reports　8　52-57　2009/03

    Publisher: Tsu : Mie University Venture Business Laboratory

  48. A unique beta-agarase, AgaA, from a marine bacterium, Vibrio sp strain PO-303

    Jinhua Dong, Yutaka Tamaru, Toshiyoshi Araki

    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　74　(6)　1248-1255　2007/04

    DOI： 10.1007/s00253-006-0781-z 　

    ISSN： 0175-7598

  49. Molecular cloning, expression, and characterization of a beta-agarase gene, agaD, from a marine bacterium, Vibrio sp strain PO-303

    Jinhua Dong, Yutaka Tamaru, Toshiyoshi Araki

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　71　(1)　38-46　2007/01

    DOI： 10.1271/bbb.60304 　

    ISSN： 0916-8451

    eISSN： 1347-6947

  50. Cloning of the novel gene encoding beta-agarase C from a marine bacterium, Vibrio sp strain PO-303, and characterization of the gene product

    Jinhua Dong, Shinnosuke Hashikawa, Takafumi Konishi, Yutaka Tamaru, Toshiyoshi Araki

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　72　(9)　6399-6401　2006/09

    DOI： 10.1128/AEM.00935-06 　

    ISSN： 0099-2240

  51. 3B10-5 Protein expression system using zebrafish embryos

    TAMARU,Yutaka, KUROKAWA,Junji, AKIYAMA,Shin-ichi, Miyake,Hideo

    平成18年度　34　2006/08/03

    Publisher: 日本生物工学会

  52. 海洋細菌Alcaligenes sp. XY-234株由来β-1,3-キシラナーゼの熱力学的安定性

    岡崎文美, 白木賢太郎, 田丸浩, 荒木利芳, 高木昌宏

    日本農芸化学会大会講演要旨集　2005　2005

  53. Cellulosomes from mesophilic bacteria

    Roy H. Doi, Akihiko Kosugi, Koichiro Murashima, Yutaka Tamaru, Sung Ok Han

    Journal of Bacteriology　185　(20)　5907-5914　2003/10

    DOI： 10.1128/JB.185.20.5907-5914.2003 　

    ISSN： 0021-9193

  54. Cellulosomes from mesophilic bacteria

    RH Doi, A Kosugi, K Murashima, Y Tamaru, SO Han

    JOURNAL OF BACTERIOLOGY　185　(20)　5907-5914　2003/10

    DOI： 10.1128/JB.185.20.5907-5914.2003 　

    ISSN： 0021-9193

    eISSN： 1098-5530

  55. Study on toxicogenomics with zebrafish

    TAMARU Yutaka, AKIYAMA Shin-ichi, TANAKA Toshio

    Bioscience & industry　61, 1, 31　(1)　31-34　2003

    Publisher: バイオインダストリ-協会

    ISSN： 0914-8981

  56. Novel carbohydrate-binding module of beta-1,3-xylanase from a marine bacterium, Alcaligenes sp strain XY-234

    F Okazaki, Y Tamaru, S Hashikawa, YT Li, T Araki

    JOURNAL OF BACTERIOLOGY　184　(9)　2399-+　2002/05

    DOI： 10.1128/JB.184.9.2399-2403.2002 　

    ISSN： 0021-9193

  57. Formation of protoplasts from cultured tobacco cells and Arabidopsis thaliana by the action of cellulosomes and pectate lyase from Clostridium cellulovorans

    Y Tamaru, S Ui, K Murashima, A Kosugi, H Chan, RH Doi, B Liu

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　68　(5)　2614-2618　2002/05

    DOI： 10.1128/AEM.68.5.2614-2618.2002 　

    ISSN： 0099-2240

    eISSN： 1098-5336

  58. Effects of Green Tea Polyphenols on Rigor Indexes and K Value of Yellowtail (Seriola quinqueradiata) during Ice Storage

    ISHIHARA Noriyuki, ARAKI Toshiyoshi, TAMARU Yutaka, INOUE Misa, NISHIMURA Akifumi, AOI Nobuyuki, CHU Djong-Chi, JUNEJA Lekh Raj, MORISHITA Tatsuo

    journal of the japanese society for cold preservation of food　28　(4)　175-181　2002

    Publisher: Japan Association of Food Preservation Scientists

    DOI： 10.5891/jafps.28.175 　

    ISSN： 1344-1213

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    Effects of green tea polyphenols (GTP), which contain (+) -catechin, (-) -epicatechin, (-) -gallocatechin, (-) -epigallocatechin, (-) -gallocatechin gallate, (-) -epicatechin gallate and (-) -epigallocatechin gallate, on rigor indexes of fish body and K values of meats in the cultured fish during round ice storage were investigated. The moist pellets supplemented with different concentrations of GTP (0, 0.02 and 0.2%) were fed to young yellowtails (Seriola quinqueradiata) of 0 (zero) -year fish. These fish were killed on the 2nd week after feeding of the moist pellets. The rigor indexes of fish body were not effected very much by GTP feeding during rigor mortis was perfected and kept up, but the decrease of them after starting of rigor resolution was slower than control group of GTP no feeding. However, the dose of supplemented GTP in the moist pellets did not show significant difference between test groups. On the changes in K values of fish meat during ice storage, there were no differences among three groups. Therefore, it was thought that the enzymatic reactions of ATP metabolism after killing fish might be not affected very much on either inhibition or acceleration by GTP feeding. Thus, it was concluded that GTP feeding would be useful for maintaining freshness of cultured fish during storage or delivery.

  59. 比較ゲノミクスと薬理ゲノミクス「新世紀の神経薬理ゲノミクス」

    Clinical Neuroscience　20巻, 1号, p.498　2002

  60. Pectate lyase A, an enzymatic subunit of the Clostridium cellulovorans cellulosome

    Y Tamaru, PH Doi

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　98　(7)　4125-4129　2001/03

    DOI： 10.1073/pnas.071045598 　

    ISSN： 0027-8424

  61. 海洋細菌Alcaligenes sp. XY-234株のβ-1,3-キシラナーゼ(TxyA)の糖質結合モジュール(CBM)に関する研究

    岡崎文美, 田丸浩, 荒木利芳

    日本生物工学会大会講演要旨集　2001　2001

  62. Study on the carbohydrate-binding module(CBM) of β-1,3-xylanase(TxyA) from a marine bacterium, Alcaligenes sp. strain XY-234.

    Okazaki Fumiyoshi, Tamaru Yutaka, Araki Toshiyoshi

    13　260-260　2001

    Publisher: 日本生物工学会

  63. The Clostridium cellulovorans cellulosome: An enzyme complex with plant cell wall degrading activity

    RH Doi, Y Tamaru

    CHEMICAL RECORD　1　(1)　24-32　2001

    DOI： 10.1002/1528-0691(2001)1:1<24::AID-TCR5>3.3.CO;2-N 　

    ISSN： 1527-8999

  64. A large gene cluster for the Clostridium cellulovorans cellulosome

    Y Tamaru, S Karita, A Ibrahim, H Chan, RH Doi

    JOURNAL OF BACTERIOLOGY　182　(20)　5906-5910　2000/10

    DOI： 10.1128/JB.182.20.5906-5910.2000 　

    ISSN： 0021-9193

  65. A large gene cluster for the Clostridium cellulovorans cellulosome

    Y Tamaru, S Karita, A Ibrahim, H Chan, RH Doi

    JOURNAL OF BACTERIOLOGY　182　(20)　5906-5910　2000/10

    DOI： 10.1128/JB.182.20.5906-5910.2000 　

    ISSN： 0021-9193

  66. The ┣DBClostridium(/)-┫DB ┣DBcellulovorans(/)-┫DB cellulosome : An enzyme complex with plant cell wall degrading activity(共著)

    The Chemical Records　2000

  67. The engL gene cluster of Clostridium cellulovorans contains a gene for cellulosomal manA

    Y Tamaru, RH Doi

    JOURNAL OF BACTERIOLOGY　182　(1)　244-247　2000/01

    DOI： 10.1128/JB.182.1.244-247.2000 　

    ISSN： 0021-9193

    eISSN： 1098-5530

  68. Three surface layer homology domains at the N terminus of the Clostridium cellulovarans major cellulosomal subunit EngE

    W Tamaru, RH Doi

    JOURNAL OF BACTERIOLOGY　181　(10)　3270-3276　1999/05

    ISSN： 0021-9193

    eISSN： 1098-5530

  69. Cellulosome and noncellulosomal cellulases of Clostridium cellulovorans

    Roy H. Doi, Jae Seon Park, Chi Chi Liu, Laercio M. Malburg, Yutaka Tamaru, Akihiko Ichiishi, Atef Ibrahim

    Extremophiles　2　(2)　53-60　1998/05

    DOI： 10.1007/s007920050042 　

    ISSN： 1431-0651

  70. Cellulosome and noncellulosomal cellulases of Clostridium cellulovorans

    RH Doi, JS Park, CC Liu, LM Malburg, Y Tamaru, A Ichiishi, A Ihrahim

    EXTREMOPHILES　2　(2)　53-60　1998/05

    DOI： 10.1007/s007920050042 　

    ISSN： 1431-0651

  71. Cloning, DNA sequencing, and expression of the beta-1,4-mannanase gene from a marine bacterium, Vibrio sp. strain MA-138

    Y Tamaru, T Araki, T Morishita, T Kimura, K Sakka, K Ohmiya

    JOURNAL OF FERMENTATION AND BIOENGINEERING　83　(2)　201-205　1997

    DOI： 10.1016/S0922-338X(97)83584-2 　

    ISSN： 0922-338X

  72. PURIFICATION AND CHARACTERIZATION OF AN EXTRACELLULAR BETA-1,4-MANNANASE FROM A MARINE BACTERIUM, VIBRIO SP STRAIN MA-138

    Y TAMARU, T ARAKI, H AMAGOI, H MORI, T MORISHITA

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY　61　(12)　4454-4458　1995/12

    ISSN： 0099-2240

  73. ISOLATION AND REGENERATION OF HAPLOID PROTOPLASTS FROM BANGIA-ATROPURPUREA (RHODOPHYTA) WITH MARINE BACTERIAL ENZYMES

    T ARAKI, M HAYAKAWA, Y TAMARU, K YOSHIMATSU, T MORISHITA

    JOURNAL OF PHYCOLOGY　30　(6)　1040-1046　1994/12

    ISSN： 0022-3646

  74. BETA-1,4-MANNANASES FROM MARINE-BACTERIA, VIBRIO SPP MA-129 AND MA-138

    T ARAKI, Y TAMARU, T MORISHITA

    JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY　38　(4)　343-351　1992/08

    DOI： 10.2323/jgam.38.343 　

    ISSN： 0022-1260

    eISSN： 1349-8037

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Books and Other Publications 10

  1. 非線形・非対称な生命現象

    田丸 浩

    日本生物工学会　2024/07

  2. 非線形バイオシステム研究の世界 ～非線形・非平衡なゆらぎと秩序～ 特集によせて

    田丸 浩

    日本生物工学会　2024/07

  3. 微生物飼料を活用した次世代陸上養殖の展開

    田丸 浩, 堀 克敏

    BIOINDUSTRY　2023

  4. バイオマス分解酵素研究の最前線 : セルラーゼ・ヘミセルラーゼを中心として

    近藤, 昭彦, 天野, 良彦, 田丸, 浩

    シーエムシー出版　2018/09

    ISBN: 9784781312927

  5. エコバイオリファイナリー : 脱石油社会へ移行するための環境ものづくり戦略

    植田, 充美, 田丸, 浩

    シーエムシー出版　2016/11

    ISBN: 9784781311258

  6. バイオマス分解酵素研究の最前線 : セルラーゼ・ヘミセルラーゼを中心として

    近藤, 昭彦, 天野, 良彦, 田丸, 浩

    シーエムシー出版　2012/03

    ISBN: 9784781305219

  7. 機能ゲノミクスへの応用「コンビナトリアル・バイオエンジニアリングの最前線」（共著）

    シーエムシー出版　2004

  8. 比較ゲノミクスへの応用「コンビナトリアル・バイオエンジニアリングの最前線」（共著）

    シーエムシー出版　2004

  9. ケモゲノミクスへの応用「コンビナトリアル・バイオエンジニアリングの最前線」（共著）

    シーエムシー出版　2004

  10. 臨床薬理ゲノミクス『先端バイオ研究の進めかた』(辻本豪三, 田中利男/編)(共著)

    羊土社　2001

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Industrial Property Rights 5

  1. 抗体の製造方法

    特許6078865

    Property Type: Patent

    More details Close

    特願2004-229931

  2. 魚類による蛋白質の製造方法

    特許4937570

    Property Type: Patent

    More details Close

    特願2004-024518

  3. トランスジェニック金魚

    特許5688849

    Property Type: Patent

    More details Close

    特願2003-138880

  4. ソフトバイオマスの分解方法

    Property Type: Patent

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    特開2002-302500

  5. アルコールの製造方法

    Property Type: Patent

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    特開2003-052354

Research Projects 23

  1. 金魚免疫系×ヒトモデル化血液脳関門チップで変革する中枢送達型抗体開発

    立川 正憲, 田丸 浩, 船本 健一

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 挑戦的研究(萌芽)

    Institution: 徳島大学

    2022/06/30 - 2025/03/31

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    核酸やタンパク質を新たなモダリティーとする高分子薬を中枢疾患治療薬として開発する場合、ヒト血液脳関門(Blood-Brain Barrier, BBB)の突破戦略の構築は重要な課題である。近年、BBB受容体に結合する抗体と薬物との複合体を創製し、受容体介在型トランスサイトーシス機構(Receptor-Mediated Transcytosis, RMT)を利用してBBB突破を図る技術が注目されている。一方で、BBBにおける標的受容体は限定的であり、新たな受容体介在型トランスサイトーシスの分子実体の同定が必要である。本研究では、ヒト脳血管内皮細胞の細胞膜画分に対する抗体を創製し、BBBにおいてRMTの第一ステップとなる受容体介在型エンドサイトーシス機能を有する受容体を同定することを目的とした。ヒトBBBモデルとして脳微小血管内皮細胞(hCMEC/D3細胞)の細胞膜画分を抗原としてマウスに免疫し、ポリクローナル抗体を含む血清を取得した。免疫沈降とプロテオミクスを組み合わせた手法を用い、hCMEC/D3細胞の細胞膜タンパク質に対する抗体と結合する受容体タンパク質を同定した。同定した受容体の介在型エンドサイトーシス機能は、標的タンパク質に対するモノクローナル抗体の内皮細胞への内在化を検出することで評価した。その結果、抗体に結合するhCMEC/D3細胞の膜タンパク質として、既知のトランスフェリン受容体を含めて新規分子を同定した。同定された分子に対するモノクローナル抗体は、hCMEC/D3細胞へ内在化活性を示し、細胞内において粒子状のシグナルが検出された。同分子をノックダウンしたhCMEC/D3細胞では、抗体の内在化活性が有意に低下した。以上から、BBBにおいて介在型エンドサイトーシス機能を有する受容体の同定に至った。

  2. Development of the system for obtaining a single-chain antibody using goldfish immunity

    Tamaru Yutaka

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Mie University

    2019/04/01 - 2022/03/31

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    A tandem repeat of plasmid carrying three hLGR5 genes was injected into zebrafish fertilized eggs. As a result, Expression of the recombinant hLGR5 in zebrafish embryos was succeeded. (Patent application #1) Next, the immunoglobulin genes in goldfish genome were investigated in comparison with the genomic information on zebrafish, carp, and rainbow trout. As a result, the genes encoding IgZ, IgZ2, and IgZ3 in goldfish genome was found in addition to IgM. Furthermore, the gene expression pattern among those Igs was observed before or after exposing Escherichia coli. As a result, although expression of IgZ and IgZ2 in Wakin type goldfish was increased, expression pattern of IgM in Wakin type goldfish was not similar to that of zebrafish IgM.

  3. Development of highly efficient and accumulated protein expression system targeted to fish eggs

    Tamaru Yutaka, Nakatani Hajime, Hori Katsutoshi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Mie University

    2016/04/01 - 2018/03/31

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    We attempted to construct a functional plasmid for CRISPR-Cas9 system in zebrafish. While the EF-1 alpha (zef1alpha) promoter from zebrafish developed by our laboratory was used for Cas9 protein expression, the U6 promoter newly cloned from zebrafish was used for the expression of guide RNA (gRNA). After an injection to fertilized eggs from zebrafish with the constructed plasmid, both EGFP expression downstream of Cas9 gene in the plasmid and Cas9 protein expression were observed among zebrafish 24 hours-per-fertilization (hpf) embryos. Furthermore, gRNAs designed by the vitellogenin gene in zebrafish genome were successfully expressed.

  4. 魚類による高効率な抗原・抗体生産システムの開発

    田丸 浩

    System: 産学が連携した研究開発成果の展開 研究成果展開事業 研究成果最適展開支援プログラム(A-STEP) 起業検証タイプ

    Institution: 三重大学

    2013 - 2014

  5. ハイスループットタンパク質生産システムの開発 Competitive

    System: ＪＳＴ先端計測分析技術・機器開発事業

    2009 - 2011

  6. ハイスループットタンパク質生産システムの開発

    田丸 浩

    Offer Organization: 科学技術振興機構

    System: 産学が連携した研究開発成果の展開 研究成果展開事業 先端計測分析技術・機器開発プログラム 一般領域 機器開発タイプ

    Institution: 三重大学

    2009 - 2011

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    魚類発現を用いた全く新しいタンパク質生産システムを開発します。本開発では、ゼブラフィッシュの受精卵を宿主とし、組織特異的なタンパク質発現ベクターを用いることで、これまで発現が困難であった膜タンパク質や細胞毒性を示すタンパク質も生産可能です。受精卵の自動回収装置と1時間に3,000個の受精卵に遺伝子導入可能な装置によりハイスループット・システムを実現します。これにより、多くのタンパク質の構造・機能解析が加速度的に進展し、創薬や医薬品製造などの産業応用が期待できます。

  7. 麹菌タンパク質高発現系を用いた効率的な魚類抗体生産技術の開発 Competitive

    System: JST地域イノベーション創出総合支援事業

    2009 - 2010

  8. 抗体生産を目指した次世代型フィッシュモデルの創出

    田丸 浩

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 挑戦的萌芽研究

    Institution: 三重大学

    2009 - 2010

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    本研究では、実験モデル動物として注目されている小型魚類のゼブラフィッシュ(Danio rerio)から次世代型モデルフィッシュとして注目した金魚(水泡眼)を用いた抗体生産系の創出を目指した。すなわち、既存の免疫哺乳動物(マウス、ウサギなど)では作製が困難な膜タンパク質に対する抗体を取得するためには、種が離れた魚類などの脊椎動物を用いることでその問題を克服できると考えた。そこで最終年度となる本年度は、金魚由来の免疫グロブリン重鎖(IgH)遺伝子のクローニングならびに塩基配列の決定を行った。さらに、水泡眼の腹腔内あるいは水泡内に抗原タンパク質(GFP-His)を直接またはアジュバンドとともに投与して追加免疫をした後、水泡内液を採取した。ポジティブコントロールとして市販の抗GFP抗体または抗Hisタグ抗体を用いたサンドイッチ法によるドットブロットを行うことで、抗原となるGFP-Hisに対する水泡液内の抗体を検出した。その結果、腹腔内へのGFP-Hisでは明らかな抗体生産の誘導が認められなかったが、アジュバンドとともにGFP-Hisを水泡内に投与した場合に強く抗体生産が誘導されることが判明した。

  9. Construction of Production of n-3 Poly Unsaturated Fatty Acid (PUFA) by Fish

    TAMARU Yutaka, SHIBATA Toshiyuki, MIYAKE Hideo

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    Institution: Mie University

    2007 - 2008

  10. ミリスチル化脂質修飾を標的とした個体レベルの時空間モニタリングとその定量解析

    田丸 浩

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 特定領域研究

    Institution: 三重大学

    2007 - 2008

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    本研究では、ゼブラフィッシュをモデル動物として、受精卵(1細胞)からの発生・分化過程という「時間的・空間的な動態」におけるミリスチル化脂質修飾酵素ならびにその標的タンパク質を介した時空間動態の定量的解析法の確立を目指した。最終年度となる今年度は、ミリスチン酸(myr)-グリシン(Gly)残基に対する抗体を作製し、ミリスチル化ペプチドに対する抗体の免疫学的力価の検討を行った。その結果、50ng以上のミリスチル化ペプチドに対して直線的な相関が得られた。さらに、大腸菌発現系を用いてゼブラフィッシュzNMT1遺伝子の組換え体酵素を精製し、標的ペプチドに対するミリスチル化の反応産物を質量分析器を用いてMyr付加の有無を検討した。その結果、組換えzNMT1は標的ペプチドをミリスチル化し、ミリスチル化ペプチドに予想通りの分子量の変動が確認された。最後に、ゼブラフィッシュ遺伝子発現系を用いて蛍光共鳴エネルギー移動(FRET)によるタンパク質間相互作用について検討を行った。当研究室で開発したpZexベクターならびに全身細胞で発現するpXIを組み合わせて、孵化腺細胞におけるFRETを観察した。その結果、受精後24-48時間において強いFRETが観察され、高等動物におけるタンパク質間相互作用解析が可能となった。 今後は、発現が困難である膜タンパク質についてのミリスチル化とタンパク質間相互作用解析を組み合わせることで、タンパク質ミリスチル化が関与する生命現象の解明を進めていく予定である。

  11. 嫌気性細菌Clostridium cellulovoransによる未利用バイオマスの有効利用 Competitive

    System: 共同研究

    2008 -

  12. ミリスチル化タンパク質の生体内モニタリングとその定量解析法の確立

    田丸 浩

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 特定領域研究

    Institution: 三重大学

    2006 - 2006

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    本研究では、ゼブラフィッシュをモデル動物として、受精卵(1細胞)からの発生・分化過程に関与するタンパク質の脂肪酸修飾を触媒するN-ミリスチル転移酵素(NMT)に焦点を絞り、ミリスチル化タンパク質の生体内モニタリングとその定量解析法の確立を目指した。 そこでまず、ゼブラフィッシュの初期発生過程におけるNMT遺伝子ならびにミリスチル化関連酵素(MetAP)についての生体内発現局在をホールマウントin situハイブリダイゼーション(WISH)法で調べた。その結果、受精後24時間の胚ではNMT遺伝子は頭部の内部に発現が見られるのに対して、MetAP遺伝子は頭部表層および全身に発現していた。さらに、受精後48時間の胚では、両遺伝子は頭部においてほぼ同様に発現しており、全身に発現していたMetAP遺伝子は消失していた。また、市販の抗ヒトNMT抗体を用いたホールマウント免疫組織染色を行った。その結果、NMT1タンパク質は受精後1日(dpf)から頭部および体幹の表層部、卵黄嚢の後端部、眼部、膜鰭に認められ、2〜3dpfでは孵化腺、胸鰭および膜鰭で発現していた。さらに、4dpf以降では内耳および体表の神経丘、ならびに眼周辺部でも発現が認められた。一方、エストラジオールを曝露した個体では血島でのNMTタンパク質の発現が増大していた。以上の結果から、NMTタンパク質はゼブラフィッシュの発生過程において広範な組織で発現し、感覚器でも発現していることが新たに明らかになった。

  13. ナノ制御マイクロインジェクション用送液系の開発

    田丸 浩

    System: 産学が連携した研究開発成果の展開 研究成果展開事業 地域事業 地域イノベーション創出総合支援事業 シーズ発掘試験

    Institution: 三重大学

    2005 - 2005

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    ポストゲノム時代における次世代技術として、解明された3~4万遺伝子の機能解析やネットワーク解析を如何に行うかに注目が集まっている。このような大量で網羅的な解析を行うには、ヒトに外挿できるモデル動物を取り扱う必要があり、この点において世界中で最も注目を浴びているのが「ゼブラフィッシュ」である。そこで本研究開発では、これまでにゼブラフィッシュ受精卵に自動インジェクションが可能な「ナノオートインジェクション装置」におけるインジェクション時の液量を100ピコリットルレベルで正確に制御が可能なシステムの開発を最終目標とする。

  14. 魚類経口ワクチンの開発 Competitive

    System: 地域先端技術共同研究開発

    2003 - 2005

  15. 魚類用ユニバーサル発現ベクターの開発

    田丸 浩

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(C)

    Institution: 三重大学

    2002 - 2004

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    本研究では、イリドウイルスの幅広い宿主域を利用して、そのプロモーターを組み込んだ発現ベクターを作成することで、様々な魚種に利用可能な発現解析系を構築することを試みた。すなわち、既存プロモーターに見られる魚種特異性の問題が解決するものと思われ、得られたイリドウイルスプロモーターは、これまで医学や理学の分野で幅広く用いられ莫大な成果をもたらしてきたSV40あるいはCMVプロモーターと同等の役割を果たすと予想される。 本年度は、(1)イリドウイルスプロモーターのクローン化、(2)蛍光タンパク質(Green Fluoresent Protein : GFP)とプロモーターを含むプラスミドの構築、(3)ゼブラフィッシュ受精卵へのインジェクション効率の検討、の3つの点に関して検討した。 (1)イリドウイルス由来のATPase遺伝子の上流域994bp(あるいは439bp)およびMCP遺伝子の上流域1411bpをPCRで増幅し、両遺伝子のプロモーターの単離に成功した。また、マダイβ-アクチン遺伝子の下流域352bpについても同様の方法でクローニングした。 (2)上記のイリドウイルス・プロモーター領域およびマダイβ-アクチンUTR領域を組み合わせて、GFPをレポーター遺伝子とする4種類のプラスミドを構築した。すなわち、(i)pEGFP/n:プロモーターのないもの、(ii)pEGFP/ATP044:ATPaseプロモーター(994bpの439bp領域)、(iii)pEGFP/ATP099:ATPaseプロモーター(994bp領域)、(iv)pEGFP/MCP141:MCPプロモーター(1411bp領域)。 (3)ゼブラフィッシュ受精卵へのインジェクション効率を算出するために、インジェクションするDNA溶液の濃度およびGFP発現効率を指標とした。コントロールとして、アフリカツメガエルEF-1αプロモーターにGFPが連結した環状プラスミドを用いた。その結果、80ng/μl濃度で33%のGFP発現効率がみられた。

  16. 魚類性決定過程を利用した内分泌撹乱物質のリスク評価

    高木 昌宏, 田丸 浩

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 特定領域研究(A)

    Institution: 北陸先端科学技術大学院大学

    2001 - 2001

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    (研究計画)有性生殖を行なう生物種において個体の遺伝的な性は受精時に決まり、それが生殖腺の性を決め、生殖付属器官や二次性徴、さらに脳、行動などの表現型の性が決定されて性が確立すると言われている。内分泌撹乱物質などの汚染物質が環境問題として重要視されている昨今、魚類の雌化、あるいは奇形魚の殆どを占める骨形成異常について遺伝子、蛋白質レベルでの解析を行い、環境要因に敏感に応答する因子を用いたバイオセンサーを構築する事を本研究の目的とした。 具体的な計画は、【1】性決定を制御する因子の序列化と探索、【2】性決定・確立に関与する遺伝子取得とマッピング、【3】骨形成過程に関与する遺伝子シグナル、細胞分化ステップの同定、【4】外的要因の受容体タンパク質を用いた環境バイオセンサーの開発。 (研究経過および成果)性決定因子の序列化には至っていないが、ゼブラフィッシュ、メダカ初期胚における卵膜の可塑性をプロテアーゼ処理により向上させることに成功し、発生時における遺伝子発現プロファイリング、アポトーシス評価が可能になった。また、ヒトアポトーシス抑制遺伝子(bc1-2)を導入したトランスジェニックゼブラフィッシュが骨形成異常を起こす点も明らかにし、骨形成異常、性決定と内分泌撹乱物質の関係を調べる基礎を築くことができたと認識している。今後、特に発生段階における性決定・骨形成におけるアポトーシスの役割を調べ、内分泌撹乱物質の関連を明らかにすることは、上述の通り環境問題、発生・分化、再生医療を論ずる上でも重要である。

  17. ゼブラフィッシュによるトキシコゲノミクス／トキシコプロテオミクス研究 Competitive

    System: 受託研究

    2000 -

  18. Study on toxicogenomics/Proteomics by Zebrafish Competitive

    System: Grant-in-Aid for Scientific Research

    2000 -

  19. タンパク質翻訳後修飾による機能ゲノムネットワーク解析 Competitive

  20. ゼブラフィッシュによる次世代型ポストゲノム研究開発 Competitive

  21. Study on Cellulosome from Marine Bacteria Competitive

  22. Study on Degradation and Synthesis of Cell Wall in Seaweed Competitive

  23. Study on Fatty Metabolism in Fish Competitive

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Works 2

  1. 環境化学物質リスク評価のためのモニタリングシステクの開発

    2002 - 2003

  2. 化学物質安全性評価のためのエンブリオアレイシステムの開発

    2003 -