Research activity information

• Bacillus velezensis S141 improves the root growth of soybean under drought conditions

  Takahiko Kondo, Surachat Sibponkrung, Panlada Tittabutr, Nantakorn Boonkerd, Shu Ishikawa, Neung Teaumroong, Ken-ichi Yoshida

  Abstract Bacillus velezensis S141 helps soybean establish specific symbiosis with strains of Bradyrhizobium diazoefficiens to form larger nodules and improve nitrogen fixation efficiency. In this study, we found that the dry weight of soybean roots increased significantly in the presence of S141 alone under drought conditions. Hence, S141 improved the root growth of soybean under limited water supply conditions. S141 can produce some auxin, which might be involved in the improved nodulation. Inactivating IPyAD of S141, which is required for auxin biosynthesis, did not alter the beneficial effects of S141, suggesting that the root growth was independent of auxin produced by S141. Under drought conditions, soybean exhibited some responses to resist osmotic and oxidative stresses; however, S141 was relevant to none of these responses. Although the mechanism remains unclear, S141 might produce some substances that stimulate the root growth of soybean under drought conditions.

  Oxford University Press (OUP), Nov. 2024, Bioscience, Biotechnology, and Biochemistry


• Bacillus subtilis grown in a “breathing” vessel without sparger aeration

  Ken-ichi Yoshida, Kyosuke Yokoyama, Ayşegül Öktem, Shu Ishikawa, Jan Maarten van Dijl, Masato Yotsuya, Ryosuke Sato

  ABSTRACT Here we present a “breathing” vessel consisting of expanded polytetrafluoroethylene, which allows gas exchange but no liquid permeation. The bacterial culture inside needs only agitation to promote air supply. Using this setup, a Bacillus subtilis cell factory for scyllo-inositol production grew to produce scyllo-inositol efficiently. The results indicate that our approach represents a sustainable “greener” approach for the cell factory.

  Oxford University Press (OUP), Sep. 2024, Bioscience, Biotechnology, and Biochemistry


• Efficient pathway-driven scyllo -inositol production from myo -inositol using thermophilic cells and mesophilic inositol dehydrogenases: a novel strategy for pathway control

  Ryota Kurashiki, Masahiro Takahashi, Yuta Okumura, Tatsuya Ono, Hirofumi Endo, Kohei Makino, Kaho Fukui, Kyosuke Yokoyama, Shu Ishikawa, Ken-ichi Yoshida, Takashi Ohshiro, Hirokazu Suzuki

  ABSTRACT Mesophilic enzymes, which are active at moderate temperatures, may dominate enzymatic reactions even in the presence of thermophilic crude enzymes. This study was conducted to investigate this hypothesis with mesophilic inositol dehydrogenases (IolG and IolX) produced in Geobacillus kaustophilus HTA426. To ensure the efficient production of mesophilic enzymes, we first screened for promoters induced at moderate temperatures using transcriptome analysis and identified four genes highly expressed at 30°C in the thermophile. We further characterized these promoters using fluorescent reporter assays to determine that the mti3 promoter could direct efficient gene expression at 40°C. We cloned the promoter into an Escherichia coli–Geobacillus shuttle plasmid and confirmed that the resulting vector functioned in G. kaustophilus and other thermophiles. We then used this vector for the cooperative expression of the iolG and iolX genes from Bacillus subtilis 168. G. kaustophilus cells carrying the expression vector were incubated at 60°C for cellular propagation and then at 40°C for the production of IolG and IolX. When the cells were permeabilized, IolG and IolX acted as catalysts to convert exogenous myo -inositol into scyllo -inositol at 30°C. In a scaled-up reaction, 10 g of myo -inositol was converted to 1.8 g of scyllo -inositol, which was further purified to yield 970 mg of pure powder. Notably, myo -inositol was degraded by intrinsic enzymes of G. kaustophilus at 60°C but not at 30°C, supporting our initial hypothesis. We indicate that this approach is useful for preparing enzyme cocktails without the need for purification. IMPORTANCE Enzyme cocktails are commonly employed for cell-free chemical synthesis; however, their preparation involves cumbersome processes. This study affirms that mesophilic enzymes in thermophilic crude extracts can function as specific catalysts at moderate temperatures, akin to enzyme cocktails. The catalyst was prepared by permeabilizing cells without the need for concentration, extraction, or purification processes; hence, its preparation was considerably simpler compared with conventional methods for enzyme cocktails. This approach was employed to produce pure scyllo -inositol from an economical substrate. Notably, this marks the first large-scale preparation of pure scyllo -inositol, holding potential pharmaceutical significance as scyllo -inositol serves as a promising agent for certain diseases but is currently expensive. Moreover, this approach holds promise for application in pathway engineering within living cells. The envisioned pathway is designed without chromosomal modification and is simply regulated by switching culture temperatures. Consequently, this study introduces a novel platform for both whole-cell and cell-free synthetic systems.

  American Society for Microbiology, Jul. 2024, Applied and Environmental Microbiology, 90(7) (7)


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

  Onuma Chumsakul, Kensuke Nakamura, Kazuki Fukamachi, Shu Ishikawa, Taku Oshima

  Springer US, Jul. 2024, Methods in Molecular Biology, 39 - 53


• High-throughput evaluation of hemolytic activity through precise measurement of colony and hemolytic zone sizes of engineered Bacillus subtilis on blood agar

  Takahiro Bamba, Rina Aoki, Yoshimi Hori, Shu Ishikawa, Ken-ichi Yoshida, Naoaki Taoka, Shingo Kobayashi, Hisashi Yasueda, Akihiko Kondo, Tomohisa Hasunuma

  Abstract Biosurfactants have remarkable characteristics, such as environmental friendliness, high safety, and excellent biodegradability. Surfactin is one of the best-known biosurfactants produced by Bacillus subtilis. Because the biosynthetic pathways of biosurfactants, such as surfactin, are complex, mutagenesis is a useful alternative to typical metabolic engineering approaches for developing high-yield strains. Therefore, there is a need for high-throughput and accurate screening methods for high-yield strains derived from mutant libraries. The blood agar lysis method, which takes advantage of the hemolytic activity of biosurfactants, is one way of determining their concentration. This method includes inoculating microbial cells onto blood-containing agar plates, and biosurfactant production is assessed based on the size of the hemolytic zone formed around each colony. Challenges with the blood agar lysis method include low experimental reproducibility and a lack of established protocols for high-throughput screening. Therefore, in this study, we investigated the effects of the inoculation procedure and media composition on the formation of hemolytic zones. We also developed a workflow to evaluate the number of colonies using robotics. The results revealed that by arranging colonies at appropriate intervals and measuring the areas of colonies and hemolytic rings using image analysis software, it was possible to accurately compare the hemolytic activity among several colonies. Although the use of the blood agar lysis method for screening is limited to surfactants exhibiting hemolytic activity, it is believed that by considering the insights gained from this study, it can contribute to the accurate screening of strains with high productivity.

  Oxford University Press (OUP), Jan. 2024, Biology Methods and Protocols, 9(1) (1)

  Link to Kobe Univ. Repository (Kernel)


• Screening to isolate <i>Bacillus subtilis</i> mutants with enhanced NADPH levels

  Yuzheng Wu, Shu Ishikawa, Ken-ichi Yoshida

  Microbiology Research Foundation, 2024, The Journal of General and Applied Microbiology

  Link to Kobe Univ. Repository (Kernel)


• Genes encoding a novel thermostable bacteriocin in the thermophilic bacterium Aeribacillus pallidus PI8

  Kyosuke Kita, Sanako Yoshida, Shunsuke Masuo, Akira Nakamura, Shu Ishikawa, Ken-ichi Yoshida

  Abstract Aim Aeribacillus pallidus PI8 is a Gram-positive thermophilic bacterium that produces thermostable antimicrobial substances against several bacterial species, including Geobacillus kaustophilus HTA426. In the present study, we sought to identify genes of PI8 with antibacterial activity. Methods and results We isolated, cloned, and characterized a thermostable bacteriocin from A. pallidus PI8 and named it pallidocyclin. Mass spectrometric analyses of pallidocyclin revealed that it had a circular peptide structure, and its precursor was encoded by pcynA in the PI8 genome. pcynA is the second gene within the pcynBACDEF operon. Expression of the full-length pcynBACDEF operon in Bacillus subtilis produced intact pallidocyclin, whereas expression of pcynF in G. kaustophilus HTA426 conferred resistance to pallidocyclin. Conclusion Aeribacillus pallidus PI8 possesses the pcynBACDEF operon to produce pallidocyclin. pcynA encodes the pallidocyclin precursor, and pcynF acts as an antagonist of pallidocyclin.

  Oxford University Press (OUP), Dec. 2023, Journal of Applied Microbiology, 134(12) (12)


• A critical role of the periplasm in copper homeostasis in Gram-negative bacteria

  Jun-ichi Ishihara, Tomohiro Mekubo, Chikako Kusaka, Suguru Kondo, Ryotaro Oiko, Kensuke Igarashi, Hirofumi Aiba, Shu Ishikawa, Naotake Ogasawara, Taku Oshima, Hiroki Takahashi

  Elsevier BV, Sep. 2023, Biosystems, 231, 104980 - 104980


• Bacillus velezensis S141, a soybean growth-promoting bacterium, hydrolyzes isoflavone glycosides into aglycones.

  Takahiko Kondo, Surachat Sibponkrung, Ken-yu Hironao, Panlada Tittabutr, Nantakorn Boonkerd, Shu Ishikawa, Hitoshi Ashida, Neung Teaumroong, Ken-ichi Yoshida

  Microbiology Research Foundation, 2023, The Journal of General and Applied Microbiology


• Constitutive glucose dehydrogenase elevates intracellular NADPH levels and luciferase luminescence in Bacillus subtilis

  Yuzheng Wu, Honami Kawabata, Kyosuke Kita, Shu Ishikawa, Kan Tanaka, Ken-ichi Yoshida

  Abstract Background Genetic modifications in Bacillus subtilis have allowed the conversion of myo-inositol into scyllo-inositol, which is proposed as a therapeutic agent for Alzheimer’s disease. This conversion comprises two reactions catalyzed by two distinct inositol dehydrogenases, IolG and IolW. The IolW-mediated reaction requires the intracellular regeneration of NADPH, and there appears to be a limit to the endogenous supply of NADPH, which may be one of the rate-determining factors for the conversion of inositol. The primary mechanism of NADPH regeneration in this bacterium remains unclear. Results The gdh gene of B. subtilis encodes a sporulation-specific glucose dehydrogenase that can use NADP⁺ as a cofactor. When gdh was modified to be constitutively expressed, the intracellular NADPH level was elevated, increasing the conversion of inositol. In addition, the bacterial luciferase derived from Photorhabdus luminescens became more luminescent in cells in liquid culture and colonies on culture plates. Conclusion The results indicated that the luminescence of luciferase was representative of intracellular NADPH levels. Luciferase can therefore be employed to screen for mutations in genes involved in NADPH regeneration in B. subtilis, and artificial manipulation to enhance NADPH regeneration can promote the production of substances such as scyllo-inositol.

  Springer Science and Business Media LLC, Dec. 2022, Microbial Cell Factories, 21(1) (1)

  Link to Kobe Univ. Repository (Kernel)


• A novel method for transforming Geobacillus kaustophilus with a chromosomal segment of Bacillus subtilis transferred via pLS20-dependent conjugation

  Kotaro Mori, Kaho Fukui, Ryotaro Amatsu, Shu Ishikawa, Valeria Verrone, Anil Wipat, Wilfried J. J. Meijer, Ken-ichi Yoshida

  Abstract Background Geobacillus kaustophilus is a thermophilic Gram-positive bacterium. Methods for its transformation are still under development. Earlier studies have demonstrated that pLS20catΔoriT mobilized the resident mobile plasmids from Bacillus subtilis to G. kaustophilus and transferred long segments of chromosome from one cell to another between B. subtilis. Results In this study, we applied mobilization of the B. subtilis chromosome mediated by pLS20catΔoriT to transform G. kaustophilus. We constructed a gene cassette to be integrated into G. kaustophilus and designed it within the B. subtilis chromosome. The pLS20catΔoriT-mediated conjugation successfully transferred the gene cassette from the B. subtilis chromosome into the G. kaustophilus allowing for the desired genetic transformation. Conclusions This transformation approach described here will provide a new tool to facilitate the flexible genetic manipulation of G. kaustophilus.

  Springer Science and Business Media LLC, Dec. 2022, Microbial Cell Factories, 21(1) (1)

  Link to Kobe Univ. Repository (Kernel)


• Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production.

  Junya Yamamoto, Onuma Chumsakul, Yoshihiro Toya, Takuya Morimoto, Shenghao Liu, Kenta Masuda, Yasushi Kageyama, Takashi Hirasawa, Fumio Matsuda, Naotake Ogasawara, Hiroshi Shimizu, Ken-Ichi Yoshida, Taku Oshima, Shu Ishikawa

  Partial bacterial genome reduction by genome engineering can improve the productivity of various metabolites, possibly via deletion of non-essential genome regions involved in undesirable metabolic pathways competing with pathways for the desired end products. However, such reduction may cause growth defects. Genome reduction of Bacillus subtilis MGB874 increases the productivity of cellulases and proteases but reduces their growth rate. Here, we show that this growth defect could be restored by silencing redundant or less important genes affecting exponential growth by manipulating the global transcription factor AbrB. Comparative transcriptome analysis revealed that AbrB-regulated genes were upregulated and those involved in central metabolic pathway and synthetic pathways of amino acids and purine/pyrimidine nucleotides were downregulated in MGB874 compared with the wild-type strain, which we speculated were the cause of the growth defects. By constitutively expressing high levels of AbrB, AbrB regulon genes were repressed, while glycolytic flux increased, thereby restoring the growth rate to wild-type levels. This manipulation also enhanced the productivity of metabolites including γ-polyglutamic acid. This study provides the first evidence that undesired features induced by genome reduction can be relieved, at least partly, by manipulating a global transcription regulation system. A similar strategy could be applied to other genome engineering-based challenges aiming toward efficient material production in bacteria.

  May 2022, DNA research : an international journal for rapid publication of reports on genes and genomes, 29(3) (3)

  Link to Kobe Univ. Repository (Kernel)


• Functional analysis of a gene cluster for putative bacteriocin deduced from the genome sequence of <i>Aeribacillus pallidus</i> PI8

  Kyosuke Kita, Sanako Yoshida, Shu Ishikawa, Ken-ichi Yoshida

  Microbiology Research Foundation, 2022, The Journal of General and Applied Microbiology, 68(2) (2), 87 - 94


• A New Tool for the Flexible Genetic Manipulation of Geobacillus kaustophilus

  Ryotaro Amatsu, Kotaro Mori, Shu Ishikawa, Wilfried Meijer, Ken-ichi Yoshida

  Geobacillus kaustophilus , a thermophilic Gram-positive bacterium, is an attractive host for the development of high-temperature bioprocesses. However, its reluctance against genetic manipulation by standard methodologies hampers its exploitation. Here, we describe a simple methodology in which an artificial DNA segment on the chromosome of Bacillus subtilis can be transferred via pLS20-mediated conjugation resulting in subsequent integration in the genome of G. kaustophilus. Therefore, we have developed a transformation strategy to design an artificial DNA segment on the chromosome of B. subtilis and introduce it into G. kaustophilus . The artificial DNA segment can be freely designed by taking advantage of the plasticity of the B. subtilis genome and combined with the simplicity of pLS20 conjugation transfer. This transformation strategy would adapt to various Gram-positive bacteria other than G. kaustophilus . Graphical abstract.

  Bio-Protocol, LLC, 2022, BIO-PROTOCOL, 12(17) (17)


• Assessment of Bacillus subtilis Plasmid pLS20 Conjugation in the Absence of Quorum Sensing Repression.

  Kotaro Mori, Valeria Verrone, Ryotaro Amatsu, Kaho Fukui, Wilfried J J Meijer, Shu Ishikawa, Anil Wipat, Ken-Ichi Yoshida

  Bacillus subtilis conjugative plasmid pLS20 uses a quorum-sensing mechanism to control expression levels of its conjugation genes, involving the repressor RcopLS20, the anti-repressor RappLS20, and the signaling peptide Phr*pLS20. In previous studies, artificial overexpression of rappLS20 in the donor cells was shown to enhance conjugation efficiency. However, we found that the overexpression of rappLS20 led to various phenotypic traits, including cell aggregation and death, which might have affected the correct determination of the conjugation efficiency when determined by colony formation assay. In the current study, conjugation efficiencies were determined under different conditions using a two-color fluorescence-activated flow cytometry method and measuring a single-round of pLS20-mediated transfer of a mobilizable plasmid. Under standard conditions, the conjugation efficiency obtained by fluorescence-activated flow cytometry was 23-fold higher than that obtained by colony formation. Furthermore, the efficiency difference increased to 45-fold when rappLS20 was overexpressed.

  Sep. 2021, Microorganisms, 9(9) (9)

  Link to Kobe Univ. Repository (Kernel)


• Identification of genes encoding a novel ABC transporter in Lactobacillus delbrueckii for inulin polymers uptake.

  Yuji Tsujikawa, Shu Ishikawa, Iwao Sakane, Ken-Ichi Yoshida, Ro Osawa

  Lactobacillus delbrueckii JCM 1002T grows on highly polymerized inulin-type fructans as its sole carbon source. When it was grown on inulin, a > 10 kb long gene cluster inuABCDEF (Ldb1381-1386) encoding a plausible ABC transporter was suggested to be induced, since a transcriptome analysis revealed that the fourth gene inuD (Ldb1384) was up-regulated most prominently. Although Bacillus subtilis 168 is originally unable to utilize inulin, it became to grow on inulin upon heterologous expression of inuABCDEF. When freshly cultured cells of the recombinant B. subtilis were then densely suspended in buffer containing inulin polymers and incubated, inulin gradually disappeared from the buffer and accumulated in the cells without being degraded, whereas levan-type fructans did not disappear. The results imply that inuABCDEF might encode a novel ABC transporter in L. delbrueckii to "monopolize" inulin polymers selectively, thereby, providing a possible advantage in competition with other concomitant inulin-utilizing bacteria.

  Aug. 2021, Scientific reports, 11(1) (1), 16007 - 16007

  Link to Kobe Univ. Repository (Kernel)


• Genome sequences of two strains of Lactococcus lactis subsp. cremoris with the same ancestry but a different capacity to produce exopolysaccharides.

  Yayoi Gotoh, Kyosuke Kita, Kosei Tanaka, Shu Ishikawa, Toshio Suzuki, Ken-Ichi Yoshida

  Strains of Lactococcus lactis subsp. cremoris are used to produce yogurt containing exopolysaccharides with a sticky texture. When strain G3-2 producing exopolysaccharides was grown at elevated temperatures, a spontaneous mutant EPSC, which had lost exopolysaccharides biosynthesis, was isolated. Genomes of the two strains were determined to be composed of a 2.4-Mb chromosome and up to eleven plasmids, and it was revealed that one of the plasmids encoding the gene cluster for exopolysaccharides biosynthesis was lost selectively in EPSC.

  Jul. 2021, The Journal of general and applied microbiology


• Identification of a repressor for the two iol operons required for inositol catabolism in Geobacillus kaustophilus

  Ken-ichi Yoshida, Yusuke Shirae, Ryo Nishimura, Kaho Fukui, Shu Ishikawa

  Geobacillus kaustophilus HTA426, a thermophilic Gram-positive bacterium, feeds on inositol as its sole carbon source, and an iol gene cluster required for inositol catabolism has been postulated with reference to the iol genes in Bacillus subtilis . The iol gene cluster of G. kaustophilus comprises two tandem operons induced in the presence of inositol; however, the mechanism underlying this induction remains unclear. B. subtilis iolQ is known to be involved in the regulation of iolX encoding scyllo-inositol dehydrogenase, and its homologue in HTA426 was found two genes upstream of the first gene (gk1899) of the iol gene cluster and was termed iolQ in G. kaustophilus . When iolQ was inactivated in G. kaustophilus , not only cellular myo-inositol dehydrogenase activity due to gk1899 expression but also the transcription of the two iol operons became constitutive. IolQ was produced and purified as a C-terminal histidine (His)-tagged fusion protein in Escherichia coli and subjected to an in vitro gel electrophoresis mobility shift assay to examine its DNA-binding property. It was observed that IolQ bound to the DNA fragments containing each of the two iol promoter regions and that DNA binding was antagonized by myo-inositol. Moreover, DNase I footprinting analyses identified two tandem binding sites of IolQ within each of the iol promoter regions. By comparing the sequences of the binding sites, a consensus sequence for IolQ binding was deduced to form a palindrome of 5′-RGWAAGCGCTTSCY-3′ (where R=A or G, W=A or T, S=G or C, and Y=C or T). IolQ functions as a transcriptional repressor regulating the induction of the two iol operons responding to myo-inositol.

  Microbiology Society, Jan. 2021, Microbiology, 167(1) (1)

  Link to Kobe Univ. Repository (Kernel)


• Complete Genome Sequence of Nitrogen-Fixing Paenibacillus sp. Strain URB8-2, Isolated from the Rhizosphere of Wild Grass

  Kyosuke Kita, Shu Ishikawa, Ken-ichi Yoshida

  We report here the complete genome sequence of nitrogen-fixing Paenibacillus sp. strain URB8-2, isolated from the rhizosphere of wild grass in Kobe, Japan, revealing that this bacterium is related to Paenibacillus rhizophilus 7197, a novel species collected recently in Inner Mongolia, China, and that it possesses two gene clusters for distinct types of nitrogenases.

  American Society for Microbiology, Sep. 2020, Microbiology Resource Announcements, 9(36) (36)

  Link to Kobe Univ. Repository (Kernel)


• Complete Genome Sequence of Thermophilic Bacterium Aeribacillus pallidus PI8

  Kyosuke Kita, Atsushi Ishida, Kosei Tanaka, Shu Ishikawa, Ken-ichi Yoshida

  Here, we report the complete genome sequence of Aeribacillus pallidus PI8, a thermophilic bacterium, isolated from soybean stem extract. The sequence was determined using Illumina and Nanopore sequencers. Bioinformatic analyses of the genome sequence revealed the presence of possible bacteriocin gene clusters.

  American Society for Microbiology, Apr. 2020, Microbiology Resource Announcements, 9(17) (17)

  Link to Kobe Univ. Repository (Kernel)


• A bacterial cell factory converting glucose into scyllo-inositol, a therapeutic agent for Alzheimer's disease.

  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.

  Mar. 2020, Communications biology, 3(1) (1), 93 - 93

  Link to Kobe Univ. Repository (Kernel)


• Production of scyllo-inositol: Conversion of rice bran into a promising disease-modifying therapeutic agaent for Alzheimer’s disease

  Yoshida, Ken-ichi, Ishikawa, Shu

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


• Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation

  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, Oct. 2018, BMC Microbiology, 18

  Link to Kobe Univ. Repository (Kernel)


• A novel method for transforming the thermophilic bacterium Geobacillus kaustophilus

  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, Aug. 2018, Microbial Cell Factories, 17

  Link to Kobe Univ. Repository (Kernel)


• Rapid conjugative mobilization of a 100kb segment of Bacillus subtilis chromosomal DNA is mediated by a helper plasmid with no ability for self-transfer

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

  BioMed Central Ltd., Jan. 2018, Microbial Cell Factories, 17(1) (1)

  Link to Kobe Univ. Repository (Kernel)


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

  Chumsakul O, Nakamura K, Ishikawa S, Oshima T

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


• Genome-Wide Analysis of ResD, NsrR, and Fur Binding in Bacillus subtilis during Anaerobic Fermentative Growth by In Vivo Footprinting

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

  Jul. 2017, JOURNAL OF BACTERIOLOGY, 199(13) (13)


• Bacillus subtilis IolQ (DegA) is a transcriptional repressor of iolX encoding NAD(+)-dependent scyllo-inositol dehydrogenase

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

  Jul. 2017, BMC MICROBIOLOGY, 17

  Link to Kobe Univ. Repository (Kernel)


• Bacillus subtilis iolU encodes an additional NADP(+)-dependent scyllo-inositol dehydrogenase

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

  May 2017, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 81(5) (5), 1026 - 1032


• A new-generation of Bacillus subtilis cell factory for further elevated scyllo-inositol production

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

  Apr. 2017, MICROBIAL CELL FACTORIES, 16

  Link to Kobe Univ. Repository (Kernel)


• Bacillus subtilis 5 '-nucleotidases with various functions and substrate specificities

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

  Oct. 2016, BMC MICROBIOLOGY, 16(1) (1), 1 - 13

  Link to Kobe Univ. Repository (Kernel)


• Replication fork progression is paused in two large chromosomal zones flanking the DNA replication origin in Escherichia coli

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

  Aug. 2016, GENES TO CELLS, 21(8) (8), 907 - 914


• H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes

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

  Jan. 2016, PLOS GENETICS, 12(1) (1)


• Enhanced dipicolinic acid production during the stationary phase in Bacillus subtilis by blocking acetoin synthesis

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

  Dec. 2015, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 79(12) (12), 2073 - 2080


• Enhanced dipicolinic acid production during the stationary phase in Bacillus subtilis by blocking acetoin synthesis

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

  Dec. 2015, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 79(12) (12), 2073 - 2080


• The Role of alpha-CTD in the Genome-Wide Transcriptional Regulation of the Bacillus subtilis Cells

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

  Jul. 2015, PLOS ONE, 10(7) (7)


• Cloning and heterologous expression of the ftfCNC-2(1) gene from Weissella confusa MBFCNC-2(1) as an extracellular active fructansucrase in Bacillus subtilis

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

  May 2015, JOURNAL OF BIOSCIENCE AND BIOENGINEERING, 119(5) (5), 515 - 520


• Cloning and heterologous expression of the ftfCNC-2(1) gene from Weissella confusa MBFCNC-2(1) as an extracellular active fructansucrase in Bacillus subtilis

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

  May 2015, JOURNAL OF BIOSCIENCE AND BIOENGINEERING, 119(5) (5), 515 - 520


• Hyperphosphorylation of DegU cancels CcpA-dependent catabolite repression of rocG in Bacillus subtilis

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

  Feb. 2015, BMC MICROBIOLOGY, 15(1) (1)


• The ResD Response Regulator, through Functional Interaction with NsrR and Fur, Plays Three Distinct Roles in Bacillus subtilis Transcriptional Control

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

  Jan. 2014, JOURNAL OF BACTERIOLOGY, 196(2) (2), 493 - 503


• The ResD Response Regulator, through Functional Interaction with NsrR and Fur, Plays Three Distinct Roles in Bacillus subtilis Transcriptional Control

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

  Jan. 2014, JOURNAL OF BACTERIOLOGY, 196(2) (2), 493 - 503


• Structural and genetic analyses reveal the protein SepF as a new membrane anchor for the Z ring

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

  Nov. 2013, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110(48) (48), E4601 - E4610


• High-Resolution Mapping of In vivo Genomic Transcription Factor Binding Sites Using In situ DNase I Footprinting and ChIP-seq

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

  Aug. 2013, DNA RESEARCH, 20(4) (4), 325 - 337


• Functions of the Hha and YdgT proteins in transcriptional silencing by the nucleoid proteins, H-NS and StpA, in escherichia coli

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

  Jun. 2013, DNA Research, 20(3) (3), 263 - 271


• Functional Analysis of the Protein Veg, Which Stimulates Biofilm Formation in Bacillus subtilis

  Ying Lei, Taku Oshima, Naotake Ogasawara, Shu Ishikawa

  Apr. 2013, JOURNAL OF BACTERIOLOGY, 195(8) (8), 1697 - 1705


• Functional Analysis of the Protein Veg, Which Stimulates Biofilm Formation in Bacillus subtilis

  Ying Lei, Taku Oshima, Naotake Ogasawara, Shu Ishikawa

  Apr. 2013, JOURNAL OF BACTERIOLOGY, 195(8) (8), 1697 - 1705


• 細菌の発現制御機構をゲノムワイドに解析する

  大島拓, 石川周

  日本農芸化学会 ; 1962-, 2013, 化学と生物, 51(10) (10), 670 - 678


• Accurate regulation of chromosome initiation is essential for maintenance of genome integrity in Bacillus subtilis

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

  Dec. 2012, GENES & GENETIC SYSTEMS, 87(6) (6), 385 - 385


• Regulation of chromosomal replication initiation by oriC-proximal DnaA-box clusters in Bacillus subtilis

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

  Jan. 2012, NUCLEIC ACIDS RESEARCH, 40(1) (1), 220 - 234


• Regulation of chromosomal replication initiation by oriC-proximal DnaA-box clusters in Bacillus subtilis

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

  Jan. 2012, NUCLEIC ACIDS RESEARCH, 40(1) (1), 220 - 234


• 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, 日本生物工学会大会講演要旨集, 64, 39 - 39


• A widespread family of bacterial cell wall assembly proteins

  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

  Dec. 2011, EMBO JOURNAL, 30(24) (24), 4931 - 4941


• Screening for sucrose phosphorylase in exopolysaccharide producing-lactic acid bacteria reveals SPaseWRS-3(1) in Leuconostoc mesenteroides isolated from sugar containing-beverage "Wedang Ronde" from Indonesia

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

  Nov. 2011, AFRICAN JOURNAL OF BIOTECHNOLOGY, 10(74) (74), 16915 - 16923


• Sequence-specific error profile of Illumina sequencers

  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

  Jul. 2011, NUCLEIC ACIDS RESEARCH, 39(13) (13)


• Transcription Factor GreA Contributes to Resolving Promoter-Proximal Pausing of RNA Polymerase in Bacillus subtilis Cells

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

  Jun. 2011, JOURNAL OF BACTERIOLOGY, 193(12) (12), 3090 - 3099


• Transcription Factor GreA Contributes to Resolving Promoter-Proximal Pausing of RNA Polymerase in Bacillus subtilis Cells

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

  Jun. 2011, JOURNAL OF BACTERIOLOGY, 193(12) (12), 3090 - 3099


• Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation

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

  Jan. 2011, NUCLEIC ACIDS RESEARCH, 39(2) (2), 414 - 428


• Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation

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

  Jan. 2011, NUCLEIC ACIDS RESEARCH, 39(2) (2), 414 - 428


• RNA Polymerase Trafficking in Bacillus subtilis Cells

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

  Nov. 2010, JOURNAL OF BACTERIOLOGY, 192(21) (21), 5778 - 5787


• RNA Polymerase Trafficking in Bacillus subtilis Cells

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

  Nov. 2010, JOURNAL OF BACTERIOLOGY, 192(21) (21), 5778 - 5787


• Noc protein binds to specific DNA sequences to coordinate cell division with chromosome segregation

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

  Jul. 2009, EMBO JOURNAL, 28(13) (13), 1940 - 1952


• Differential Binding Profiles of StpA in Wild-Type and hns Mutant Cells: a Comparative Analysis of Cooperative Partners by Chromatin Immunoprecipitation-Microarray Analysis

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

  Apr. 2009, JOURNAL OF BACTERIOLOGY, 191(7) (7), 2388 - 2391


• The functional analysis of YabA, which interacts with DnaA and regulates initiation of chromosome replication in Bacillus subtils

  Eunha Cho, Naotake Ogasawara, Shu Ishikawa

  Apr. 2008, GENES & GENETIC SYSTEMS, 83(2) (2), 111 - 125


• 細菌の細胞分裂の分子メカニズム (特集 原核細胞の細胞骨格)

  石川周, 小笠原直毅

  共立出版, 2008, 蛋白質核酸酵素, 53(13) (13), 1725 - 1731


• Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method

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

  Aug. 2007, DNA RESEARCH, 14(4) (4), 155 - 168


• Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method

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

  Aug. 2007, DNA RESEARCH, 14(4) (4), 155 - 168


• Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase

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

  Aug. 2006, DNA RESEARCH, 13(4) (4), 141 - 153


• A new FtsZ-interacting protein, YlmF, complements the activity of FtsA during progression of cell division in Bacillus subtilis

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

  Jun. 2006, MOLECULAR MICROBIOLOGY, 60(6) (6), 1364 - 1380


• A new FtsZ-interacting protein, YlmF, complements the activity of FtsA during progression of cell division in Bacillus subtilis

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

  Jun. 2006, MOLECULAR MICROBIOLOGY, 60(6) (6), 1364 - 1380


• 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

  秀潤社, 2006, 細胞工学, 25(10) (10), 1155 - 1160


• Synergistic regulation of competence development in Bacillus subtilis by two Rap-Phr systems

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

  Jul. 2005, JOURNAL OF BACTERIOLOGY, 187(13) (13), 4353 - 4361


• Synergistic regulation of competence development in Bacillus subtilis by two Rap-Phr systems

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

  Jul. 2005, JOURNAL OF BACTERIOLOGY, 187(13) (13), 4353 - 4361


• Transcriptional, functional and cytochemical analyses of the veg gene in Bacillus subtilis

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

  Apr. 2003, JOURNAL OF BIOCHEMISTRY, 133(4) (4), 475 - 483


• Essential Bacillus subtilis genes

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

  Apr. 2003, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100(8) (8), 4678 - 4683


• Transcriptional, functional and cytochemical analyses of the veg gene in Bacillus subtilis

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

  Apr. 2003, JOURNAL OF BIOCHEMISTRY, 133(4) (4), 475 - 483


• Transcriptional, functional and cytochemical analyses of the veg gene in Bacillus subtilis

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

  Apr. 2003, JOURNAL OF BIOCHEMISTRY, 133(4) (4), 475 - 483


• Production of long-chain levan by a sacC insertional mutant from Bacillus subtilis 327UH

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

  Jul. 2002, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 66(7) (7), 1555 - 1558


• Production of long-chain levan by a sacC insertional mutant from Bacillus subtilis 327UH

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

  Jul. 2002, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 66(7) (7), 1555 - 1558


• Production of long-chain levan by a sacC insertional mutant from Bacillus subtilis 327UH

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

  Jul. 2002, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 66(7) (7), 1555 - 1558


• Biochemical characterization of aspartyl phosphate phosphatase interaction with a phosphorylated response regulator and its inhibition by a pentapeptide

  S Ishikawa, L Core, M Perego

  Jun. 2002, JOURNAL OF BIOLOGICAL CHEMISTRY, 277(23) (23), 20483 - 20489


• A free terminal carboxylate group is required for PhrA pentapeptide inhibition of RapA phosphatase

  LJ Core, S Ishikawa, M Perego

  Oct. 2001, PEPTIDES, 22(10) (10), 1549 - 1553


• Cloning and expression of two autolysin genes, cwIU and cwIV, which are tandemly arranged on the chromosome of Bacillus polymyxa var. colistinus

  S Ishikawa, S Kawahara, J Sekiguchi

  Dec. 1999, MOLECULAR AND GENERAL GENETICS, 262(4-5) (4-5), 738 - 748, English


• Peptidoglycan hydrolase LytF plays a role in cell separation with Cw1F during vegetative growth of Bacillus subtilis

  R Ohnishi, S Ishikawa, J Sekiguchi

  May 1999, JOURNAL OF BACTERIOLOGY, 181(10) (10), 3178 - 3184, English


• Peptidoglycan hydrolase LytF plays a role in cell separation with Cw1F during vegetative growth of Bacillus subtilis

  R Ohnishi, S Ishikawa, J Sekiguchi

  May 1999, JOURNAL OF BACTERIOLOGY, 181(10) (10), 3178 - 3184, English


• Genome analysis and germination related genes of Bacillus subtilis

  Fukushima Tatsuya, Ishikawa Shu, Yamamoto Hiroki, Sekiguchi Junichi

  日本生物工学会, 1999, 日本生物工学会大会講演要旨集, 11, 90 - 90, Japanese


• [Formation, structure and germination of the spore of Bacillus subtilis]

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

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

  [Refereed]


• Regulation of a new cell wall hydrolase gene, cwlF, which affects cell separation in Bacillus subtilis

  S Ishikawa, Y Hara, R Ohnishi, J Sekiguchi

  May 1998, JOURNAL OF BACTERIOLOGY, 180(9) (9), 2549 - 2555, English


• Regulation of a new cell wall hydrolase gene, cwlF, which affects cell separation in Bacillus subtilis

  S Ishikawa, Y Hara, R Ohnishi, J Sekiguchi

  May 1998, JOURNAL OF BACTERIOLOGY, 180(9) (9), 2549 - 2555


• Regulation and characterization of a newly deduced cell wall hydrolase gene (cwlJ) which affects germination of Bacillus subtilis spores

  S Ishikawa, K Yamane, J Sekiguchi

  Mar. 1998, JOURNAL OF BACTERIOLOGY, 180(6) (6), 1375 - 1380


• Regulation and characterization of a newly deduced cell wall hydrolase gene (cwlJ) which affects germination of Bacillus subtilis spores

  S Ishikawa, K Yamane, J Sekiguchi

  Mar. 1998, JOURNAL OF BACTERIOLOGY, 180(6) (6), 1375 - 1380


• Localization of proteins onto the cell surface of Bacillus subtilis with a cell wall binding domain of autolysin

  Tsuchiya Atsushi, Ishikawa Shu, Sekiguchi Junichi

  日本生物工学会, 1998, 日本生物工学会大会講演要旨集, 10, 11 - 11


• Purification and characterization of an autolysin of Bacillus polymyxa var. colistinus which is most active at acidic pH

  S Kawahara, C Utsunomiya, S Ishikawa, J Sekiguchi

  1997, JOURNAL OF FERMENTATION AND BIOENGINEERING, 83(5) (5), 419 - 422


• Study on a Bacillus subtilis autolysin, Cw1F, which appears during vegetative growth

  Hara Yoshiko, Ohnishi Ryo, Ishikawa Shu, Sekiguchi Junichi

  日本生物工学会, 1997, 日本生物工学会大会講演要旨集, 9, 22 - 22


• Study on a cw1J gene which affects germination of Bacillus subtilis spores

  Ishikawa Shu, Yamane Kunio, Sekiguchi Junichi

  日本生物工学会, 1997, 日本生物工学会大会講演要旨集, 9, 22 - 22

• 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, 日本ゲノム微生物学会年会要旨集, 10th, 63


• 枯草菌ゲノム縮小株によるケミカル代替素材の生産

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

  2014, 日本農芸化学会大会講演要旨集(Web), 2014


• 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

  05 Mar. 2013, 日本農芸化学会大会講演要旨集(Web), 2013, 4B11A10 (WEB ONLY)


• 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, 日本ゲノム微生物学会年会要旨集, 7th, 80


• 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

  The Society for Biotechnology, Japan, Oct. 2012, 日本生物工学会大会講演要旨集, 64, 39 - 39


• Functional analysis of the Veg protein that stimulates biofilm formation in Bacillus subtilis

  LEI YING, ISHIKAWA SHU, OGASAWARA NAOTAKE

  2012, 日本ゲノム微生物学会年会要旨集, 6th, 85


• Transcription factor GreA contributes to resolving promoter-proximal pausing of RNA polymerase in Bacillus subtilis cells

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

  Jun. 2011, Journal of Bacteriology, 193(12) (12), 3090 - 3099


• Bacillus subtilis degU32(hy) proactively cancels catabolite repression

  IWASAKI KANA, ISHIKAWA SHU, OGASAWARA NAOTAKE, TAKENAKA SHINJI, YOSHIDA KEN-ICHI

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


• Identification of Novel Nucleoid-associated Proteins in Bacillus subtilis

  LEI YING, ISHIKAWA SHU, OGASAWARA NAOTAKE

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


• Studies on in vivo dynamics of Bacillus subtilis RNA polymerase through ChAP-chip analysis of RpoA

  MURAYAMA SATOHIKO, OSHIMA TAKU, ISHIKAWA SHU, OGASAWARA NAOTAKE

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


• Search of nucleoid proteins in Bacillus subtilis: comparative analysis using ChAP(ChIP)-chip analysis between in B. subtilis and E. coli.

  CHUMSAKUL ONUMA, UYAL EBRU, ISHIKAWA SHU, OSHIMA TAKU, OGASAWARA NAOTAKE

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


• 大腸菌のタイリングアレイ解析により明らかになったゲノム進化

  大島 拓, 小笠原 直毅, 石川 周, 黒川 顕, 饗場 浩文

  25 Feb. 2007, 日本細菌学雑誌, 62(1) (1), 46 - 46


• 1E12-1 Expression analysis of metal responsive genes in the moderately halophilic bacterium, Halomonas elongate OUT30018

  KOGA Ayumi, SUSUKI Koudai, OSHIMA Taku, ISHIKAWA Shu, KUROKAWA Ken, OGASAWARA Naotaka, SHINMYO Atsuhiko, YOSHIDA Kazuya, NAKAYAMA Hideki

  日本生物工学会, 2007, 日本生物工学会大会講演要旨集, 19, 116 - 116


• 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

  Aug. 1999, 蛋白質核酸酵素, 44(10) (10), 14 - 20


• Formation, Structure and Germination of the Spore of Bacillus subtilis.

  SATO TSUTOMU, NANAMIYA HIDEAKI, OHASHI YOSHIAKI, KAWAMURA FUJIO, TAKAMATSU HIROMU, KODAMA TAKEKO, WATABE KAZUHITO, ISHIKAWA SHU, SEKIGUCHI JUN'ICHI

  共立出版, Aug. 1999, 蛋白質 核酸 酵素, 44(10) (10), 1460 - 1466


• Localization of proteins onto the cell surface of Bacillus subtilis with a cell wall binding domain of autolysin.

  TSUCHIYA ATSUSHI, ISHIKAWA SHU, SEKIGUCHI JUN'ICHI

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


• Study on a cwlJ gene which affects germination of Bacillus subtilis spores.

  ISHIKAWA SHU, YAMANE KUNIO, SEKIGUCHI JUN'ICHI

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


• Study on a Bacillus subtilis autolysin, CwlF, which appears during vegetative growth.

  HARA YOSHIKO, ONISHI RYO, ISHIKAWA SHU, SEKIGUCHI JUN'ICHI

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


• Bacillus colistinusの自己溶解酵素遺伝子cw1Vに関する研究 : 微生物

  石川 周, 宇都宮 千恵, 関口 順一, 河原 伸二

  社団法人日本農芸化学会, 05 Jul. 1995, 日本農藝化學會誌, 69, 228 - 228


• Study on a Bacillus colistinus autolysin gene, cwlU

  Ishikawa Shu, Kawahara Shinji, Rashid M. H., Sekiguchi Junichi

  日本生物工学会, 1995, 日本生物工学会大会講演要旨集, 7, 82 - 82

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

  Onuma Chumsakul, Kensuke Nakamura, ISHIKAWA SHU, Taku Oshima

  Humana Press, New York, NY, 2018


• 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

  羊土社, Sep. 2014


• 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

  日本農芸化学会, Oct. 2013


• 細菌の細胞分裂の分子メカニズム

  石川 周, 小笠原 直毅

  共立出版, Oct. 2008


• 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

  共立出版, Aug. 1999

• Study of the mechanism of bacterial growth inhibition by citrate

  Shu Ishikawa

  The;th Annual Meeting of the Society for Antibacterial and Antifungal Agents, Japan, Sep. 2021

• The Society for Biotechnology, Japan

  Apr. 2021 - Present


• Society of Genome Microbiology, Japan


• JAPAN SOCIETY FOR LACTIC ACID BACTERIA


• グラム陽性菌ゲノム機能会議

• L体およびD体のホモポリ-γ-L-グルタミン酸の合成とメカニズム解明

  石川 周

  科学研究費補助金／挑戦的研究（開拓）, Jun. 2018 - Mar. 2023


• 新たなゲノム機能調節機構の解明につながる好熱バチルスの制御因子Crhの解析

  吉田 健一

  科学研究費補助金／基盤研究(B), Apr. 2018 - Mar. 2022


• The role of nucleoid structure in bacterial transcriptional regulation

  Oshima Taku, YAMAMOTO Kaneyoshi, ISHIKAWA Shu

  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Nara Institute of Science and Technology, Apr. 2014 - Mar. 2017

  We performed the modified high resolution ChIP-seq analysis of E. coli nucleoid proteins to identify the binding regions of nucleoid proteins in base pair resolution. The results indicated that some nucleoid proteins recognize specific sequences at over 3000 regions in E. coli genome, while we could not find the specific recognition sequences of H-NS and HU. Our results also suggested that each nucleoid protein may independently interact with genomic DNA. However, because the independent interaction of each nucleoid protein affects to the functions of other nucleoid proteins, there is the inter-relation of nucleoid proteins to form functional nucleoid structure in E. coli cells.


• 枯草菌における細胞の繊維状化システムの解明

  Shu ISHIKAWA

  Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(基盤研究(C)), 2015 - 2017


• 汎用的高効率バイオプロセス細胞の創製

  Notake OGASAWARA

  Japan Science and Technology Agency (JST), Advanced Low Carbon Technology (ALCA), 2010 - 2016

  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。


• Study of regulatory mechanism of bacterial cell division machinary

  Shu ISHIKAWA

  Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(基盤研究(C)), 2012 - 2014

  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。


• Characterization and comparison of nucleoid proteins in different bacterial species

  Naotake OGASAWARA

  Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(基盤研究(A)), 2011 - 2013

  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。


• Elucidation of localization mechanism of the cell surface proteins in bacteria

  Hiroki YAMAMOTO

  Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(基盤研究(C)), Grant-in-Aid for Scientific Research (C), Shinshu University, 2011 - 2013

  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。


• Elucidation of roles of actin-like cytoskeletons in the teichoic acid modification of the bacterial cell wall

  Hiroki YAMAMOTO

  Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(基盤研究(C)), Grant-in-Aid for Scientific Research (C), Shinshu University, 2007 - 2009

  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。


• Fundamental Network of Genes and Proteins for Bacterial Cell Growth

  Naotake OGASAWARA

  Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(若手研究(B)), Grant-in-Aid for Scientific Research on Priority Areas, Nara Institute of Science and Technology, 2005 - 2009

  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


• 細菌の細胞分裂初期の分子メカニズムの解明

  Shu ISHIKAWA

  Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(特定領域研究), 若手研究(B), 奈良先端科学技術大学院大学, 2006 - 2007

  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。


• Functional analysis of the Bacillus subtilis GTP-binding protein family

  Naotake OGASAWARA

  Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(基盤研究(A)), Grant-in-Aid for Scientific Research (A), Nara Institute of Science and Technology, 2005 - 2007

  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


• 枯草菌における2成分シグナル伝達系ネットワークの解析

  石川 周

  日本学術振興会, 科学研究費助成事業, 特別研究員奨励費, 奈良先端科学技術大学院大学, 2001 - 2002

  枯草菌では11種の2成分制御系調節蛋白質(Response Regulator Aspartate Phosphatase、Rap)の脱リン酸化酵素RapA〜RapKの存在が知られているが、大部分のものについて、特異的な機能は明らかになってない。 前年度では、酵母2ハイブリッド法を用いて枯草菌のゲノムライブラリーから脱リン酸化酵素と相互作用をする蛋白質をスクリーニングし、Rapと相互作用する蛋白質を同定することができた。その中には、予想していたように2成分制御系調節蛋白質や脱リン酸化酵素を特異的に阻害するペプチドなども検出することができた。しかし、脱リン酸化酵素RapAと2成分制御系調節蛋白質SpoOFの既知の相互作用を検出することができなかったこと、数個のbaitに関しては2成分制御系調節蛋白質との相互作用が見られなかったことなど、問題点が残った。 今年度では、これらの問題点を解決するために、全てのRapと全ての2成分制御系調節蛋白質との相互作用を検証した。その結果、全ての既知の相互作用(RapA-SpoOF、RapB-SpoOF)と予測されていた相互作用(RapE-SpoOF、RapC-ComA、RapF-ComA)、さらに未知の相互作用(RapG-SpoOF&ComA、RapH-ComA、RapJ-SpoOF)が確認できた。おどろくことに、35種類ある2成分制御系調節蛋白質のうちRapと相互作用するのは、SpoOFとComAだけであることがわかった。さらに、前年度のゲノムライブラリーからのスクリーニング結果を合わせると、ComAがRapと相互作用する領域が、リン酸化されるrecievorドメインではなく、DNA結合ドメインであるということもわかった。 また、ComAをDNA binding domainとリン酸化されるreceiver domainと全てのRapとの相互作用を酵母2ハイブリッド法で確認したところ、ComAは前述したRapのDNA binding domainとのみ相互作用することを確認した。このことは、SpoOFには脱リン酸化を通して2成分制御系をコントロールしているが、ComAに関してはDNA結合を阻害することにより2成分制御系をコントロールしているという新しい事実を示唆している。

• 超高分子ガンマ-ポリグルタミン酸、該ポリグルタミン酸を産生するバチルス属細菌変異株及び該バチルス属細菌変異株のスクリーニング方法

  石川 周, 山本 純也, チュムサクル オヌマ

  特願2022-159018, 30 Sep. 2022, 国立大学法人神戸大学, 特開2024-052354, 11 Apr. 2024

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• 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, 28 Oct. 2015, 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, 18 May 2017, 特許第6791623号, 09 Nov. 2020

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• 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, 28 Oct. 2015, 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, 18 May 2017, 特許第6693723号, 20 Apr. 2020

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• 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, 19 Nov. 2015, 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, 01 Jun. 2017, 特許第6660718号, 13 Feb. 2020

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