九州大学 研究者情報
論文一覧
土居 克実(どい かつみ) データ更新日:2021.06.15

教授 /  農学研究院 生命機能科学部門 遺伝子資源開発学講座


原著論文
1. Sirinthorn Sunthornthummas, Katsumi Doi, Yasuhiro Fujino, Achariya Rangsiruji, Siriruk Sarawaneeyaruk, Kedvadee Insian, Onanong Pringsulaka, Genomic characterisation of Lacticaseibacillus paracasei phage ΦT25 and preliminary analysis of its derived endolysin, International Dairy Journal, 10.1016/j.idairyj.2020.104968, 116, 2021.05.
2. Nguyen Cong Thanh, Yasuhiro Fujino, Yasuaki Hiromasa , Katsumi Doi, Draft Genome Sequence of Enterobacter kobei M4-VN, Isolated from Potatoes with Soft Rot Disease, Microbiology resource announcements, 10.1128/MRA.00908-20., 9, 36, 2020.09.
3. Yasuhiro Fujino, Shuichiro Goda, Yuri Suematsu, Katsumi Doi, Development of a new gene expression vector for Thermus thermophilus using a silica‑inducible promoter, Microbial Cell Factories, 10.1186/s12934-020-01385-2, 19, 126, 2020.06.
4. Nguyen Cong Thanh, Yuko Nagayoshi, Yasuhiro Fujino, Kazuhiro Iiyama, Naruto Furuya, Yasuaki Hiromasa, Takeo Iwamoto, Katsumi Doi, Characterization and Genome Structure of Virulent Phage EspM4VN to Control Enterobacter sp. M4 Isolated From Plant Soft Rot, Frontiers in Microbiology, https://doi.org/10.3389/fmicb.2020.00885, 11, 885, 2020.06.
5. Sirinthorn Sunthornthummas, Katsumi Doi, Achariya Rangsiruji, Sukhumaporn Krajangsung, Siriruk Sarawaneeyaruk, Onanong Pringsulaka, Isolation and characterization of spontaneous phage-resistant mutants of Lactobacillus paracasei, Food Control, 10.1016/j.foodcont.2018.12.037, 99, 114-123, 2019.05, [URL], Spontaneous phage-resistant mutants were isolated from Lactobacillus paracasei LPC by agar plate (AP) and secondary-culture (SC) methods. They were characterized by cell and colony morphologies, carbohydrate fermentation patterns, phage resistance stability, efficiency of plaquing (EOP), acidifying and milk acidification kinetics. Only 98 out of 175 isolates (56%) proved to be true phage-resistant mutants and the SC method was more efficient than the AP method. Although the phage resistance stability varied among the mutants isolated, the EOP values were mostly very high (<10
−11
). Three phage-resistant strains were selected based on their extreme resistance capacity to the phage ΦT25 (EOP<10
−10
) and their nonlysogenic property. Acidifying activity did not differ between phage-sensitive strains and their three respective phage-resistant derivatives. Most of the mutants were completely or partially unable to adsorb phage particles. Restriction-modification type systems were not detected in all phage-resistant derivatives. All three selected mutants were identical to the corresponding parent strain of L. paracasei LPC in the cell and colony morphologies. The comparison of random amplified polymorphic DNA profiles obtained with four arbitrary primers also revealed the highest similarity coefficient (87%) among the parent strain and the three mutants, indicating that each mutant has been derived from this parent strain. A good performance during milk fermentation and the subsequent refrigerated storage were obtained when these mutants were employed. These phage-resistant derivatives could be used as improved strains or for strain rotation programs when commercial strains become sensitive to the phages present in industrial environments..
6. Hirokazu Suzuki, Tomoaki Abe, Katsumi Doi, Toshihisa Ohshima, Azoreductase from alkaliphilic Bacillus sp. AO1 catalyzes indigo reduction, Applied Microbiology and Biotechnology, 10.1007/s00253-018-9284-y, 102, 21, 9171-9181, 2018.11, [URL], Indigo is an insoluble blue dye historically used for dyeing textiles. A traditional approach for indigo dyeing involves microbial reduction of polygonum indigo to solubilize it under alkaline conditions; however, the mechanism by which microorganisms reduce indigo remains poorly understood. Here, we aimed to identify an enzyme that catalyzes indigo reduction; for this purpose, from alkaline liquor that performed microbial reduction of polygonum indigo, we isolated indigo carmine-reducing microorganisms. All isolates were facultative anaerobic and alkali-tolerant Bacillus spp. An isolate termed AO1 was found to be an alkaliphile that preferentially grows at pH 9.0–11.0 and at 30–35 °C. We focused on flavin-dependent azoreductase as a possible enzyme for indigo carmine reduction and identified its gene (azoA) in Bacillus sp. AO1 using homology-based strategies. azoA was monocistronic but clustered with ABC transporter genes. Primary sequence identities were < 50% between the azoA product (AzoA) and previously characterized flavin-dependent azoreductases. AzoA was heterologously produced as a flavoprotein tolerant to alkaline and organic solvents. The enzyme efficiently reduced indigo carmine in an NADH-dependent manner and showed strict specificity for electron acceptors. Notably, AzoA oxidized NADH in the presence, but not the absence, of indigo. The reaction rate was enhanced by adding organic solvents to solubilize indigo. Absorption spectrum analysis showed that indigo absorption decreased during the reaction. These observations suggest that AzoA can reduce indigo in vitro and potentially in Bacillus sp. AO1. This is the first study that identified an indigo reductase, providing a new insight into a traditional approach for indigo dyeing..
7. Sunthornthummas, S., Doi, K., Rangsiruji, A., Sarawaneeyaruk, S., Pringsulaka, O., Isolation and characterization of Lactobacillus paracasei LPC and phage ΦT25 from fermented milk, Food Control, 10.1016/j.foodcont.2016.10.052, 73, 1353-1361, 2017.03, [URL].
8. 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.
9. Sonam Tamrakar, Hai Bang Tran, Marina Nishida, Satoru Kaifuchi, Hiroto Suhara, Katsumi Doi, Katsuya Fukami, Gopal Prasad Parajuli, Kuniyoshi Shimizu, Antioxidative activities of 62 wild mushrooms from Nepal and the phenolic profile of some selected species, Journal of Natural Medicines, 10.1007/s11418-016-1013-1, 70, 4, 769-779, 2016.10, [URL], Mushrooms have garnered immense popularity for their nutritional as well as medicinal values. The therapeutic potential of mushrooms in Nepal, a country well known for its biodiversity and natural medicinal resources, remains largely unstudied. Therefore, this study attempts to unveil the antioxidative properties of Nepalese wild mushrooms. Sixty-two wild mushroom samples were collected from several forests in different parts of Nepal. Ethanol and water extracts of the dried samples were tested for their antioxidative activities using total phenolic content (TPC), oxygen radical absorbance capacity (ORAC) assay, 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and reducing power (RP) assays. Ethanol extracts of samples belonging to the order Hymenochaetales showed significantly high activity in all the assays. Inonotus clemensiae had an exceptionally high TPC of 643.2 mg gallic acid equivalent (GAE)/g extract and also exhibited the lowest EC50 values in DPPH (0.081 mg/mL), ABTS (0.409 mg/mL), and EC0.5 value in reducing power (RP; 0.031 mg/mL) assays. High-performance liquid chromatography (HPLC) analysis of the top ten samples with the highest TPC was done to identify the phenolic compounds in the extracts, followed by liquid chromatography–mass spectrometry (LC–MS) analysis for some unknown compounds. These findings highlight the very strong antioxidative activity of Nepalese mushrooms, and paves the way for further research to explore their economic potential..
10. 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, [URL].
11. 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, [URL].
12. 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.
13. 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..
14. 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.
15. 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.
16. Jumpei KOBAYASHI, Jotaro YUKIMOTO, Yasuhiro SHIMIZU, Taketo OHOMORI, Hirokazu SUZUKI, Katsumi DOI, Toshihisa OHSHIMA, Characterization of Lactobacillus salivarius alanine racemase: short-chain carboxylate-activation and the role of A131, SpringerPlus, 2015.06.
17. Hirokazu SUZUKI, Jumpei KOBAYASHI, Keisuke WADA, Megumi FURUKAWA, Katsumi DOI, Thermoadaptation-Directed Enzyme Evolution in an Error-Prone Thermophile Derived from Geobacillus kaustophilus HTA426, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 10.1128/AEM.02577-14, 81, 1, 149-158, 2015.01.
18. 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, [URL].
19. 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, [URL].
20. 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, [URL].
21. 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, [URL].
22. 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, [URL].
23. 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.
24. 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, [URL].
25. 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, [URL].
26. 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, [URL].
27. 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.
28. 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, [URL].
29. 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, [URL].
30. 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, [URL].
31. 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,
.
32. 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, [URL].
33. 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, [URL], 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. .
34. 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, [URL], 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..
35. 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, [URL], 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..
36. 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, [URL], 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..
37. 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, [URL], 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..
38. 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, [URL].
39. 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, [URL].
40. 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, [URL], 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..
41. 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.
42. 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, [URL].
43. 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, [URL].
44. 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.
45. 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.
46. 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, [URL].
47. 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].
48. 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].
49. 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].
50. 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, [URL].
51. 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.
52. 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].
53. 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.
54. 土居克実、西崎陽祐、大桃定洋、緒方靖哉, 分子系統解析による西南暖地型サイレージ乳酸菌株の多様性の究明, 生物工学会誌, 82, 9, 436-437, 2004.09.
55. 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.
56. 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.
57. 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.
58. 土居克実、岩武敦司、江口智子、大桃定洋、緒方靖哉, サイレージ発酵におけるバクテリオシンの有効利用と高生産性の追究, 生物工学会誌, 80(12), 578-580., 2002.12.
59. 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.
60. 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.
61. 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.
62. 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.
63. 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.
64. 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.
65. 土居克実、江口智子、島純、西山孝、大桃定洋、緒方靖哉, サイレージ乳酸菌の機能開発 -サイレージ乳酸菌が保持するプラスミドの特性と利用開発-, 生物工学会誌, 79(6), 177-179., 2001.06.
66. 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.
67. 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.
68. 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.
69. 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.
70. 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.
71. 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.
72. 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.
73. 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.
74. 土居克実、江口智子、崔聖賢、大桃定洋、緒方靖哉, サイレージ乳酸菌の機能開発 -高温環境に適応したバクテリオシン生産株の分離と利用-, 生物工学会誌, 77(11), 472-474, 1999.11.
75. 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.
76. 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.
77. 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.
78. 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.
79. 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.
80. 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.
81. 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.
82. 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.
83. 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.
84. 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.
85. 土居克実、江口智子、田中治、森勝美、大桃定洋、緒方靖哉, サイレージ乳酸菌の機能開発  -ファージタイピングによる簡便な同定法の開発および高機能サイレージ菌株作出-, 生物工学会誌, 75(5), 361-363, 1997.05.
86. F. Inagaki, S. Hayashi, K. Doi, Y. Motomura, E. Izawa and S. Ogata, Microbial participation in the formation of siliceous deposits from geothermal water and analysis of the extremely thermophilic bacterial community, FEMS Microbiol. Ecol., 10.1111/j.1574-6941.1997.tb00421.x, 24, 1, 41-48, 24, 41-48., 1997.01.
87. 土居克実、田中治、大桃定洋、緒方靖哉, サイレージ乳酸菌の機能開発, 生物工学会誌, 74(4), 294-297, 1996.04.
88. E. Yokoyama, K. Doi, M. Kimura and S. Ogata, Detection of the single-stranded DNA of Streptomyces plasmid pSA1.1 and a binding histone-like protein, FEMS Microbiol. Lett., 10.1111/j.1574-6968.1996.tb08156.x, 138, 2-3, 197-200, 138, 197-200, 1996.02.
89. S. Ogata, K. Doi and E. Yokoyama, Streptomyces episomal factors; Characterization and application for gene technology, Current Trends in Biotechnology, 139-180, 1996.01.
90. C. Kinoshita-Iramina, M. Kitahara, Y. Harada, K. Doi and S. Ogata, Formation of Spontaneously Developing Pocks Regulated by Two Unhomologous Plasmids in Streptomyces laurentii, J. Fac. Agr., Kyushu Univ., 40, 1-2, 167-178, 40(1・2), 167-178, 1995.10.
91. E. Yokoyama, Y. Ono, K. Doi and S. Ogata, Study on the spoIIIE-like gene in Streptomyces azureus, Microb. Util. Renew. Resour., 9, 326-333, 1995.08.
92. C. Kinoshita-Iramina, M. Kitahara, Y. Harada, K. Doi and S. Ogata, Two plasmids Related to Spontaneously Developing Pocks in Streptomyces laurentii ATCC31255, Biosci. Biotech. Biochem., 59(6), 1040-1043, 1995.06.
93. K. Doi, E. Yokoyama, Y. Nakano, S. Tokunaga and S. Ogata, Transfer Function of spi Gene in Plasmid pSA1.1 of Streptomyces azureus ATCC14921, Actinomycetologica, 9(1), 44-48, 1995.06.
94. K. Doi, M. C. Saeki, Y. Ono and S. Ogata, Plasmid formation and its relation to the formation of spontaneously developing pocks in Streptomyces azureus ATCC14921, J. Appl. Bacteriol., 10.1111/j.1365-2672.1995.tb03132.x, 79, 3, 237-243, 79, 237-243, 1995.06.
95. O. Tanaka, S. Ohmomo, Y. Zong, K. Nishiyama, K. Doi and S. Ogata, Relationship between Fermentation Quality of Silage and Presence of Phages for Silage-Making Lactobacilli, Bull. Natl. Grassl. Res. Inst., 51, 31-39, 1995.03.
96. M. Rodprapakorn, K. Doi and S. Ogata, Protoplast Regeneration and Transformation of Thiostrepton-Producing Streptomyces laurentii ATCC31255, J. Fac. Agr., Kyushu Univ., 39, 3-4, 167-174, 39(3・4), 167-174, 1995.03.
97. 金重尚子、張曄、西山加奈子、土居克実、田中治、大桃定洋、緒方靖哉, イタリアンライグラスサイレージにおける乳酸桿菌ファージの検出頻度と発酵品質, 日本農芸化学会誌, 68(8)、1219-1221, 1994.08.
98. K. Doi, T. Tomura, H. Kishino, T. Hara, S. Kuhara, K. Kanda and S. Ogata, Introduction of Kanamycin Resistant Gene to Pock-forming Plasmid pSA1.1 of Streptomyces azureus and Identification of spoIIIE-like Gene in the Recombinant Plasmid, J. Fac. Agr., Kyushu Univ., 38, 3-4, 193-205, 38(3・4), 193-205, 1994.03.
99. T. Tomura, H. Kishino, K. Doi, T. Hara, S. Kuhara and S. Ogata, Sporulation-inhibitory gene in pock-forming plasmid pSA1.1 of Streptomyces azureus, Biosci. Biotech. Biochem.,, 57, 3, 438-443, 57 (3), 438-443., 1993.03.
100. Ogata, S. Yamada, K. Doi, S. Tokunaga, H. Matsubara and T. Hara, Inhibition of Spore Formation and Thiostrepton Production by Accumulated Intermediates of Purine Biosynthesis and the Suppression by AICA (5-Amino-4-Imidazole Carboxamide) in Purine Auxotrophic Mutants of Streptomyces azureus ATCC14921, J. Fac. Agr., Kyushu Univ.,, 35, 3-4, 161-167, Vol.35,No. 3・4, p. 161-167, 1991.03.
101. S. Ogata, K. Doi and S. Yamada, Effect of Adenine and Related Compounds on Spore Formation and Thiostrepton Production by Purine Auxotrophic Mutants of Streptomyces azureus ATCC14921, Actinomycetologica, Vol.4, No. 2, p. 89-91, 1990.12.
102. M. Rodprapakorn, Y. Nakano, K. Doi and S. Ogata, Taxonomic study of feed additive-producing strains of genus Streptomyces, Microb. Util. Renew. Resour., 9, 165-173.

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