Kyushu University Academic Staff Educational and Research Activities Database
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Katsumi DOI Last modified date:2018.06.11



Graduate School
Undergraduate School
Other Organization


E-Mail
Homepage
http://www.agr.kyushu-u.ac.jp/lab/MiBR/english.html
Phone
092-642-3059
Fax
092-642-3059
Academic Degree
Doctor of Philosophy (Agricultural science)
Field of Specialization
Applied Microbiology
Outline Activities
(1) Research activity:

Utilization of Microbial Genetic Resources.

The goal of the research is to ensure that the genetic diversity of agriculturally important microorganisms is maintained to enhance and increase agricultural efficiency and profitability. The Research will collect, authenticate and characterize potentially useful microbial germplasm stock; preserve microbial genetic diversity; and facilitate distribution and utilization of microbial germplasm for research and industry.

Main targets of the Research are Streptomyces species, Lactic acid bacteria and hyperthermophilic bacteria.

(2) Educational activity:

Professional education and moral tutor for foregin students.

University and graduate school education on the Depertment of Genetic Resources Technology in the Graduate School of Bioresource and Bioenvironmental Sciences and School of Agriculture.

(3) Social activity:

Part-time lecturer of Towa University (Faculty of Engineering), Kyushu University (Faculty of Low),
Fukuoka Agricultural Science School (Department of Food Science) and Daiichi University (College of Pharmaceutical Sciences).
Research
Research Interests
  • Investigation and isolation of bioresources from geothermal water
    keyword : Extreamphiles, Hyperthermophiles, bioresources
    2010.09.
  • Isolation and identification of virus infected to hyperthermopiles
    keyword : Extreamphiles, Hyperthermophiles, virus, phage
    2007.04.
  • Study of biosilicification with Thermus species
    keyword : Thermus, biosilicification, silica-induced protein, silica
    1995.04.
  • Structural and functional analysis of extrachromosomal elements in bacteria
    keyword : plasmis, bacteriophage, DNA translocation, site-specific recombination, gene targeting, evolution, conjugation
    1990.04.
  • Investigation of environmentally-sound agricultural and livestock system using lactic acid bacteria
    keyword : silage, Lactic acid bacteria, bacteriocin, probiotics, identification
    1994.01.
  • Spatial and temporal analysis of gene regulation for morphological and metabolic differentiation in Streptomyces
    keyword : Streptomyces, morphological and metabolic differentiation, gene regulation
    1990.04.
Current and Past Project
  • Biochemical investigation of thermophilic microorganisms is main scope of JSPS project.
    Especially, my scope is isolation and characterization of a high bacteriocin producing thermophilic lactic acids bacteria from Thailand.

    Enterococcus sp. K-4, with a bacteriocin-like activity against E. faecium, was isolated from grass silage in Thailand. Morphological, physiological, and phylogenetic studies clearly identified strain K-4 as a strain of E. faecalis. Strain K-4 produced a maximal amount of bacteriocin at 43-45C. We purified, for the first time, the bacteriocin produced at high temperature by E. faecalis to homogeneity, using adsorption on cells of the producer strain and reversed-phase liquid chromatography. The bacteriocin, designated enterocin SE-K4, is a peptide of about 5 kDa as measured by SDS-PAGE, and Mass spectrometry analysis found the molecular mass of 5356.2, which is in good agreement. The amino acid sequencing of the N-terminal end of enterocin SE-K4 showed apparent sequence similarity to class IIa bacteriocins. Enterocin SE-K4 was active against E. faecium, E. faecalis, B. subtilis, Clostridium beijerinckii, and Listeria monocytogenes. Enterocin SE-K4 is very heat stable.
    Strain K-4 carries two plasmids, pEK4S (approximately 60 kb) and pEK4L (approximately 75 kb). Plasmid-curing experiments showed that pEK4S was involved in the production of and immunity to enterocin SE-K4 in strain K-4. A derivative strain, M6, with pEK4S produced a higher amount of enterocin SE-K4 than the parental strain K-4, although its growth rate was lower than that of parental strain K-4. Phenotypic changes in strain M6 are attributed to an increase in plasmid copy number.

    References:
    Eguchi et al., Biosci. Biotechnol. Biochem., 64 (2), 247-253 (2001)
    Doi et al., J. Biosci. Bioeng., 93 (4), 434-436 (2002)
Academic Activities
Books
1. 土居 克実, 藤野 泰寛, Thermophilic Microbes in Environmental and Industrial Biotechnology: Biotechnology of Thermophiles, Springer, 233-247., 2013.03.
2. Bacteriophages in lactic acid bacteria.
Papers
1. FUJINO Yasuhiro, NAGAYOSHI Yuko, OHSHIMA Toshihisa, OGATA Seiya, DOI Katsumi, Complete genome sequence of Thermus thermophilus TMY, isolated from a geothermal power plant, Genome Announcements, 10.1128/genomeA.01596-16, 5, 5, e01596-16, 2017.02, [URL].
2. Yasuhiro Fujino, Ryo Tanoue, Takushi Yokoyama, Katsumi DOI, A tightly regulated expression system for E. coli using supersaturated silicic acid, Biotechnol. Lett., 10.1007/s10529-016-2118-z, 38, 8, 1381-1387, 2016.08.
3. DOI Katsumi, FUJINO Yasuhiro, NAGAYOSHI Yuko, OHSHIMA Toshihisa, OGATA Seiya, Complete genome sequence of thiostrepton producing Streptomyces laurentii ATCC 31255, Genome Announcements, 10.1128/genomeA.00360-16, 4, 3, e00360-16, 2016.06.
4. FUJINO Yasuhiro, NAGAYOSHI Yuko, IWASE Makoto, Takushi Yokoyama, OHSHIMA Toshihisa, Katsumi DOI, Silica-induced protein (Sip) in thermophilic bacterium, Thermus thermophilus, responds to low iron availability, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, in press, 2016.03.
5. NAGAYOSHI Yuko, KUMAGAE Kenta, Mori Kazuki, KOSUKE TASHIRO, NAKAMURA Ayano, FUJINO Yasuhiro, Yasuaki Hiromasa, IWAMOTO Takeo, Satoru Kuhara, OHSHIMA Toshihisa, Katsumi DOI, Physiological properties and genome structure of the hyperthermophilic filamentous phage φOH3 which infects Thermus thermophilus HB8, Frontiers in Microbiology, 7, 50, 2016.02, A filamentous bacteriophage, φOH3, was isolated from hot spring sediment in Obama hot spring in Japan with the hyperthermophilic bacterium Thermus thermophilus HB8 as its host. Phage φOH3, which was classified into the Inoviridae family, consists of a flexible filamentous particle 830 nm long and 8 nm wide. φOH3 was stable at temperatures ranging from 70 to 90°C and at pHs ranging from 6 to 9. A one-step growth curve of the phage showed a 60-min latent period beginning immediately postinfection, followed by intracellular virus particle production during the subsequent 40 min. The released virion number of φOH3 was 109. During the latent period, both single stranded DNA (ssDNA) and the replicative form (RF) of phage DNA were multiplied from min 40 onward. During the release period, the copy numbers of both ssDNA and RF DNA increased sharply. The size of the φOH3 genome is 5688 bp, and eight putative open reading frames (ORFs) were annotated. These ORFs were encoded on the plus strand of RF DNA and showed no significant homology with any known phage genes, except ORF 5, which showed 60% identity with the gene VIII product of the Thermus filamentous phage PH75. All the ORFs were similar to predicted genes annotated in the Thermus aquaticus Y51MC23 and Meiothermus timidus DSM 17022 genomes at the amino acid sequence level. This is the first report of the whole genome structure and DNA multiplication of a filamentous T. thermophilus phage within its host cell..
6. SAKIHARA Kengo, MAEDA Jumpei, KOSUKE TASHIRO, FUJINO Yasuhiro, Satoru Kuhara, OHSHIMA Toshihisa, OGATA Seiya, Katsumi DOI, Draft genome sequence of thiostreptone producing Streptomyces azureus ATCC 14921, Genome Announcements, 3, 5, 01183-15, 2015.10.
7. Hirokazu Suzuki, Keisuke Wada, Jumpei Kobayashi, OHSHIMA Toshihisa, Katsumi DOI, Megumi Furukawa, A thiostrepton resistance gene and its mutants serve as selectable markers in Geobacillus kaustophilus HTA426, Bioscience, Biotechnology, and Biochemistry, 80, 2, 368-375, 2015.09.
8. Hironaga AKITA, Yoshifumi IMAIZUMI, Katsumi DOI, Toshihisa OHSHIMA, Hirokazu SUZUKI, Spectrophotometric assay of D-isoleucine using an artificially created D-amino acid dehydrogenase, Biotechnol. Lett., 10.1007/s10529-014-1597-z, 36, 11, 2245-2248, 2014.11.
9. Ryutaro Ogura, Taisuke Wakamatsu, Yuta Mutaguchi, Katsumi Doi, Toshihisa Ohshima, Biochemical characterization of an L-tryptophan dehydrogenase from the photoautotrophic cyanobacterium Nostoc punctiforme, Enzyme Microb. Tech., http://dx.doi.org/10.1016/j.enzmictec.2014.04.002, 60, 40-46, 2014.06.
10. Tran Hai Ban, Hiroto Suhara, Katsumi Doi, Hiroya Ishikawa, Katsuya Fukami, Gopal Prasad Parajuli, Yoshinori Katakura, Shuntaro Yamashita, Kazuo Watanabe, Mahesh Kumar Adhikari, Hira Kaji Manandhar, RYUICHIRO KONDO, kuniyoshi shimizu, Wild Mushrooms in Nepal: Some Potential Candidates as Antioxidant and ACE-Inhibition Sources, Evid. Based Complement. Alternat. Med., http://dx.doi.org/10.1155/2014/195305, 2014, ID: 195305, 2014.01.
11. Hironaga AKITA, Hirokazu SUZUKI, Katsumi DOI, Toshihisa OHSHIMA, Efficient synthesis of D-branched-chain amino acids and their labeled compounds with stable isotopes using D-amino acid dehydrogenase., Appl. Microbiol. Biotechnol., 10.1007/s00253-013-4902-1, 98, 3, 1135-1143, 2013.05.
12. Hirokazu SUZUKI, Keisuke WADA, Megumi FURUKAWA, Katsumi DOI, Toshihisa OHSHIMA, A ternary conjugation system to construct DNA libraries in Geobacillus kaustophilus HTA426, Biosci. Biotechnol. Biochem., http://dx.doi.org/10.1271/bbb.130492, 77, 11, 2316-2318, 2013.11.
13. Yuta MUTAGUCHI, Taketo OHMORI, Hirofumi AKANO, Katsumi DOI, Toshihisa OHSHIMA, Distribution of D-amino acids in vinegars and involvement of lactic acid bacteria in the production of D-amino acids, SpringerPlus, 10.1186/2193-1801-2-691, 2, 691, 2013.12.
14. Katsumi DOI, Yousuke NISHIZAKI, Hidetoshi KIMURA, Maki KITAHARA, Yasuhiro FUJINO, Sadahiro OHMOMO, Toshihisa OHSHIMA, Seiya OGATA, Identification of thermo tolerant lactic acid bacteria isolated from silage prepared in the hot and humid climate of Southwestern Japan, SpringerPlus, 10.1186/2193-1801-2-485, 2, 485, 2013.09.
15. Katsumi DOI, Ong Thi Ahn PHUONG, Fagyun KAWATOU, Yuko NAGAYOSHI, Yasuhiro FUJINO, Toshihisa OHSHIMA, Identification and characterization of lactic acid bacteria isolated from fermented rice bran product, Adv. Microbiol., 10.4236/aim.2013.33038, 3, 3, 265-272, 2013.07.
16. Yuta MUTAGUCHI, Taketo OHMORI, Taisuke WAKAMATSU, Katsumi DOI, Toshihisa OHSHIMA, Identification, purification, and characterization of a novel amino acid racemase, isoleucine 2-epimerase, from Lactobacillus species., J. Bacteriol., 10.1128/JB.00709-13 , 94, 5207-5215, 2013.11.
17. Junpei KOBAYASHI, Yasuhiro SHIMIZU, Yuta MUTAGUCHI, Katsumi DOI, Toshihisa OHSHIMA, Characterization of D-amino acid aminotransferase from Lactobacillus salivarius,, J. Mol. Catal. B: Enzym., http://dx.doi.org/10.1016/j.molcatb.2013.04.013, 94, 15-22, 2013.10.
18. Katsumi DOI, Kazuki MORI, Yuta MUTAGUCHI, KOSUKE TASHIRO, Yasuhiro FUJINO, Satoru KUHARA, Toshihisa OHSHIMA, Draft Genome Sequence of D-branched-chain amino acids producing Lactobacillus otakiensis JCM 15040T isolated from a traditional Japanese pickle, , Genome Announcements, 10.1128/genomeA.00156-12 , 1, 4, e00546-13-e00546-13, 2013.01.
19. Taisuke WAKAMATSU, Chisato HIGASHI, Taketo OHMORI, Katsumi DOI, Toshihisa OHSHIMA, Biochemical characterization of two glutamate dehydrogenases with different cofactor specificities from a hyperthermophilic archaeon Pyrobaculum calidifontis, Extremophiles, 17, 3, 379-389, 2013.05, [URL].
20. Katsumi DOI, Mori Kazuki, KOSUKE TASHIRO, FUJINO Yasuhiro, Yuko Nagayoshi, Yoshiharu Hayashi, Satoru Kuhara, Toshihisa Ohshima, Draft Genome Sequence of Pediococcus lolii NGRI 0510QT isolated from ryegrass silage, Genome Announcements, 10.1128/genomeA.00156-12 , 1, 3, 00156-12 -00156-12 , 2013.01.
21. Ying Zhao, 若松 泰介, Katsumi DOI, Haruhiko Sakuraba, Toshihisa Ohshima, A psychrophilic leucine dehydrogenase from Sporosarcina psychrophila: Purification, characterization, gene sequencing and crystal structure analysis, J. Mol. Catal. B: Enzym., 83, 65-72, 2012.11,
.
22. 大森 勇門, YUta Mutaguchi, Katsumi DOI, Toshihisa Ohshima, Effects of alkali or acid treatment on the isomerization of amino acids, J. Biosci. Bioeng., 114, 4, 457-459, 2012.10.
23. K. Doi, Y. Ohyama, E. Yokoyama, T. Nishiyama, Y. Fujino, Y. Nagayoshi, T. Ohshima and S. Ogata , Expression analysis of the spi gene in the pock-forming plasmid pSA1.1 from Streptomyces azureus and localization of its product during differentiation
, Appl Microbiol Biotechnol, 10.1007/s00253-012-4000-9, 2012.05, The sporulation inhibitory gene spi in the pock-forming conjugative plasmid pSA1.1 of Streptomyces azureus was introduced into cells via a high or low copy number vector to examine the effect of gene dosage on the growth of Streptomyces lividans TK24 as a host. In transformants carrying a high spi copy number, nutrient mycelial growth was inhibited, as was morphological differentiation from substrate mycelium to aerial mycelium on solid media. The degree of inhibition depended on the spi gene dosage, but the presence of pSA1.1 imp genes, which encode negative repressor proteins for spi, relieved the inhibition. Confocal images of Spi tagged with enhanced green fluorescent protein in cells on solid media revealed that spi expression was initiated at the time of elongation of substrate mycelium, that its expression increased dramatically at septation in aerial hyphae, and that the expression was maximal during prespore formation. Expression of spi covered the whole of the hyphae, and the level of expression at the tip of the hyphae during prespore formation was about sixfold greater than during substrate mycelial growth and threefold greater than during aerial mycelial growth. Thus, localized expression of spi at particular times may inhibit sporulation until triggering imp expression to repress its inhibitory effects..
24. H. Akita, K. Doi, Y. Kawarabayasi and T. Ohshima , Creation of a thermostable NADP(+)-dependent D: -amino acid dehydrogenase from Ureibacillus thermosphaericus strain A1 meso-diaminopimelate dehydrogenase by site-directed mutagenesis, Biotechnology Letters , 10.1007/s10529-012-0952-1 , 2012.05, TA thermostable, NADP?-dependent D- amino acid dehydrogenase (DAADH) was created from the meso-diaminopimelate dehydrogenase of Ureibacillus thermosphaericus strain A1 by introducing five point mutations into amino acid residues located in the active site. The recombinant protein, expressed in Escherichia coli, was purified to homogeneity using a two-step separation procedure and then characterized. In the presence of NADP?, the protein catalyzed the oxidative deamination of several D-amino acids, including D-cyclohexylalanine, D-isoleucine and D-2-aminooctanoate, but not meso- diaminopimelate, confirming the creation of a NADP-dependent DAADH. For the reverse reaction, the corresponding 2-oxo acids were aminated in the presence of NADPH and ammonia. In addition, the D-amino acid dehydrogenase showed no loss of activity at 65 °C, indicating the mutant enzyme was more thermostable than its parental meso-diaminopimelate dehydrogenase. .
25. S. Bai, G. Naren, H. Noma, M. Etou, H. Ohashi, Y. Fujino, K. Doi, Y. Okaue, T. Yokoyama , Silica deposition induced by isolated aluminum ions bound on chelate resin as a model compound of the surface of microbes, Colloids Surf B Biointerfaces, 10.1016/j.colsurfb.2012.02.044, 95, 208-213, 2012.03, To elucidate the mechanism of silica biodeposition in hot spring water, which is induced by Al(3+) ions bound to the surface of microbes, a chelate resin (Chelex 100) was used as a model compound of the surface of microbes. No silicic acid was adsorbed on the Na type Chelex 100, whereas silicic acids were significantly adsorbed to the Al type Chelex 100. In the Al type Chelex 100, the Al(3+) ions were present as 1:1 tridentate complex with iminodiacetate (IDA) group. After adsorption of silicic acid to Al type Chelex 100, a IDAAlOSi(OH)(3) site formed. The site acted as a template for the successive adsorption of silicic acids to form silica sheets around Al type Chelex 100 particles. In conclusion, Al(3+) ions bound to the surface of microbes play a key role as a trigger for the biodeposition of silica in hot spring water..
26. T. Hirajima, Y. Aiba, M.Farahat, N. Okibe, K. Sasaki, T. Tsuruta and K. Doi , Effect of microorganisms on flocculation of quartz, Int. J. Miner. Process, 10.1016/j.minpro.2011.10.001, 102-103, 107–111, 2012.01, Application of microorganisms as surface modifiers in flocculation has generated a great deal of interest in recent times. The surface properties such as zeta-potential and hydrophobicity of minerals and microorganisms play a major role in determining the adsorption of microorganisms onto the minerals and hence the efficiency of flocculation. The utility of microorganisms, including Escherichia coli (wild-type and genetically modified strain Sip), Arthrobacter nicotianae, Bacillus licheniformis, and Pseudomonas maltophilia, has been evaluated by measuring their zeta-potentials and carrying out adsorption and flocculation experiments. Of the tested microorganisms, adsorption of E. coli strain Sip significantly modified the quartz surface. The zeta-potential of the quartz became highly positive at acidic pH, and its IEP (isoelectric point) was shifted from pH < 2 to pH 4.3. Moreover, the settling velocity of the bio-treated quartz reached its maximum value at this pH. The number of cells adsorbed onto quartz was low at pH above the IEP due to the identical surface charges of the mineral and bacterial cells. This led to a repulsive force between the mineral particles and bacterial cells, which hindered the adsorption process. For all of the studied strains, the settling velocity of bio-treated quartz was high at their respective IEPs. An interaction model of microorganisms is proposed to explain the flocculation behavior of bio-treated quartz. Potential energies were calculated using the DLVO theory, and the results were found to be in good agreement with the flocculation tests. The settling velocity of the bio-treated quartz was maximized at pH close to the IEP of microbial cells. Interaction between cells is identified as the most likely cause of flocculation of bio-treated quartz..
27. H. Akita, Y. Fujino, K. Doi and T. Ohshima , Highly stable meso-diaminopimelate dehydrogenase from an Ureibacillus thermosphaericus strain A1 isolated from a Japanese compost: purification, characterization and sequencing, AMB Express, 10.1186/2191-0855-1-43, 1, 43, 2011.11, We screened various thermophiles for meso-diaminopimelate dehydrogenase (meso-DAPDH, EC 1.4.1.16), which catalyzes the NAD(P)-dependent oxidative deamination of meso-diaminopimelate, and found the enzyme in a thermophilic bacterium isolated from compost in Japan. The bacterium grew well aerobically at around 55°C and was identified as Ureibacillus thermosphaericus strain A1. We purified the enzyme about 47-fold to homogeneity from crude cell extract using five successive purification steps. The molecular mass of the purified protein was about 80 kDa, and the molecule consists of a homodimer with the subunit molecular mass of about 40 kDa. The optimum pH and temperature for the catalytic activity of the enzyme are about 10.5 and 65°C, respectively. The enzyme is highly selective for meso-diaminopimelate as the electron donor, and NADP but not NAD can serve as the electron acceptor. The Km values for meso-diaminopimelate and NADP at 50°C and pH 10.5 are 1.6 mM and 0.13 mM, respectively. The nucleotide sequence of this meso-DAPDH gene encodes a 326-amino acid peptide. When the gene was cloned and overexpressed in Escherichia coli Rosetta (DE3), the specific activity in the crude extract of the recombinant cells was about 18.0-fold higher than in the extract from U. thermosphaericus strain A1. This made more rapid and simpler purification of the enzyme possible..
28. K. Doi, Y. Fujino, T. Yokoyama, S. Iwai, T. Ohshima and S. Ogata , Role of silica-induced protein in biosilicification in Thermus thermophils, Metal ions biology and medicine , 11, 288, 2011.06.
29. Y. Fujino, T. Yokoyama, T. Ohshima and K. Doi, Biodeposition of silica in geothermal system: Transcriptional analysis of silica-induced protein, Metal ions biology and medicine , 11, 289, 2011.06.
30. T. Ohmori, Y. Mutaguchi, S. Yoshikawa, K. Doi and T. Ohshima, Amino acid components of lees in salmon fish sauce are tyrosine and phenylalanine, J. Biosci. Bioeng., org/10.1016/j.jbiosc.2011.05.009, 112, 3, 256–258., 2011.03, We report that the lees in salmon fish sauce consist of Tyr and Phe. The concentration of free l-Tyr (2.0mM) was almost same as the saturated concentration (2.4mM) in water at 20°C. This result shows that lees are formed by Tyr precipitation due to its saturation in the sauce..
31. Mutaguchi Y, Ohmori T, Sakuraba H, Yoneda K, Doi K, Ohshima T., Visible wavelength spectrophotometric assays of L-aspartate and D-aspartate using hyperthermophilic enzyme systems., Anal. Biochem. , 409, 1, 1-6, 2011.02.
32. Y. Fujino, T. Ohshima, T. Yokoyama and K. Doi, Transcriptional analysis of the response to supersaturated silicic acid in Thermus thermophilus
, Geochim Cosmochim Ac, 74, 12, A309, 2010.12.
33. K. Doi, Y. Fujino, T. Ohshima and T. Yokoyama, Characterization of a silica-induced protein in Thermus thermophilus related to biosilicification
, Geochim Cosmochim Ac, 74, 12, A238, 2010.12.
34. Satomura T, Zhang XD, Hara Y, Doi K, Sakuraba H, Ohshima T., Characterization of a novel dye-linked L -proline dehydrogenase from an aerobic hyperthermophilic archaeon, Pyrobaculum calidifontis., Appl Microbiol Biotechnol., 2010.10.
35. S. IWAI, K. DOI, Y. FUJINO, T. NAKAZONO, K. FUKUDA, Y. MOTOMURA AND S. OGATA, Silica deposition and phenotypic changes to Thermus thermophilus cultivated in the presence of supersaturated silica, The ISME Journal, 4, 6, 809-816 , 2010.04.
36. M. Farahat, T. Hirajima, K. Sasaki, K. Doi, Adhesion of Escherichia coli onto quartz, hematite and corundum: Extended DLVO theory and flotation behavior., Colloids Surf B Biointerfaces, 10.1016/j.colsurfb.2009.07.009 , 74, 1, 140-149, 2009.11.
37. Katsumi Doi, Yousuke Nishizaki, Yasuhiro Fujino, Toshihisa Ohshima, Sadahiro Ohmomo and Seiya Ogata, Pediococcus lolii sp. nov., isolated from ryegrass silage, Int. J. Syst. Evol. Microbiol., 59, 1007-1010, 2009.04, [URL].
38. Hisaaki Yanai, Katsumi Doi, Toshihisa Ohshima, Sulfolobus tokodaii ST0053 Produces a Novel Thermostable, NAD-Dependent Medium-Chain Alcohol Dehydrogenase, Appl. Environ. Microbiol., Vol. 75, No. 6, p. 1758-1763, 2009.04, [URL].
39. Katsumi Doi, Yasuhiro Fujino, Fumio Inagaki, Ryouichi Kawatsu, Miki Tahara, Toshihisa Ohshima, Yoshihiro Okaue, Takushi Yokoyama, Satoru Iwai, Seiya Ogata , Stimulation of Expression of a Silica-Induced Protein (Sip) in Thermus thermophilus by Supersaturated Silicic Acid
, Appl. Environ. Microbiol., Vol. 75, No.8, 2406-2413, 2009.04, [URL].
40. M. Farahat, T. Hirajima, K. Sasaki, Y. Aiba, K. Doi, Adsorption of SIP E. coli onto quartz and its applications in froth flotation , Minerals Engineering, 10.1016/j.mineng.2007.10.019 , 21, 5, 389-395, 2008.04.
41. Shimizu Y, Sakuraba H, Doi K, Ohshima T., Molecular and functional characterization of D-3-phosphoglycerate dehydrogenase in the serine biosynthetic pathway of the hyperthermophilic archaeon Sulfolobus tokodaii, Arch Biochem Biophys, 470(2):120-128, 2008.02.
42. Y. Fujino, R. Kawatsu, F. Inagaki, A. Umeda, T. Yokoyama, Y. Okaue, S. Iwai, S. Ogata, T. Ohshima and K. Doi, Thermus thermophilus TMY isolated from silica scale taken from a geothermal power plant, J. Appl. Microbiol., Vol. 104, Issue 1, 70-78 , 2008.01, [URL].
43. Katsumi DOI, Study on Temporal and Spatial Expression of the Sporulation-inhibitory Gene of Conjugative Plasmid During Differentiation in Streptomyces., Actinomycetologica, 19(1), 27-32, 2005.07.
44. K . Doi, Z. Ye, Y. Nishizaki, A.Umeda, S. Ohmomo and S. Ogata, A Comparative Study of Silage-Making Lactobacillus Bacteriophages and Phage Typing, J. Biosci. Bioeng., 95(5), 549-560, 2003.05.
45. S. Yamada, H. Suenaga, K. Doi, S. Yoshino and S. Ogata, Stimulatory and Inhibitory Responses of Formation of Spontaneously Developing Pocks to UV-doses in Streptomyces azureus ATCC14921, Biosci. Biotech. Biochem., 67(4), 797-802, 2003.04.
46. H. Sakemi, S. Nishitake, M. Rodprapakorn, T. Shirakami, S. Takechi, K. Doi and S. Ogata, Nucleotide Sequence of Conjugative and Integrating Plasmid pSLS from Streptomyces laurentii ATCC31255, J. Fac. Agr., Kyushu Univ., 47, 2, 407-417, 47(2), 407-417, 2003.02.
47. O. Pringsulaka, S. Chavanich, K. Doi and S. Ogata, Changes in the population of a wide host range actinophage isolated from Thai soil and host streptomycetes in Thai and Japanese soil, Actinomycetol., 16(2), 21-25, 2002.12.
48. K. Doi, S. Nitisinprasert, S. Ohmomo and S. Ogata, Isolation and characterization of a high enterocin SE-K4 producing thermophilic enterococci, Enterococcus faecalis K-4 from Thai silage, The 3rd joint seminar on development of thermotolerant microbial resources and their applications (Chiangmai, Thailand), p.143., 2002.11.
49. K. Doi, T. Eguchi, S-H. Choi, A. Iwatake, S. Ohmomo and S.Ogata, Isolation of Enterocin SE-K4-Encoding Plasmid and a High Enterocin SE-K4 Producing Strain of Enterococcus faecalis K-4, J. Biosci. Bioeng., 10.1263/jbb.93.434, 93, 4, 434-436, 93(4), 434-436, 2002.04.
50. F. Inagaki, Y. Motomura, K. Doi, S. Taguchi, E. Izawa D. R. Lowe and S. Ogata, Silified Microbial Community at Steep Cone Hot Spring, Yellowstone National Park, Microb. Environ., 16(2), 125-130, 2001.11.
51. E. Yokoyama, K. Doi, M. Kimura and S. Ogata, Disruption of the hup gene encoding a histone-like protein HS1 and detection of HS12 of Streptomyces lividans, Res. Microbiol., 10.1016/S0923-2508(01)01252-9, 152, 8, 717-723, 152, 717-723, 2001.09.
52. A. Ishizaki, E. Takese, S. Kumai, R. Nagano, K. Sonomoto, K. Doi, S. Ogata, Y. Kawamura and T. Ezaki, Taxonomic position of new bacteriocin (nukacin ISK-1) producer isolated from long-aged Nukadoko, J. Gen. Appl. Microbiol, 10.2323/jgam.47.143, 47, 3, 143-147, 47, 143-147, 2001.07.
53. S. Eguchi, K. Kaminaka, J. Shima, S. Kawamoto, K. Mori, S-. H. Choi, K. Doi, S. Ohmomo and S. Ogata, Isolation and characterization of enterocin SE-K4 produced by thermophilic enterococci, Enterococcus faecalis K-4,, Biosci. Biotech. Biochem., 10.1271/bbb.65.247, 65, 2, 247-253, 65(2), 247-253, 2001.02.
54. K. Doi, T. Eguchi, M. Rodprapakorn, J. Shima, S. Ohmomo and S. Ogata, Genetic analysis of plasmids in the silage-making lactic acids bacteria and application for the preparation of high quality silage, The 2nd joint seminar on development of thermotolerant microbial resources and their applications (Yamaguchi, Japan), p.59, 2000.10.
55. Nitisinprasert, V. Nilphai, P. Sukyai, P. Bunyun, K. Doi and K. Sonomoto, Isolation and selection of thermotolerant lactic acid bacteria showing antimicrobial activity from chicken intestines, The 2nd joint seminar on development of thermotolerant microbial resources and their applications (Yamaguchi, Japan), p.54., 2000.10.
56. T. Nishiyama, Y. Kamachi, E. Yokoyama, K. Doi and S. Ogata, Characterization of cloned chromosomal fragment affecting differentiation in Streptomyces azureus ATCC14921, J. Fac. Agr., Kyushu Univ., 45(1), 225-236, 2000.09.
57. S. Nitisinprasert, V. Nilphai, P. Bunyun, P. Sukyai, K. Doi and K. Sonomoto, Screening and Identification of Effective Thermotolerant Lactic Acid Bacteria Producing Antimicrobial Activity Against Escherchia coli and Salmonella sp. Resistant to Antibiotics, Kasetsart J., 34, 387-400, 2000.08.
58. T. Nishiyama, H. Sakemi, H. Sumi, S. Tokunaga, K. Doi and S. Ogata, A chromosomal locus encoding a phosphoserine phosphatase- and a truncated MinD-like protein affects differentiation in Streptomyces azureus ATCC14921, FEMS Microbiol. Lett., 10.1111/j.1574-6968.2000.tb09275.x, 190, 1, 133-139, 190, 133-139, 2000.06.
59. T. Eguchi, K. Doi, K. Nishiyama, S. Ohmomo and S. Ogata, Characterization of a phage resistance plasmid, pLKS, of silage-making Lactobacillus plantarum NGRI0101, Biosci. Biotech. Biochem., 10.1271/bbb.64.751, 64, 4, 751-756, 64(4), 751-756., 2000.04.
60. F. Inagaki, R. Kawatsu, Y. Motomura, K. Doi, E. Izawa and S. Ogata, Effect of Thermophilic Bacteria on the Siliceous Deposition and Phylogenetic Analysis of the Bacterial Diversity in Silica Scale, J. Fac. Agr., Kyushu Univ., 44, 3-4, 309-316, 44(3・4), 309-316, 2000.02.
61. G. Fan, E. Takahashi, K. Doi, S. matsuo, O. Tanaka, S. Ohmomo and S. Ogata, Transformation of silage-making Lactobacillus strains by electroporation with plasmid vectors, J. Fac. Agr., Kyushu Univ., 43, 1-2, 217-225, 1999.11.
62. S. Ogata, T. Nishiyama, K. Doi, S. Yoshino, F. Kato and H-W. Ackermann, A Giant Phage Taillike Particle of Clostridium saccharoperbutylacetonicum ATCC13564, J. Fac. Agr., Kyushu Univ., 44, 1-2, 127-135, 44(1・2), 127-135, 1999.10.
63. A. K. Okba, T. Ogata, H. Matsubara, Y. Tawara, A. Abou-Shousha, S. Matsuo, K. Doi and S. Ogata, Stimulatory Effects of Bacitracin on Submerged Sporulation and Mycelial Growth in Thiostrepton-Producing Streptomyces cyaneus ATCC14921 and Streptomyces laurentii ATCC31255, J. Fac. Agr., Kyushu Univ., 43, 3-4, 461-472, 43(4・3), 461-472, 1999.03.
64. E. Yokoyama, Y. Matsuzaki, K. Doi and S. Ogata, Gene encoding a replication initiator protein and replication origin of conjugative plasmid pSA1.1 of Streptomyces cyaneus ATCC 14921, FEMS Microbil. Lett., 10.1111/j.1574-6968.1998.tb13305.x, 169, 1, 103-109, 169, 103-109., 1999.02.
65. A. K. Okba, T. Ogata, H. Matsubara, S. Matsuo, K. Doi and S. Ogata, Effects of Bacitracin and Excess Mg2+ on Submerged Mycelial Growth of Streptomyces azureus, J. Ferment. Bioeng., 10.1016/S0922-338X(98)80029-9, 86, 1, 28-33, 86(1), 28-33, 1998.07.
66. F. Inagaki, T. Yokoyama, K. Doi, E. Izawa and S. Ogata, Bio-deposition of Amorphous Silica by an Extremely Thermophilic bacterium, Thermus spp., Biosci. Biotech. Biochem., 10.1271/bbb.62.1271, 62, 6, 1271-1272, 62(6), 1271-1272., 1998.06.
67. K. Doi, Y. Ono, E. Yokoyama, Y. Tsukagoe and S. Ogata (1998), Whole sequence of spoIIIE-like, sporulation-inhibitory, and transfer gene (spi) in a conjugative plasmid, pSA1.1, of Streptomyces azureus and detection of spi-like gene in the actinomycete chromosome, Biosci. Biotech. Biochem., 10.1271/bbb.62.1597, 62, 8, 1597-1600, 62(6), 1597-1600, 1998.06.
68. E. Yokoyama, K. Doi, M. Kimura and S. Ogata, Histone-like protein of Streptomyces lividans, J. Fac. Agr., Kyushu Univ., 42, 3-4, 473-482, 43(3・4), 473-482, 1998.03.
69. C. Kinoshita-Iramina, M. Kitahara, K. Doi and S. Ogata, A conjugative linear plasmid in Streptomyces laurentii ATCC31255, Biosci. Biotech. Biochem., 61, 9, 1469-1473, 61(9), 1469-1473, 1997.09.
70. E. Yokoyama, K. Doi and S. Ogata, Cloning and sequencing of the hup gene encoding the histone-like protein HSl of Streptomyces lividans, Biochimica et Biophysica Acta, 10.1016/S0167-4781(97)00089-4, 1353, 2, 103-106, 1353,103-106, 1997.08.
Presentations
1. Sirinthorn Sunthornthummas,Onanong Pringsulaka,Yasuhiro Fujino, Katsumi Doi, Characterization of Lactobacillus paracasei phageΦT25 from fermented milk in Thailand, 日本農芸化学会関西・中四国・西日本支部2017年度合同大阪大会, 2017.09.
2. Keita Chiba, Michiru Kuroki, Gakuro Harada, Yoshinori Katakura, Katsumi DOI, Apoptotic death of cancer cells using holin, lytic protein from bacteriophage, AFELiSA 2016, 2016.11.
3. Mina KIM, Hindra MARTONO, Yuko NAGAYOSHI, Junpei MAEDA, Yasuhiro FUJINO, Katsumi DOI, Characterization of thermostable lytic proteins from Thermus bacteriophage φOH2, AFELiSA 2016, 2016.11.
4. KAYUMBA JIMMY, JUNPEI MAEDA, YASUHIRO FUJINO, KATSUMI DOI, IDENTIFICATION AND CHARACTERIZATION OF LAB ISOLATED FROM RWANDAN CHEESE AND JAPANESE FERMENTED TEA LEAVES (GOISHI-CHA), 第53回化学関連支部合同九州大会, 2016.07.
5. Nguyen Cong Thanh, 永吉 佑子, 藤野 泰寛, 土居 克実, Isolation and characterization of bacteriophage of Enterobacter asburiae, a cause of soft rot disease of plants in Vietnam, 第52回化学関連支部合同九州大会, 2015.06.
6. Martono Hindra, Yuko Nagayoshi, Toshihisa Ohshima, Yasuhiro Fujino, Katsumi Doi, Characterization of Novel Thermostable Endolysin from Phage φOH2

, 2014 Molecular Genetics of Bacteria and Phages Meeting, 2014.08, This research attempts to clone a novel endolysin from phage φOH2 and to perform characterization and functional analysis of the enzyme. φOH2 endolysin is found to be an extremely thermostable enzyme carrying PGRP domain, capable of degrading cell wall of bacteria other than phage’s host and withstand treatment in various pH buffers. Further work on this particular enzyme could help in understanding heat resistant mechanism of thermostable endolysin and developing a new antibacterial agent that could target antibiotic-resistant bacteria.
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7. Yuko NAGAYOSHI, Kenta KUMAGAE, Yasuhiro FUJINO, Toshihisa OHSHIMA, Katsumi DOI, Isolation and characrization of Thermus thermophilus phage φOH3, AFELiSA 2013, 2013.11.
8. Hirokazu SUZUKI, Junpei KOBAYASHI, Keisuke WADA, Megumi FURUKAWA, Katsumi DOI, Thermostabilization-directed gene evolution using adaptive mutations in the thermophile Geobacillus kaustophilus HTA426, BioMicroWorld 2013, 2013.10.
9. Hironaga AKITA, Hirokazu SUZUKI, Katsumi DOI, Toshihisa OHSHIMA, Efficient synthesis and stable isotope-labeling of D-branched-chain amino acids using thermostable D-amino acid dehydrogenase, Thermophiles2013, 2013.09.
10. , [URL].
11. The genus Thermus are defined as aerobic, heterotrophic, non-motile, pigmented, non-spore-forming, and Gram- negative rods that can grow at temperatures over 70 °C. Previously, we isolated Thermus thermuohilus TMY from the geothermal power plant in Japan and reported that strain TMY induces the precipitation of supersaturated silicic acid during exponeatial growth phase.
Notably, supersaturated silicic acid markedly stimulated expression of one cell envelope protein, which is named as silica-induced protein (Sip). The amino acid sequence of Sip showed significant
similarity with the solute-binding protein of Fe3+ ABC transporters observed in other Thermus strains, however, little is known about the regulation of gene expression in response to supersaturated silicic acid. To determine the regulation of Sip expression, the transdriptional regulation mechanisms were investigated.
Althogh sip operon comprises sip (solute-binding protein), permiase and ATPase, only sip gene was strongly transcribed in the silica-stressed condition. This might result from the fact that the palindromic structure located immidiately downstream of sip could function as the terminator of sip. Primer extension analysis revealed that transcription initiation site of sip is
located at 34 bases upstream of start codon. -35 and -10 element of the sip promoter showed meaningful similarity to those of &A promoters commonly seen in T. thermophilus. Sip trnscription was enhanced by the addition of supersaturated silicic acid, however, sip was also transcribed in the iron-condition. Due to the negative charge of colloidal silica in silica-stressed condition, iron ions might be trapped by colloidal silica. Thermus cells might receive the signals of the existence of supersaturated silicic acid as the iron deficiency caused by colloidal silica. This mechanism of silica-responsible promoter could serve us more convenient and effective genetic tools for thermophile and must shed new light on bacterial biosilicification studies.
, [URL].
12. Thermus thermophilus TMY, an extreme thermophile, was isolated from a siliceous deposit formed from geothermal water at a geothermal power plant. At concentrations higher than the solubility of amorphous silica (400 to 700 ppm SiO2, at 750), a silica-induced protein (Sip) was expressed in the cell envelope of log-phase cells grown in the presence of supersaturated silicic acid. Molecular weightand pI of Sip were about 35 kDa and 9.5, respectively. Induction of Sip expression occurred within 1 h after the addition of a supersaturating concentration of silicic acid to broth. Production of Sip and its upregulation were in excellent temporal agreement with the silica precipitation, which was observed at silicic acid concentrations greater than 400 ppm in the medium at 75°C.
The amino acid sequence of Sip was similar to that of the predicted solute-binding protein of the Fe3+ -ABC transporter in T. thermophilus HB8 and HB27 [2]. Within the genome, sip is situated as a component of the Fbp-type ABC transporter operon, which contains a palindromic structure immediately downstream of sip. This structure is conserved in other T. thermophilus genomes and may function as a terminator that causes definitive Sip expression in response to silica stress.
     The sip gene was cloned in pET32 and expressed in E. coli. Transformant grown in LB containing 600 ppm silica precipitated silica during their growth (Fig. 1). Purified and heat-treated Sip protein also precipitated silica effectively. Therefore Sip might exhibit their silica precipitation ability.

, [URL].
Membership in Academic Society
  • American Society for Microbiology
Educational
Educational Activities
・Faculty of Agriculture, Graduate school of Bioresource and Bioenvironmental Sciences:

Japanese Classes for Foreign students: Introduction to Japanese Agriculture (2 credits),
Introduction to Japanese Agricultural Sciences and Technologies (2 credits),
Advanced Topics on Japanese Agricultural Sciences and Technologies (2 credits)
Research in Japanese Agriculture (1 credit)

English Class for Foreign students: Advanced Topics on Genetic Resources Technology (part)
                                                              Advanced Technology in Agriculture (part)

Orientation and Instruction for Foreign students

・Laboratory of Microbial Genetics : Supervising of dissertation for Master's course and Doctor's course students.
Other Educational Activities
  • 2006.08.
Social
Professional and Outreach Activities
(1) Professional education and moral tutor for foregin students.

Lectures are Introduction for Japanese Agriculture I (IJA-1) and Introduction for Japanese Agriculture II (IJA-2) in Japanese. Aims of these lecture are acquisition of technical term in Agricultural Science field and improvement in the ability to high-quality presentation using Japanese language for foreign students.

(2) University and graduate school education on the Depertment of Genetic Resources Technology in the Graduate School of Bioresource and Bioenvironmental Sciences and School of Agriculture.

Research and Technological Guidance for students in the Microbial Genetic Technology such as thesis and research work..