研究者紹介システム

石川 周
イシカワ シュウ
大学院科学技術イノベーション研究科 科学技術イノベーション専攻
准教授
農学関係
Last Updated :2021/04/12

研究者情報

所属

  • 【主配置】

    大学院科学技術イノベーション研究科 科学技術イノベーション専攻
  • 【配置】

    農学部 生命機能科学科, 大学院農学研究科 生命機能科学専攻, 先端バイオ工学研究センター

学位

  • 博士(学術), 信州大学

授業科目

ジャンル

  • 科学・技術 / バイオテクノロジー
  • 科学・技術 / 生命科学

コメントテーマ

  • 高効率バイオプロセス細胞
  • 枯草菌
  • 乳酸菌の加速進化機構
  • 有用遺伝子
  • 分子生物学
  • ゲノム生物学

研究活動

プロフィール情報

  • プロフィール

    枯草菌をつかって、細胞分裂、転写などの生育に必須な機能の分子メカニズムを研究してきた。その知見に基づき「汎用的高効率バイオプロセス細胞の創製」を目指している。
    それに利用するために、乳酸菌の加速進化機構の解明や、メタゲノムから効率的に有用遺伝子を取得する方法の開発も行っている。

研究キーワード

  • 微生物学
  • 分子生物学
  • タンパク質複合体
  • リボゾーム
  • 遺伝子発現制御
  • 必須タンパク質
  • 転写制御
  • ゲノム
  • テイコ酸
  • GTP結合蛋白質
  • 大腸菌
  • ChIP-chip解析
  • タイリングチップ
  • 細胞骨格蛋白質
  • 細胞システム
  • システム生物学
  • 細菌細胞
  • 枯草菌
  • 生体分子
  • 細胞分裂
  • 細菌
  • 蛋白質

研究分野

  • ライフサイエンス / ゲノム生物学
  • ライフサイエンス / 分子生物学
  • ライフサイエンス / 応用微生物学

委員歴

  • 2015年 - 2017年, 日本ゲノム微生物学会, 評議員

論文

  • Christophe Michon, Choong-Min Kang, Sophia Karpenko, Kosei Tanaka, Shu Ishikawa, Ken-Ichi Yoshida

    A rare stereoisomer of inositol, scyllo-inositol, is a therapeutic agent that has shown potential efficacy in preventing Alzheimer's disease. Mycobacterium tuberculosis ino1 encoding myo-inositol-1-phosphate (MI1P) synthase (MI1PS) was introduced into Bacillus subtilis to convert glucose-6-phosphate (G6P) into MI1P. We found that inactivation of pbuE elevated intracellular concentrations of NAD+·NADH as an essential cofactor of MI1PS and was required to activate MI1PS. MI1P thus produced was dephosphorylated into myo-inositol by an intrinsic inositol monophosphatase, YktC, which was subsequently isomerized into scyllo-inositol via a previously established artificial pathway involving two inositol dehydrogenases, IolG and IolW. In addition, both glcP and glcK were overexpressed to feed more G6P and accelerate scyllo-inositol production. Consequently, a B. subtilis cell factory was demonstrated to produce 2 g L-1 scyllo-inositol from 20 g L-1 glucose. This cell factory provides an inexpensive way to produce scyllo-inositol, which will help us to challenge the growing problem of Alzheimer's disease in our aging society.

    2020年03月02日, Communications biology, 3 (1), 93 - 93, 英語, 国際誌

    [査読有り]

  • Yoshida, Ken-ichi, Ishikawa, Shu

    2019年, J Nutr Sci Vitaminol, 65, S139 - S142, 英語

    [査読有り]

  • Nishihata Shogo, Kondo Takahiko, Tanaka Kosei, Ishikawa Shu, Takenaka Shinji, Kang Choong-Min, Yoshida Ken-ichi

    Background Bradyrhizobium diazoefficiens USDA110 nodulates soybeans for nitrogen fixation. It accumulates poly-3-hydroxybutyrate (PHB), which is of physiological importance as a carbon/energy source for survival during starvation, infection, and nitrogen fixation conditions. PHB accumulation is orchestrated by not only the enzymes for PHB synthesis but also PHB-binding phasin p

    BMC, 2018年10月, BMC Microbiology, 18, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Miyano Megumi, Tanaka Kosei, Ishikawa Shu, Mori Kotaro, Miguel-Arribas Andres, Meijer Wilfried J. J, Yoshida Ken-ichi

    Background: Bacterial strains of the genus Geobacillus grow at high temperatures of 50-75 °C and could thus be useful for biotechnological applications. However, genetic manipulation of these species is difficult because the current techniques for transforming Geobacillus species are not efficient. In this study, we developed an easy and efficient method for transforming Geobac

    BMC, 2018年08月, Microbial Cell Factories, 17, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Miyano Megumi, Tanaka Kosei, Ishikawa Shu, Takenaka Shinji, Miguel-Arribas Andres, Meijer Wilfried J. J, Yoshida Ken-ichi

    2018年01月27日, MICROBIAL CELL FACTORIES, 17

    [査読有り]

  • Chumsakul O, Nakamura K, Ishikawa S, Oshima T

    2018年, Methods in molecular biology (Clifton, N.J.), 1837, 33 - 47

    [査読有り]

  • Miyano Megumi, Tanaka Kosei, Ishikawa Shu, Takenaka Shinji, Miguel-Arribas Andres, Meijer Wilfried J. J, Yoshida Ken-ichi

    Background: The conjugative plasmid, pLS20, isolated from Bacillus subtilis natto, has an outstanding capacity for rapid self-transfer. In addition, it can function as a helper plasmid, mediating the mobilization of an independently replicating co-resident plasmid. Results: In this study, the oriT sequence of pLS20cat (oriT(LS20)) was eliminated to obtain the plasmid, pLS20catΔ

    BioMed Central, 2018年01月, Microbial Cell Factories, 17, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Onuma Chumsakul, Divya P. Anantsri, Tai Quirke, Taku Oshima, Kensuke Nakamura, Shu Ishikawa, Michiko M. Nakano

    Upon oxygen limitation, the Bacillus subtilis ResE sensor kinase and its cognate ResD response regulator play primary roles in the transcriptional activation of genes functioning in anaerobic respiration. The nitric oxide (NO)-sensitive NsrR repressor controls transcription to support nitrate respiration. In addition, the ferric uptake repressor (Fur) can modulate transcription under anaerobic conditions. However, whether these controls are direct or indirect has been investigated only in a gene-specific manner. To gain a genomic view of anaerobic gene regulation, we determined the genome-wide in vivo DNA binding of ResD, NsrR, and Fur transcription factors (TFs) using in situ DNase I footprinting combined with chromatin affinity precipitation sequencing (ChAP-seq; genome footprinting by high-throughput sequencing [GeF-seq]). A significant number of sites were targets of ResD and NsrR, and a majority of them were also bound by Fur. The binding of multiple TFs to overlapping targets affected each individual TF's binding, which led to combinatorial transcriptional control. ResD bound to both the promoters and the coding regions of genes under its positive control. Other genes showing enrichment of ResD at only the promoter regions are targets of direct ResD-dependent repression or antirepression. The results support previous findings of ResD as an RNA polymerase (RNAP)binding protein and indicated that ResD can associate with the transcription elongation complex. The data set allowed us to reexamine consensus sequence motifs of Fur, ResD, and NsrR and uncovered evidence that multiple TGW (where W is A or T) sequences surrounded by an A- and T-rich sequence are often found at sites where all three TFs competitively bind. IMPORTANCE Bacteria encounter oxygen fluctuation in their natural environment as well as in host organisms. Hence, understanding how bacteria respond to oxygen limitation will impact environmental and human health. ResD, NsrR, and Fur control transcription under anaerobic conditions. This work using in situ DNase I footprinting uncovered the genome-wide binding profile of the three transcription factors (TFs). Binding of the TFs is often competitive or cooperative depending on the promoters and the presence of other TFs, indicating that transcriptional regulation by multiple TFs is much more complex than we originally thought. The results from this study provide a more complete picture of anaerobic gene regulation governed by ResD, NsrR, and Fur and contribute to our further understanding of anaerobic physiology.

    AMER SOC MICROBIOLOGY, 2017年07月, JOURNAL OF BACTERIOLOGY, 199 (13), 英語

    [査読有り]

    研究論文(学術雑誌)

  • Dong-Min Kang, Christophe Michon, Tetsuro Morinaga, Kosei Tanaka, Shinji Takenaka, Shu Ishikawa, Ken-ichi Yoshida

    Background: Bacillus subtilis is able to utilize at least three inositol stereoisomers as carbon sources, myo-, scyllo-, and D-chiro-inositol (MI, SI, and DCI, respectively). NAD(+)-dependent SI dehydrogenase responsible for SI catabolism is encoded by iolX. Even in the absence of functional iolX, the presence of SI or MI in the growth medium was found to induce the transcription of iolX through an unknown mechanism. Results: Immediately upstream of iolX, there is an operon that encodes two genes, yisR and iolQ (formerly known as degA), each of which could encode a transcriptional regulator. Here we performed an inactivation analysis of yisR and iolQ and found that iolQ encodes a repressor of the iolX transcription. The coding sequence of iolQ was expressed in Escherichia coli and the gene product was purified as a His-tagged fusion protein, which bound to two sites within the iolX promoter region in vitro. Conclusions: IolQ is a transcriptional repressor of iolX. Genetic evidences allowed us to speculate that SI and MI might possibly be the intracellular inducers, however they failed to antagonize DNA binding of IolQ in in vitro experiments.

    BIOMED CENTRAL LTD, 2017年07月, BMC MICROBIOLOGY, 17, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Dong-Min Kang, Kosei Tanaka, Shinji Takenaka, Shu Ishikawa, Ken-ichi Yoshida

    Bacillus subtilis genes iolG, iolW, iolX, ntdC, yfiI, yrbE, yteT, and yulF belong to the Gfo/Idh/MocA family. The functions of iolG, iolW, iolX, and ntdC are known; however, the functions of the others are unknown. We previously reported the B. subtilis cell factory simultaneously overexpressing iolG and iolW to achieve bioconversion of myo-inositol (MI) into scyllo-inositol (SI). YulF shares a significant similarity with IolW, the NADP(+)-dependent SI dehydrogenase. Transcriptional abundance of yulF did not correlate to that of iol genes involved in inositol metabolism. However, when yulF was overexpressed instead of iolW in the B. subtilis cell factory, SI was produced from MI, suggesting a similar function to iolW. In addition, we demonstrated that recombinant His(6)-tagged YulF converted scyllo-inosose into SI in an NADPH-dependent manner. We have thus identified yulF encoding an additional NADP(+)-dependent SI dehydrogenase, which we propose to rename iolU.

    TAYLOR & FRANCIS LTD, 2017年05月, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 81 (5), 1026 - 1032, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Kosei Tanaka, Ayane Natsume, Shu Ishikawa, Shinji Takenaka, Ken-ichi Yoshida

    Background: A stereoisomer of inositol, scyllo-inositol (SI), has been regarded as a promising therapeutic agent for Alzheimer's disease. However, this compound is relatively rare, whereas another stereoisomer of inositol, myo-inositol (MI) is abundant in nature. Bacillus subtilis 168 has the ability to metabolize inositol stereoisomers, including MI and SI. Previously, we reported a B. subtilis cell factory with modified inositol metabolism that converts MI into SI in the culture medium. The strain was constructed by deleting all genes related to inositol metabolism and overexpressing key enzymes, IolG and IolW. By using this strain, 10 g/l of MI initially included in the medium was completely converted into SI within 48 h of cultivation in a rich medium containing 2% (w/v) Bacto soytone. Results: When the initial concentration of MI was increased to 50 g/l, conversion was limited to 15.1g/l of SI. Therefore, overexpression systems of IolT and PntAB, the main transporter of MI in B. subtilis and the membrane-integral nicotinamide nucleotide transhydrogenase in Escherichia coli respectively, were additionally introduced into the B. subtilis cell factory, but the conversion efficiency hardly improved. We systematically determined the amount of Bacto soytone necessary for ultimate conversion, which was 4% (w/v). As a result, the conversion of SI reached to 27.6 g/l within 48 h of cultivation. Conclusions: The B. subtilis cell factory was improved to yield a SI production rate of 27.6 g/l/48 h by simultaneous overexpression of IolT and PntAB, and by addition of 4% (w/v) Bacto soytone in the conversion medium. The concentration of SI was increased even in the stationary phase perhaps due to nutrients in the Bacto soytone that contribute to the conversion process. Thus, MI conversion to SI may be further optimized via identification and control of these unknown nutrients.

    BIOMED CENTRAL LTD, 2017年04月, MICROBIAL CELL FACTORIES, 16, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Ayako Terakawa, Ayane Natsume, Atsushi Okada, Shogo Nishihata, Junko Kuse, Kosei Tanaka, Shinji Takenaka, Shu Ishikawa, Ken-ichi Yoshida

    Background: In Escherichia coli, nagD, yrfG, yjjG, yieH, yigL, surE, and yfbR encode 5'-nucleotidases that hydrolyze the phosphate group of 5'-nucleotides. In Bacillus subtilis, genes encoding 5'-nucleotidase have remained to be identified. Results: We found that B. subtilis ycsE, araL, yutF, ysaA, and yqeG show suggestive similarities to nagD. Here, we expressed them in E. coli to purify the respective His(6)-tagged proteins. YcsE exhibited significant 5'-nucleotidase activity with a broader specificity, whereas the other four enzymes had rather weak but suggestive activities with various capacities and substrate specificities. In contrast, B. subtilis yktC shares high similarity with E. coli suhB encoding an inositol monophosphatase. YktC exhibited inositol monophosphatase activity as well as 5'-nucleotidase activity preferential for GMP and IMP. The ycsE, yktC, and yqeG genes are induced by oxidative stress and were dispensable, although yqeG was required to maintain normal growth on solid medium. In the presence of diamide, only mutants lacking yktC exhibited enhanced growth defects, whereas the other mutants without ycsE or yqeG did not. Conclusions: Accordingly, in B. subtilis, at least YcsE and YktC acted as major 5'-nucleotidases and the four minor enzymes might function when the intracellular concentrations of substrates are sufficiently high. In addition, YktC is involved in resistance to oxidative stress caused by diamide, while YqeG is necessary for normal colony formation on solid medium.

    BIOMED CENTRAL LTD, 2016年10月, BMC MICROBIOLOGY, 16 (1), 1 - 13, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Masahiro Tatsumi Akiyama, Taku Oshima, Onuma Chumsakul, Shu Ishikawa, Hisaji Maki

    Although the speed of nascent DNA synthesis at individual replication forks is relatively uniform in bacterial cells, the dynamics of replication fork progression on the chromosome are hampered by a variety of natural impediments. Genome replication dynamics can be directly measured from an exponentially growing cell population by sequencing newly synthesized DNA strands that were specifically pulse-labeled with the thymidine analogue 5-bromo-2-deoxyuridine (BrdU). However, a short pulse labeling with BrdU is impracticable for bacteria because of poor incorporation of BrdU into the cells, and thus, the genomewide dynamics of bacterial DNA replication remain undetermined. Using a new thymidine-requiring Escherichia coli strain, eCOMB, and high-throughput sequencing, we succeeded in determining the genomewide replication profile in bacterial cells. We also found that fork progression is paused in two similar to 200-kb chromosomal zones that flank the replication origin in the growing cells. This origin-proximal obstruction to fork progression was overcome by an increased thymidine concentration in the culture medium and enhanced by inhibition of transcription. These indicate that DNA replication near the origin is sensitive to the impediments to fork progression, namely a scarcity of the DNA precursor deoxythymidine triphosphate and probable conflicts between replication and transcription machineries.

    WILEY-BLACKWELL, 2016年08月, GENES TO CELLS, 21 (8), 907 - 914, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Koichi Higashi, Toru Tobe, Akinori Kanai, Ebru Uyar, Shu Ishikawa, Yutaka Suzuki, Naotake Ogasawara, Ken Kurokawa, Taku Oshima

    Bacteria can acquire new traits through horizontal gene transfer. Inappropriate expression of transferred genes, however, can disrupt the physiology of the host bacteria. To reduce this risk, Escherichia coli expresses the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes to control their expression. Once expression is optimized, the horizontally transferred genes may actually contribute to E. coli survival in new habitats. Therefore, we investigated whether and how H-NS contributes to this optimization process. A comparison of H-NS binding profiles on common chromosomal segments of three E. coli strains belonging to different phylogenetic groups indicated that the positions of H-NS-bound regions have been conserved in E. coli strains. The sequences of the H-NS-bound regions appear to have diverged more so than H-NS-unbound regions only when H-NS-bound regions are located upstream or in coding regions of genes. Because these regions generally contain regulatory elements for gene expression, sequence divergence in these regions may be associated with alteration of gene expression. Indeed, nucleotide substitutions in H-NS-bound regions of the ybdO promoter and coding regions have diversified the potential for H-NS-independent negative regulation among E. coli strains. The ybdO expression in these strains was still negatively regulated by H-NS, which reduced the effect of H-NS-independent regulation under normal growth conditions. Hence, we propose that, during E. coli evolution, the conservation of H-NS binding sites resulted in the diversification of the regulation of horizontally transferred genes, which may have facilitated E. coli adaptation to new ecological niches.

    PUBLIC LIBRARY SCIENCE, 2016年01月, PLOS GENETICS, 12 (1), 英語

    [査読有り]

    研究論文(学術雑誌)

  • TOYA Yoshihiro, HIRASAWA Takashi, ISHIKAWA Shu, CHUMSAKUL Onuma, MORIMOTO Takuya, LIU Shenghao, MASUDA Kenta, KAGEYAMA Yasushi, OZAKI Katsuya, OGASAWARA Naotake, SHIMIZU Hiroshi

    2015年12月, Biosci Biotechnol Biochem, 79 (12), 2073 - 2080, 英語

    [査読有り]

    研究論文(学術雑誌)

  • MALIK Amarila, HAPSARI Maria Tyas, OHTSU Iwao, ISHIKAWA Shu, TAKAGI Hiroshi

    2015年05月, J Biosci Bioeng, 119 (5), 515 - 520, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Murayama Satohiko, Ishikawa Shu, Chumsakul Onuma, Ogasawara Naotake, Oshima Taku

    2015年, Plos One, 10 (7)

    [査読有り]

  • Tanaka Kosei, Iwasaki Kana, Morimoto Takuya, Matsuse Takatsugu, Hasunuma Tomohisa, Takenaka Shinji, Chumsakul Onuma, Ishikawa Shu, Ogasawara Naotake, Yoshida Ken-ichi

    2015年, Bmc Microbiology, 15 (1)

    [査読有り]

  • Toya Yoshihiro, Hirasawa Takashi, Ishikawa Shu, Chumsakul Onuma, Morimoto Takuya, Liu Shenghao, Masuda Kenta, Kageyama Yasushi, Ozaki Katsuya, Ogasawara Naotake, Shimizu Hiroshi

    2015年, Bioscience Biotechnology and Biochemistry, 79 (12), 2073 - 2080

    [査読有り]

  • Malik Amarila, Hapsari Maria Tyas, Ohtsu Iwao, Ishikawa Shu, Takagi Hiroshi

    2015年, Journal of Bioscience and Bioengineering, 119 (5), 515 - 520

    [査読有り]

  • Bernadette Henares, Sushma Kommineni, Onuma Chumsakul, Naotake Ogasawara, Shu Ishikawa, Michiko M. Nakano

    The ResD response regulator activates transcription of diverse genes in Bacillus subtilis in response to oxygen limitation. ResD regulon genes that are the most highly induced during nitrate respiration include the nitrite reductase operon (nasDEF) and the flavohemoglobin gene (hmp), whose products function in nitric oxide (NO) metabolism. Transcription of these genes is also under the negative control of the NO-sensitive NsrR repressor. Recent studies showed that the NsrR regulon contains genes with no apparent relevance to NO metabolism and that the ResD response regulator and NsrR coordinately regulate transcription. To determine whether these genes are direct targets of NsrR and ResD, we used chromatin affinity precipitation coupled with tiling chip (ChAP-chip) and ChAP followed by quantitative PCR (ChAP-qPCR) analyses. The study showed that ResD and NsrR directly control transcription of the ykuNOP operon in the Fur regulon. ResD functions as an activator at the nasD and hmp promoters, whereas it functions at the ykuN promoter as an antirepressor of Fur and a corepressor for NsrR. This mechanism likely participates in fine-tuning of transcript levels in response to different sources of stress, such as oxygen limitation, iron limitation, and exposure to NO.

    AMER SOC MICROBIOLOGY, 2014年01月, JOURNAL OF BACTERIOLOGY, 196 (2), 493 - 503, 英語

    [査読有り]

    研究論文(学術雑誌)

  • HENARES Bernadette, KOMMINENI Sushma, CHUMSAKUL Onuma, OGASAWARA Naotake, ISHIKAWA Shu, NAKANO Michiko M

    The ResD response regulator activates transcription of diverse genes in Bacillus subtilis in response to oxygen limitation. ResD regulon genes that are the most highly induced during nitrate respiration include the nitrite reductase operon (nasDEF) and the flavohemoglobin gene (hmp), whose products function in nitric oxide (NO) metabolism. Transcription of these genes is also under the negative control of the NO-sensitive NsrR repressor. Recent studies showed that the NsrR regulon contains genes with no apparent relevance to NO metabolism and that the ResD response regulator and NsrR coordinately regulate transcription. To determine whether these genes are direct targets of NsrR and ResD, we used chromatin affinity precipitation coupled with tiling chip (ChAP-chip) and ChAP followed by quantitative PCR (ChAP-qPCR) analyses. The study showed that ResD and NsrR directly control transcription of the ykuNOP operon in the Fur regulon. ResD functions as an activator at the nasD and hmp promoters, whereas it functions at the ykuN promoter as an antirepressor of Fur and a corepressor for NsrR. This mechanism likely participates in fine-tuning of transcript levels in response to different sources of stress, such as oxygen limitation, iron limitation, and exposure to NO.

    AMER SOC MICROBIOLOGY, 2014年01月, J Bacteriol, 196 (2), 493 - 503, 英語

    [査読有り]

    研究論文(学術雑誌)

  • LEI Ying, OSHIMA Taku, OGASAWARA Naotake, ISHIKAWA Shu

    2013年04月, J Bacteriol, 195 (8), 1697 - 1705, 英語

    [査読有り]

    研究論文(学術雑誌)

  • 大島拓, 石川周

    2013年, 化学と生物, 51 (10), 670 - 678

    [査読有り]

  • Duman Ramona, Ishikawa Shu, Celik Ilkay, Strahl Henrik, Ogasawara Naotake, Troc Paulina, Loewe Jan, Hamoen Leendert W

    2013年, Proceedings of the National Academy of Sciences of the United States of America, 110 (48), 4601 - 4610

    [査読有り]

  • Chumsakul Onuma, Nakamura Kensuke, Kurata Tetsuya, Sakamoto Tomoaki, Hobman Jon L, Ogasawara Naotake, Oshima Taku, Ishikawa Shu

    2013年, DNA Research, 20 (4), 325 - 337

    [査読有り]

  • Ueda Takeshi, Takahashi Hiroki, Uyar Ebru, Ishikawa Shu, Ogasawara Naotake, Oshima Taku

    2013年, DNA Research, 20 (3), 263 - 271

    [査読有り]

  • Lei Ying, Oshima Taku, Ogasawara Naotake, Ishikawa Shu

    2013年, Journal of Bacteriology, 195 (8), 1697 - 1705

    [査読有り]

  • Okumura Hajime, Yoshimura Mika, Ueki Mikako, Oshima Taku, Ogasawara Naotake, Ishikawa Shu

    2012年, Nucleic Acids Research, 40 (1), 220 - 234

    [査読有り]

  • OKUMURA Hajime, YOSHIMURA Mika, UEKI Mikako, OSHIMA Taku, OGASAWARA Naotake, ISHIKAWA Shu

    2012年, Nucleic Acids Res, 40 (1), 220 - 234, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Ishikawa Shu, Okumura Hajime, Yoshimura Mika, Ueki Mikako, Oshima Taku, Ogasawara Naotake

    2012年, Genes & Genetic Systems, 87 (6), 385

    [査読有り]

  • 2Ap03 Bacillus subtilis cell factory for production of scyllo-inositol promising for Alzheimer's disease (Bio-Based Production) :

    YOSHIDA Ken-ichi, ONUMA Chumsakul, ISHIKAWA Shu, OGASAWARA Naotake

    日本生物工学会, 2012年, 日本生物工学会大会講演要旨集, 64, 英語

    研究論文(研究会,シンポジウム資料等)

  • Yoshikazu Kawai, Jon Marles-Wright, Robert M. Cleverley, Robyn Emmins, Shu Ishikawa, Masayoshi Kuwano, Nadja Heinz, Nhat Khai Bui, Christopher N. Hoyland, Naotake Ogasawara, Richard J. Lewis, Waldemar Vollmer, Richard A. Daniel, Jeff Errington

    Teichoic acids and acidic capsular polysaccharides are major anionic cell wall polymers (APs) in many bacteria, with various critical cell functions, including maintenance of cell shape and structural integrity, charge and cation homeostasis, and multiple aspects of pathogenesis. We have identified the widespread LytR-Cps2A-Psr (LCP) protein family, of previously unknown function, as novel enzymes required for AP synthesis. Structural and biochemical analysis of several LCP proteins suggest that they carry out the final step of transferring APs from their lipid-linked precursor to cell wall peptidoglycan (PG). In Bacillus subtilis, LCP proteins are found in association with the MreB cytoskeleton, suggesting that MreB proteins coordinate the insertion of the major polymers, PG and AP, into the cell wall. The EMBO Journal (2011) 30, 4931-4941. doi: 10.1038/emboj.2011.358; Published online 30 September 2011

    NATURE PUBLISHING GROUP, 2011年12月, EMBO JOURNAL, 30 (24), 4931 - 4941, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Amarila Malik, Shu Ishikawa, Muhamad Sahlan, Naotake Ogasawara, Uyen Quynh Nguyen, Herman Suryadi

    Sucrose phosphorylase has been known for its activity to generate some intermediate drug precursors. In spite of the broad acceptor specificity of the enzyme, the difference in enzyme specificity between bacterial species was recognized. A number of lactic acid bacteria strains known as exopolysaccharide producer isolated previously from local foods, beverages and soil samples from Indonesia's biosphere were screened for gene encode sucrose phosphorylase using polymerase chain reaction (PCR). A 1476-bp gene fragment from Leuc mesenteroides MBFWRS-3(1) isolated from sugar containing-beverage from Solo, Central Java, called Wedang Ronde, was successfully cloned encoding 492 amino acid residues of sucrose phosphorylase SPaseWRS-3(1) (AN. HM536929). Its predicted molecular mass was found to be closed to the confirmed one by sodium dodecyl sulfate polyacrylamide gel electrophresis (SDS-PAGE) gel (approximately 57 kDa). Although, it revealed high similarity in amino acid sequences to the existing ones (99% identity to 1355SPase), this is the first report on SPase from Indonesia's biosphere. The recombinant SPaseWRS-3(1) expressed by Escherichia coli BL21 Star (TM) showed lower activity as compared to the reference SPase, which is 50%.

    ACADEMIC JOURNALS, 2011年11月, AFRICAN JOURNAL OF BIOTECHNOLOGY, 10 (74), 16915 - 16923, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Kensuke Nakamura, Taku Oshima, Takuya Morimoto, Shun Ikeda, Hirofumi Yoshikawa, Yuh Shiwa, Shu Ishikawa, Margaret C. Linak, Aki Hirai, Hiroki Takahashi, Md. Altaf-Ul-Amin, Naotake Ogasawara, Shigehiko Kanaya

    We identified the sequence-specific starting positions of consecutive miscalls in the mapping of reads obtained from the Illumina Genome Analyser (GA). Detailed analysis of the miscall pattern indicated that the underlying mechanism involves sequence-specific interference of the base elongation process during sequencing. The two major sequence patterns that trigger this sequence-specific error (SSE) are: (i) inverted repeats and (ii) GGC sequences. We speculate that these sequences favor dephasing by inhibiting single-base elongation, by: (i) folding single-stranded DNA and (ii) altering enzyme preference. This phenomenon is a major cause of sequence coverage variability and of the unfavorable bias observed for population-targeted methods such as RNA-seq and ChIP-seq. Moreover, SSE is a potential cause of false single-nucleotide polymorphism (SNP) calls and also significantly hinders de novo assembly. This article highlights the importance of recognizing SSE and its underlying mechanisms in the hope of enhancing the potential usefulness of the Illumina sequencers.

    OXFORD UNIV PRESS, 2011年07月, NUCLEIC ACIDS RESEARCH, 39 (13), 英語

    [査読有り]

    研究論文(学術雑誌)

  • Yoko Kusuya, Ken Kurokawa, Shu Ishikawa, Naotake Ogasawara, Taku Oshima

    Bacterial Gre factors associate with RNA polymerase (RNAP) and stimulate intrinsic cleavage of the nascent transcript at the active site of RNAP. Biochemical and genetic studies to date have shown that Escherichia coli Gre factors prevent transcriptional arrest during elongation and enhance transcription fidelity. Furthermore, Gre factors participate in the stimulation of promoter escape and the suppression of promoter-proximal pausing during the beginning of RNA synthesis in E. coli. Although Gre factors are conserved in general bacteria, limited functional studies have been performed in bacteria other than E. coli. In this investigation, ChAP-chip analysis (chromatin affinity precipitation coupled with DNA microarray) was conducted to visualize the distribution of Bacillus subtilis GreA on the chromosome and to determine the effects of GreA inactivation on core RNAP trafficking. Our data show that GreA is uniformly distributed in the transcribed region from the promoter to coding region with core RNAP, and its inactivation induces RNAP accumulation at many promoter or promoter-proximal regions. Based on these findings, we propose that GreA would constantly associate with core RNAP during transcriptional initiation and elongation and resolves its stalling at promoter or promoter-proximal regions, thus contributing to the even distribution of RNAP along the promoter and coding regions in B. subtilis cells.

    AMER SOC MICROBIOLOGY, 2011年06月, JOURNAL OF BACTERIOLOGY, 193 (12), 3090 - 3099, 英語

    [査読有り]

    研究論文(学術雑誌)

  • KUSUYA Yoko, KUROKAWA Ken, ISHIKAWA Shu, OGASAWARA Naotake, OSHIMA Taku

    Bacterial Gre factors associate with RNA polymerase (RNAP) and stimulate intrinsic cleavage of the nascent transcript at the active site of RNAP. Biochemical and genetic studies to date have shown that Escherichia coli Gre factors prevent transcriptional arrest during elongation and enhance transcription fidelity. Furthermore, Gre factors participate in the stimulation of promoter escape and the suppression of promoter-proximal pausing during the beginning of RNA synthesis in E. coli. Although Gre factors are conserved in general bacteria, limited functional studies have been performed in bacteria other than E. coli. In this investigation, ChAP-chip analysis (chromatin affinity precipitation coupled with DNA microarray) was conducted to visualize the distribution of Bacillus subtilis GreA on the chromosome and to determine the effects of GreA inactivation on core RNAP trafficking. Our data show that GreA is uniformly distributed in the transcribed region from the promoter to coding region with core RNAP, and its inactivation induces RNAP accumulation at many promoter or promoter-proximal regions. Based on these findings, we propose that GreA would constantly associate with core RNAP during transcriptional initiation and elongation and resolves its stalling at promoter or promoter-proximal regions, thus contributing to the even distribution of RNAP along the promoter and coding regions in B. subtilis cells.

    AMER SOC MICROBIOLOGY, 2011年06月, J Bacteriol, 193 (12), 3090 - 3099, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Onuma Chumsakul, Hiroki Takahashi, Taku Oshima, Takahiro Hishimoto, Shigehiko Kanaya, Naotake Ogasawara, Shu Ishikawa

    AbrB is a global transcriptional regulator of Bacillus subtilis that represses the expression of many genes during exponential growth. Here, we demonstrate that AbrB and its homolog Abh bind to hundreds of sites throughout the entire B. subtilis genome during exponential growth. Comparison of regional binding of AbrB and Abh in wild-type, delta abrB and delta abh backgrounds revealed that they bind as homomer and/or heteromer forms with different specificities and affinities. We found four AbrB and Abh binding patterns were major. Three of these contain pairs of TGGNA motifs connected by A/T-rich sequences, differing in arrangement and spacing. We also assessed the direct involvement of these complexes in the control of gene expression. Our data indicate that AbrB usually acts as a repressor, and that the ability of Abh to act as a transcriptional regulator was limited. We found that changes to AbrB/Abh levels affect their binding at several promoters and consequently transcriptional regulation. Surprisingly, most AbrB/Abh binding events had no impact on transcription, suggesting an interesting possibility that AbrB/Abh binding is analogous to nucleoid-associated protein binding in Escherichia coli.

    OXFORD UNIV PRESS, 2011年01月, NUCLEIC ACIDS RESEARCH, 39 (2), 414 - 428, 英語

    [査読有り]

    研究論文(学術雑誌)

  • CHUMSAKUL Onuma, TAKAHASHI Hiroki, OSHIMA Taku, HISHIMOTO Takahiro, KANAYA Shigehiko, OGASAWARA Naotake, ISHIKAWA Shu

    AbrB is a global transcriptional regulator of Bacillus subtilis that represses the expression of many genes during exponential growth. Here, we demonstrate that AbrB and its homolog Abh bind to hundreds of sites throughout the entire B. subtilis genome during exponential growth. Comparison of regional binding of AbrB and Abh in wild-type, delta abrB and delta abh backgrounds revealed that they bind as homomer and/or heteromer forms with different specificities and affinities. We found four AbrB and Abh binding patterns were major. Three of these contain pairs of TGGNA motifs connected by A/T-rich sequences, differing in arrangement and spacing. We also assessed the direct involvement of these complexes in the control of gene expression. Our data indicate that AbrB usually acts as a repressor, and that the ability of Abh to act as a transcriptional regulator was limited. We found that changes to AbrB/Abh levels affect their binding at several promoters and consequently transcriptional regulation. Surprisingly, most AbrB/Abh binding events had no impact on transcription, suggesting an interesting possibility that AbrB/Abh binding is analogous to nucleoid-associated protein binding in Escherichia coli.

    OXFORD UNIV PRESS, 2011年01月, Nucleic Acids Res, 39 (2), 414 - 428, 英語

    [査読有り]

    研究論文(学術雑誌)

  • ISHIKAWA Shu, OSHIMA Taku, KUROKAWA Ken, KUSUYA Yoko, OGASAWARA Naotake

    2010年11月, J Bacteriol, 192 (21), 5778 - 5787, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Ishikawa Shu, Oshima Taku, Kurokawa Ken, Kusuya Yoko, Ogasawara Naotake

    2010年, Journal of Bacteriology, 192 (21), 5778 - 5787

    [査読有り]

  • Wu Ling Juan, Ishikawa Shu, Kawai Yoshikazu, Oshima Taku, Ogasawara Naotake, Errington Jeff

    2009年, Embo Journal, 28 (13), 1940 - 1952

    [査読有り]

  • Uyar Ebru, Kurokawa Ken, Yoshimura Mika, Ishikawa Shu, Ogasawara Naotake, Oshima Taku

    2009年, Journal of Bacteriology, 191 (7), 2388 - 2391

    [査読有り]

  • 石川周, 小笠原直毅

    2008年, 蛋白質核酸酵素, 53 (13), 1725 - 1731

    [査読有り]

  • Cho Eunha, Ogasawara Naotake, Ishikawa Shu

    2008年, Genes & Genetic Systems, 83 (2), 111 - 125

    [査読有り]

  • ISHIKAWA Shu, OGURA Yoshitoshi, YOSHIMURA Mika, OKUMURA Hajime, CHO Eunha, KAWAI Yoshikazu, KUROKAWA Ken, OSHIMA Taku, OGASAWARA Naotake

    2007年08月, DNA Res, 14 (4), 155 - 168, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Ishikawa Shu, Ogura Yoshitoshi, Yoshimura Mika, Okumura Hajime, Cho Eunha, Kawai Yoshikazu, Kurokawa Ken, Oshima Taku, Ogasawara Naotake

    2007年, DNA Research, 14 (4), 155 - 168

    [査読有り]

  • ISHIKAWA Shu, KAWAI Yoshikazu, HIRAMATSU Konosuke, KUWANO Masayoshi, OGASAWARA Naotake

    2006年06月, Mol Microbiol, 60 (6), 1364 - 1380, 英語

    [査読有り]

    研究論文(学術雑誌)

  • タイリングアレイを用いた細菌ゲノム機能研究の可能性

    小笠原直毅, 石川周, 黒川顕, 大島拓

    2006年, 細胞工学, 25, 1155 - 1160, 日本語

    [招待有り]

  • Oshima Taku, Ishikawa Shu, Kurokawa Ken, Aiba Hirofumi, Ogasawara Naotake

    2006年, DNA Research, 13 (4), 141 - 153

    [査読有り]

  • Ishikawa S, Kawai Y, Hiramatsu K, Kuwano M, Ogasawara N

    2006年, Molecular Microbiology, 60 (6), 1364 - 1380

    [査読有り]

  • BONGIORNI Cristina, ISHIKAWA Shu, STEPHENSON Sophie, OGASAWARA Naotake, PEREGO Marta

    2005年07月, J Bacteriol, 187 (13), 4353 - 4361, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Bongiorni C, Ishikawa S, Stephenson S, Ogasawara N, Perego M

    2005年, Journal of Bacteriology, 187 (13), 4353 - 4361

    [査読有り]

  • FUKUSHIMA T, ISHIKAWA S, YAMAMOTO H, OGASAWARA N, SEKIGUCHI J

    2003年04月, J Biochem, 133 (4), 475 - 483, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Fukushima Tatsuya, Ishikawa Shu, Yamamoto Hiroki, OGASAWARA Naotake, SEKIGUCHI Junichi

    Japanese Biochemical Society, 2003年04月, The journal of biochemistry, 133 (4), 475 - 483, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Fukushima T, Ishikawa S, Yamamoto H, Ogasawara N, Sekiguchi J

    2003年, Journal of Biochemistry, 133 (4), 475 - 483

    [査読有り]

  • Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Debarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauel C, Meima R, Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura M, Ohanan T, O'Reilly M, O'Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP, Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E, Schumann W, Seegers JFML, Sekiguchi J, Sekowska A, Seror SJ, Simon M, Stragier P, Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, van Dijl JM, Watabe K, Wipat A, Yamamoto H, Yamamoto M, Yamamoto Y, Yamane K, Yata K, Yoshida K, Yoshikawa H, Zuber U, Ogasawara N

    2003年, Proceedings of the National Academy of Sciences of the United States of America, 100 (8), 4678 - 4683

    [査読有り]

  • Shida Toshio, Mukaijo Kohsuke, Ishikawa Shu, YAMAMOTO Hiroki, SEKIGUCHI Junichi

    A hyper extracellular protein producer, Bacillus subtilis 327UH, produced large amounts of levan in a medium containing 20% sucrose, and the yield of levan after 10 hours was more than 60%, when based on the fructose amount of sucrose. After transformation of 327UH with a levanase-deficient 168SC (sacC : : Cm^r) chromosomal DNA, a Cm^r transformant 327UHSC (sacC : : Cm^r degSU(

    社団法人日本農芸化学会, 2002年07月, Bioscience, biotechnology, and biochemistry, 66 (7), 1555 - 1558, 英語

    [査読有り]

    研究論文(学術雑誌)

  • SHIDA T, MUKAIJO K, ISHIKAWA S, YAMAMOTO H, SEKIGUCHI J

    2002年07月, Biosci Biotechnol Biochem, 66 (7), 1555 - 1558, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Shida T, Mukaijo K, Ishikawa S, Yamamoto H, Sekiguchi J

    2002年, Bioscience Biotechnology and Biochemistry, 66 (7), 1555 - 1558

    [査読有り]

  • Ishikawa S, Core L, Perego M

    2002年, Journal of Biological Chemistry, 277 (23), 20483 - 20489

    [査読有り]

  • Core LJ, Ishikawa S, Perego M

    2001年, Peptides, 22 (10), 1549 - 1553

    [査読有り]

  • ペプチドグリカンヒドロラーゼLytFは枯草菌の栄養増殖期におけるCwlFによる細胞分離に役割がある

    OHNISHI R, ISHIKAWA S, SEKIGUCHI J

    1999年05月, J Bacteriol, 181 (10), 3178 - 3184, 英語

    [査読有り]

    研究論文(学術雑誌)

  • Ohnishi R, Ishikawa S, Sekiguchi J

    1999年, Journal of Bacteriology, 181 (10), 3178 - 3184

    [査読有り]

  • Ishikawa S, Kawahara S, Sekiguchi J

    1999年, Molecular and General Genetics, 262 (4/5), 738 - 748

    [査読有り]

  • 519 枯草菌ゲノム解析と発芽関連遺伝子

    福島 達也, 石川 周, 山本 博規, 関口 順一

    日本生物工学会, 1999年, 日本生物工学会大会講演要旨集, 11, 日本語

    [査読有り]

    研究論文(研究会,シンポジウム資料等)

  • Sekiguchi J, Sato T, Nanamiya H, Ohashi Y, Kawamura F, Takamatsu H, Kodama T, Watabe K, Ishikawa S

    1999年, Tanpakushitsu Kakusan Koso, 44 (10), 1460 - 6

    [査読有り]

  • Bacillus subtilisにおける細胞分離に影響する新規な細胞壁ヒドロラーゼ遺伝子cwlFの制御

    ISHIKAWA S, HARA Y, OHNISHI R, SEKIGUCHI J

    1998年05月, J Bacteriol, 180 (9), 2549 - 2555, 英語

    [査読有り]

    研究論文(学術雑誌)

  • 枯草菌胞子の発芽に影響を与える,新たに推定された細胞壁ヒドロラーゼ遺伝子(cwlJ)の調節および解析

    ISHIKAWA S, YAMANE K, SEKIGUCHI J

    1998年03月, J Bacteriol, 180 (6), 1375 - 1380, 英語

    [査読有り]

    研究論文(学術雑誌)

  • S63 オートリシンの細胞壁結合ドメインを用いた枯草菌表層への蛋白の局在化

    土屋 篤史, 石川 周, 関口 順一

    日本生物工学会, 1998年, 日本生物工学会大会講演要旨集, 10, 日本語

    研究論文(研究会,シンポジウム資料等)

  • Ishikawa S, Hara Y, Ohnishi R, Sekiguchi J

    1998年, Journal of Bacteriology, 180 (9), 2549 - 2555

    [査読有り]

  • Ishikawa S, Yamane K, Sekiguchi J

    1998年, Journal of Bacteriology, 180 (6), 1375 - 1380

    [査読有り]

  • Kawahara S, Utsunomiya C, Ishikawa S, Sekiguchi J

    1997年, Journal of Fermentation and Bioengineering, 83 (5), 419 - 422

    [査読有り]

  • 140 B.subtilisの対数増殖期におけるオートリシン、Cw1Fの研究

    原 佳子, 大西 亮, 石川 周, 関口 順一

    日本生物工学会, 1997年, 日本生物工学会大会講演要旨集, 9, 日本語

    研究論文(研究会,シンポジウム資料等)

  • 139 枯草菌の胞子発芽に影響する遺伝子、cw1Jに関する研究

    石川 周, 山根 國男, 関口 順一

    日本生物工学会, 1997年, 日本生物工学会大会講演要旨集, 9, 日本語

    研究論文(研究会,シンポジウム資料等)

MISC

  • H‐NSによる転写抑制を介した大腸菌ゲノムの多様性獲得機構

    東光一, 戸邉亨, 石川周, 鈴木穣, 小笠原直毅, 黒川顕, 黒川顕, 大島拓

    2016年, 日本ゲノム微生物学会年会要旨集, 10th, 63, 日本語

  • 枯草菌ゲノム縮小株を用いた組換えタンパク質生産における転写,代謝フラックス解析

    戸谷吉博, 河崎優樹, 平沢敬, 増田健太, 森本拓也, ONUMA Chumsakul, 石川周, 大島拓, 影山泰, 尾崎克也, 小笠原直毅, 清水浩

    2013年03月05日, 日本農芸化学会大会講演要旨集(Web), 2013, 4B11A10 (WEB ONLY), 日本語

  • 大腸菌Hha,YdgTタンパク質による外来性遺伝子の転写抑制

    上田剛士, 高橋弘喜, 石川周, 小笠原直毅, 大島拓

    2013年, 日本ゲノム微生物学会年会要旨集, 7th, 80, 日本語

  • 2Ap03 Bacillus subtilis cell factory for production of scyllo-inositol promising for Alzheimer's disease (Bio-Based Production)

    YOSHIDA Ken-ichi, ONUMA Chumsakul, ISHIKAWA Shu, OGASAWARA Naotake

    公益社団法人日本生物工学会, 2012年10月, 日本生物工学会大会講演要旨集, 64, 英語

    講演資料等(セミナー,チュートリアル,講習,講義他)

  • Bacillus subtilisにおいてバイオフィルム形成を刺激するVeg蛋白質の機能解析

    LEI Ying, ISHIKAWA Shu, OGASAWARA Naotake

    2012年, 日本ゲノム微生物学会年会要旨集, 6th, 85, 英語

    講演資料等(セミナー,チュートリアル,講習,講義他)

  • 転写因子GreAはB.subtilis細胞におけるRNAポリメラーゼのプロモーター近医停止を解決する

    KUSUYA Yoko, OSHIMA Taku, ISHIKAWA Shu, KUROKAWA Ken, OGASAWARA Naotake

    2011年, 日本分子生物学会年会プログラム・要旨集(Web), 34th, 3P - 0215 (WEB ONLY), 英語

    講演資料等(セミナー,チュートリアル,講習,講義他)

  • 枯草菌のdegU32(hy)はカタボライトレプレッションを積極的に解除する

    IWASAKI Kana, ISHIKAWA Shu, OGASAWARA Naotake, TAKENAKA Shinji, YOSHIDA Ken‐Ichi

    2011年, 日本分子生物学会年会プログラム・要旨集(Web), 34th, 2P - 0003 (WEB ONLY), 日本語

    講演資料等(セミナー,チュートリアル,講習,講義他)

  • 枯草菌における新規核様体蛋白質の同定

    LEI Ying, ISHIKAWA Shu, OGASAWARA Naotake

    2009年, 日本分子生物学会年会講演要旨集, 32nd (Vol.1), 126, 英語

    講演資料等(セミナー,チュートリアル,講習,講義他)

  • ChAP‐chip解析を用いたin vivoにおける枯草菌RNA polymerase α subunit(RpoA)と相互作用するゲノム部位の網羅解析

    MURAYAMA Satohiko, OSHIMA Taku, ISHIKAWA Shu, OGASAWARA Naotake

    2009年, 日本分子生物学会年会講演要旨集, 32nd (Vol.4), 92, 英語

    講演資料等(セミナー,チュートリアル,講習,講義他)

  • Bacillus subtilisにおける核様体蛋白質の探索:B.subtilisとE.coliとの間のChAP(ChIP)チップ解析を用いた比較解析

    CHUMSAKUL Onuma, UYAL Ebru, ISHIKAWA Shu, OSHIMA Taku, OGASAWARA Naotake

    2009年, 日本分子生物学会年会講演要旨集, 32nd (Vol.1), 27, 英語

    講演資料等(セミナー,チュートリアル,講習,講義他)

  • 枯草菌ゲノムの分子生物学 枯草菌の胞子形成,胞子,発芽

    佐藤勉, 七宮英晃, 大橋由明, 河村富士夫, 高松宏治, 児玉武子, 渡部一仁, 石川周, 関口順一

    1999年08月, 蛋白質 核酸 酵素, 44 (10), 1460 - 1466, 日本語

    [査読有り]

    記事・総説・解説・論説等(学術雑誌)

  • オートリシンの細胞壁結合ドメインを用いた枯草菌表層への蛋白の局在化

    土屋篤史, 石川周, 関口順一

    1998年, 日本生物工学会大会講演要旨集, 1998, 11, 日本語

    講演資料等(セミナー,チュートリアル,講習,講義他)

  • 枯草菌の胞子発芽に影響する遺伝子,cwlJに関する研究

    石川周, 山根国男, 関口順一

    1997年, 日本生物工学会大会講演要旨集, 1997, 22, 日本語

    講演資料等(セミナー,チュートリアル,講習,講義他)

  • B.subtilisの対数増殖期におけるオートリシン,CwlFの研究

    原佳子, 大西亮, 石川周, 関口順一

    1997年, 日本生物工学会大会講演要旨集, 1997, 22, 日本語

    講演資料等(セミナー,チュートリアル,講習,講義他)

書籍等出版物

  • GeF-seq: A Simple Procedure for Base Pair Resolution ChIP-seq

    Onuma Chumsakul, Kensuke Nakamura, 石川 周, Taku Oshima

    共著, Humana Press, New York, NY, 2018年, 英語

    学術書

  • 高精度で結合領域を決定するGeF-seq

    大島 拓, 石川 周, Chumsakul Onuma, 中村 建介

    共著, 羊土社, 2014年09月, 日本語

    学術書

  • 細菌の発現制御機構をゲノムワイドに解析する :次世代シーケンサーを用いた高精度な網羅的解析の可能性

    大島 拓, 石川 周

    単著, 日本農芸化学会, 2013年10月, 日本語

    学術書

  • 細菌の細胞分裂の分子メカニズム

    石川 周, 小笠原 直毅

    共著, 共立出版, 2008年10月, 日本語

    学術書

  • 枯草菌の胞子形成,胞子,発芽

    佐藤 勉, 七宮 英晃, 大橋 由明, 河村 富士夫, 高松 宏治, 児玉 武子, 渡部 一仁, 石川 周, 関口 順一

    共著, 共立出版, 1999年08月, 日本語

    学術書

所属学協会

  • 日本ゲノム微生物学会

  • 日本乳酸菌学会

  • グラム陽性菌ゲノム機能会議

共同研究・競争的資金等の研究課題

  • 石川 周

    科学研究費補助金/挑戦的研究(開拓), 2018年06月 - 2023年03月, 研究代表者

    競争的資金

  • 吉田 健一

    科学研究費補助金/基盤研究(B), 2018年04月 - 2022年03月

    競争的資金

  • 石川 周

    文部科学省, 科学研究費補助金(基盤研究(C)), 2015年 - 2017年, 研究代表者

    競争的資金

  • 汎用的高効率バイオプロセス細胞の創製

    小笠原 直毅

    独立行政法人科学技術振興機構(JST), 先端的低炭素化技術開発(ALCA), 2010年 - 2016年

    化学プロセスによる諸有用ケミカル素材の工業的生産を、バイオプロセスによる生産へ転換するために、革新的な「汎用的高効率バイオプロセス細胞」を創出します。具体的には、現在、諸有用分子の工業的合成等に用いられている枯草菌について、その増殖メカニズムの制御により細胞を素材生産期に導き、維持し、同時に、代謝フラックスの制御によって多様な産物を効率的に生産できる汎用性を備えたバイオプロセス技術を開発します。

    競争的資金

  • 石川 周

    文部科学省, 科学研究費補助金(基盤研究(C)), 2012年 - 2014年, 研究代表者

    細菌の細胞分裂はFtsZが中心となり行われるが、FtsZは細胞膜に結合できないので、細胞膜に繋ぎとめる蛋白質が必須である。大腸菌ではFtsAが、シアノバクテリアではSepFがその役割を担うと考えられるが、増殖に必須である。枯草菌は両方の因子を備え、さらに同様の役割をすると考えられるEzrAも有するので、各々が破壊可能である。本研究では、酵母2ハブリッド解析、結晶構造、電子顕微鏡観察など多面的に調べ、SepFがFtsZを膜につなぎとめるメカニズムを解明した。また、EzrAがFtsZと直接結合せず、FtsAとの結合を介してZ-ringのダイナミズムを促進している、というモデルを提案した。

    競争的資金

  • 小笠原 直毅

    文部科学省, 科学研究費補助金(基盤研究(A)), 2011年 - 2013年

    我々は、1bpの解像度でDNA結合タンパク質とゲノムDNAとの結合領域を網羅的に解析可能なGeF-seq法を新たに開発し、進化的に大きく異なる細菌、大腸菌と枯草菌の核様体タンパク質について解析を行った。その結果、配列非特異的な結合様式を示すHUタンパク質は、枯草菌、大腸菌で同様の結合様式を示すものの、大腸菌では、DNAが屈曲あるいはヘアピン状の構造を取りうるDNA配列に、FisおよびIHFタンパク質が結合し、DNAと構造を取ることが示唆された。これらのタンパク質は枯草菌には存在しないことから、細菌種ごとに核様体構造が大きく異なる可能性が示された。

    競争的資金

  • 山本 博規

    文部科学省, 科学研究費補助金(基盤研究(C)), 2011年 - 2013年

    枯草菌が桿状形態を維持して増殖するためには、細胞壁溶解酵素の活性が必要である。本研究では、これらの酵素の機能を制御する因子の解明を試みた。まず、LytEのシグナルペプチド(SPLytE)を用いてLytFを発現する株(SPLytE-LytF)では、分泌されたLytFは本来のセプタムと極だけでなく細胞側壁にも局在していた。また、lytEとcwlOの合成致死性についても、部分的ではあるものの相補できるようになっていた。以上の結果から、シグナルペプチドが細胞壁溶解酵素の局在性と機能を支配している可能性が示唆された。さらに詳細に調べた結果、SPLytEの疎水性領域の前半部分が重要であることがわかった。

    競争的資金

  • 山本 博規

    文部科学省, 科学研究費補助金(基盤研究(C)), 2007年 - 2009年

    レクチンの一種であるConcanavalin Aの蛍光標識物(ConA-TMR)を用いることにより、枯草菌の細胞壁テイコ酸(WTA)を特異的に検出する方法を確立した。種々のテイコ酸修飾遺伝子変異株を用いて観察を行った結果、ConA-TMRはmajor WTAのグルコース修飾を効率よく検出し、minor WTAやリポテイコ酸は検出できないことが明らかになった。また、major WTAのグルコース修飾に関与するtagE条件変異株を用いて、細胞側壁におけるWTA修飾が螺旋状に行われていることを明らかにした。さらに側壁のWTA修飾制御には、細胞骨格蛋白質のひとつであるMreBが関与している可能性が示唆された。

    競争的資金

  • 小笠原 直毅

    文部科学省, 科学研究費補助金(若手研究(B)), 2005年 - 2009年

    FtsZは自己縮合してポリマー構造、さらにはリング構造を形成し、細菌の細胞分裂の基盤となる。この様な反応には、枯草菌ではFtsZと直接結合するFtsA、YlmF、ZapAとの結合が重要である。そこで、このような細胞分裂初期の分子メカニズムを解明するために、FtsZにランダムに変異を導入し、相互作用を失う変異FtsZを酵母2ハイブリッド解析により同定し、どのアミノ酸がFtsZ自身やFtsA、YlmF、ZapAとの結合に関わっているかを決定した。FtsZは、Plus End領域、T7 loop、Minus End領域、保存されていない領域、保存性の高いC末端配列からなる。Methanococcus JannaschiiのFtsZの結晶構造解析などから、FtsZポリマーは、異なるFtsZのPlusとMinus Endが結合して形成されると考えられていたが、本研究で得られた変異FtsZの結果はこれとよく一致しており、このようなモデルが枯草菌FtsZにも当てはまることがわかった。また、保存性の高いC末端配列に欠損、もしくは変異を持つ変異FtsZでは、FtsAとYlmFとの結合能を失うこと

    競争的資金

  • 石川 周

    文部科学省, 科学研究費補助金(特定領域研究), 2006年 - 2007年, 研究代表者

    細菌細胞の増殖を支える遺伝子・タンパク質のネットワークがどのように構築されているか、その基本原理の解明を目指して、2大モデル細菌である枯草菌・大腸菌を対象として、タイリングチップを用いたChIP-chip解析や質量分析法を用いた複合来解析等の新たな研究手法の導入を進め、新たな必須遺伝子機能、必須遺伝子産物間の機能ネットワーク、転写調節タンパク質と核様体タンパク質による転写制御ネットワーク、核様体タンパク質による細胞周期制御、代謝ネットワークのモデル化等について、多くの新たな知見を明らかにした。

    競争的資金

  • 小笠原 直毅

    文部科学省, 科学研究費補助金(基盤研究(A)), 2005年 - 2007年

    枯草菌は、モデル生物として、ゲノム機能解析が進んでいる。その中で、ゲノム配列決定によって見出された機能未知、あるいは、未解析である遺伝子の破壊株ライブラリーの作成が、研究代表者を中心として行われた(Proc Natl Acad Sci USA,100,4678-4683,2003)。その結果、LB培地・37度という培養条件で、その破壊が致死となる必須遺伝子は271であるということが明らかとなった。その内、機能が不明確なものは22遺伝子であった。興味深いことに、その中の7遺伝子は、分子スイッチとして働くと考えられるGTP結合蛋白質をコードしていた(Microbiology,148,3539-3552,2002)。GTP結合蛋白質には、GTP結合型とGDP結合型の2つの状態があり、それぞれに特異的なeffectorに作用することにより分子スイッチとして働く。GTP-GDP型の変換は内在性のGTPase活性により行われるが、GTPase活性化因子、GTP-GDP交換促進因子等による調節を受けている。従って、GTP結合蛋白質の機能を解明するためには、そのGTPase活性を調節する因

    競争的資金

産業財産権

  • 枯草菌変異株及びその利用

    増田 健太, 劉 生浩, 森本 拓也, 小笠原 直毅, 石川 周, チュムサクル オンウマ

    特願2015-226957, 2015年11月19日, 花王株式会社, 国立大学法人 奈良先端科学技術大学院大学, 特開2017-093321, 2017年06月01日

    特許権

  • 組換え微生物及びその利用

    増田 健太, 劉 生浩, 森本 拓也, 小笠原 直毅, 石川 周, チュムサクル オンウマ

    特願2015-211548, 2015年10月28日, 花王株式会社, 国立大学法人 奈良先端科学技術大学院大学, 特開2017-079640, 2017年05月18日

    特許権

  • 枯草菌変異株及びその利用

    増田 健太, 劉 生浩, 森本 拓也, 小笠原 直毅, 石川 周, チュムサクル オンウマ

    特願2015-211547, 2015年10月28日, 花王株式会社, 国立大学法人 奈良先端科学技術大学院大学, 特開2017-079639, 2017年05月18日

    特許権