List of Publications

[2014] [2013] [2012] [2011] [2010] [2009] [2008-2005] [2004-2000] [1999-1995] [1994-1968]


2014

  • “Characterization of water-soluble dark-brown pigment from Antarctic bacterium,Lysobacter oligotrophicus .”T. Kimura, W. Fukuda, T. Sanada and T. Imanaka,J. Biosci. Bioeng., (in press)

  • “Evaluation of metabolome sample preparation methods regarding leakage reduction for the oleaginous yeastYarrowia lipolytica.” C. Zhao, K. Nambou, L. Wei, J. Chen, T. Imanaka, and Q. Hua ,Biochem. Eng. J., 82, 63-70, 2014

  • “Designing of a "cheap to run" fermentation platform for an enhanced production of single cell oil from Yarrowia lipolytica as a potential feedstock for biodiesel.” K. Nambou, C. Zhao, L. Wei, J. Chen, T. Imanaka, Q. Hua ,Bioresource Technol., (in press)

  • “The X-ray crystal structure of the euryarchaeal RNA polymerase in an open clamp configuration.” K. Murakami, S-H Jun, A. Hirata, T. Kanai, T. Santangelo, and T. Imanaka,Nature Communications, 2014 . doi: 10.1038/ncomms6132.

  • “Genetic Examination and Mass Balance Analysis of Pyruvate/Amino Acids Oxidation Pathways in the Hyperthermophilic Archaeon Thermococcus kodakarensis.” K. Nohara, I. Orita, S. Nakamura, T. Imanaka, T. Fukui,J. Bacteriol., 196(22), 3831-3839, 2014.

  • “超好熱菌を用いた水素連続生産系の構築” 金井　保、跡見晴幸、今中忠行、酵素工学会誌、71号、18-24、2014

  • “Cysteine desulfurase plays an important role in environmental adaptation of the hyperthermophilic archaeon Thermococcus kodakarensis.” R. Hidese, T. Inoue, T. Imanaka, S. Fujiwara,Mol. Microbiol., 93(2), 331-345, 2014.

  • “Stepwise and combinatorial optimization of enantioselectivity for the asymmetric hydrolysis of 1-(3’,4’-methylenedioxypyhenyl)ethyl acetate under use of a cold-adapted Bacillus amyloliquefaciens esterase.” J.-Y. Liu, G.-W. Zheng, T. Imanaka, J.-H. Xu,Biotechnol. Bioprocess Eng.,19, 442-448, 2014

  • “The tryptophan synthase β-subunit paralogs TrpB1 and TrpB2 in Thermococcus kodakarensis are both involved in Trp biosynthesis and indole salvage.” T. Hiyama, T. Sato, T. Imanaka, H. Atomi,FEBS J., 281(14), 3113-3125, 2014.

  • “Characterization and gene deletion analysis of four homologues of group 3 pyridine nucleotide disulfide oxidoreductases from Thermococcus kodakarensis.”
    P. Harnvoravongchai, H. Kobori, I. Orita, S. Nakamura, T. Imanaka, T. Fukui, Extremophiles, 18(3), 603-616, 2014.

  • “Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from antarctic white rock.” W. Fukuda, Y. Chino, S. Araki, Y. Kondo, H. Imanaka, T. Kanai, H. Atomi, T. Imanaka,Int. J. Syst. Evol. Microbiol., 64, 2034-2040, 2014.

  • “Identification of a novel aminopropyltransferase involved in the synthesis of branched-chain polyamines in hyperthermophiles.” K. Okada, R. Hidese, W. Fukuda, M. Niitsu, K. Takao, Y. Horai, N. Umezawa, T. Higuchi, T. Oshima, Y. Yoshikawa, T. Imanaka, S. Fujiwara, J. Bacteriol., 196(10), 1866-1876, 2014.

  • “Different roles of two transcription factor B proteins in the hyperthermophilic archaeon Thermococcus kodakarensis.” R. Hidese, R. Nishikawa, L. Gao, M. Katano, T. Imai, S. Kato, T. Kanai, H. Atomi, T. Imanaka, S. Fujiwara, Extremophiles, 18(3), 573-588, 2014.

  • “Atomic Force Microscopic Study of Chitinase Binding onto Chitin and Cellulose Surfaces.” Y. Kikkawa, M. Fukuda, T. Kimura, A. Kashiwada, K. Matsuda, M. Kanesato, M. Wada, T. Imanaka, T. Tanaka, Biomacromolecules, 15(3), 1074-1077, 2014.

  • “Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis.” A. Kita, T. Ishibashi, H. Tomita, Y. Yokoooji, T. Imanaka, H. Atomi, K. Miki, Proteins, 2014 . doi: 10.1002/prot.24546.

  • “An archaeal glutamate decarboxylase homolog functions as an aspartate decarboxylase and is involved in β-alanine and CoA biosynthesis. ” H. Tomita, Y. Yokooji, T. Ishibashi, T. Imanaka, H. Atomi, J. Bacteriol., 196(6), 1222-1230, 2014.

  • “Characterization of two members among the five ADP-forming acyl-CoA synthetases reveals the presence of a 2-(imidazol-4-yl)acetyl-CoA synthetase in Thermococcus kodakarensis.” T. Awano, A. Wilming, H. Tomita, Y. Yokooji, T. Fukui, T. Imanaka, and H. Atomi, J. Bacteriol., 196(1), 140-147, 2014


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2013

  • “Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation.” T. Tominaga, S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, and K. Miki, Pro. Natl. Acad. Sci. U. S. A., 110(51), 20485-20490, 2013.

  • “Importance and determinants of induction of cold-induced DEAD RNA helicase in the hyperthermophilic archaeon Thermococcus kodakarensis.” E. Nagaoka, R. Hidese, T. Imanaka, S. Fujiwara,J. Bacteriol., 195(15), 3442-3450, 2013.

  • “Identification and characterization of an archaeal ketopantoate reductase and its involvement
    in regulation of coenzyme A biosynthesis” H. Tomita, T.i Imanaka, and H.Atomi, Mol. Microbiol.,
    90(2), 307-321, 2013

  • “Hydrogen production by the hyperthermophilic archaeon Thermococcus kodakarensis.” T. Kanai,
    T. Imanaka, and H. Atomi, J. Japan Petroleum Institute, 56 (5), 267-279, 2013.

  • “Structural change of DNA induced by nucleoid proteins: Growth phase-specific Fis and stationary phase-specific Dps.”,Y. T. Sato, S. Watanabe, T. Kenmotsu, M. Ichikawa, Y. Yoshikawa, J.Teramoto, T. Imanaka, A. Ishihama and K. Yoshikawa, Biophys. J., 105(4), 1037-1044, 2013.

  • “バイオサーファクタント生産菌の分離とバイオレメディエーションへの利用”, 高松邦明, 山津敦史, 今中忠行、環境バイオテクノロジー学会誌、13、47-49、2013.

  • “Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization" Y. Nishitani, R. Aono, A. Nakamura, T. Sato, H. Atomi, T. Imanaka, K. Miki,J. Mol. Biol., 425, 2709-2721, 2013.

  • “Identification and structure of a novel archaeal HypB for [NiFe] hydrogenase maturation" D. Sasaki, S. Watanabe, R. Matsumi, T. Shoji, A. Yasukochi, K. Tagashira, W. Fukuda, T. Kanai, H. Atomi, T. Imanaka, K. Miki,J. Mol. Biol., 425(10), 1627-1640, 2013.

  • "Lysobacter oligotrophicus sp. nov., a bacterium isolated from a freshwater lake in Skarvsnes, Antarctica. " W. Fukuda, T. Kimura, S. Araki, Y. Miyoshi, H. Atomi T. Imanaka,Int. J. Syst. Evol. Microbiol., 63, 3313-3318, 2013

  • “CoA biosynthesis in archaea.” H. Atomi, H. Tomita, T. Ishibashi, Y. Yokooji, T. Imanaka,Biochem. Soc. Trans., 41(1), 427-431, 2013

  • “Genetic examination of initial amino acid oxidation and glutamate catabolism in the hyperthermophilic archaeon Thermococcus kodakarensis.” Y. Yokooji, T. Sato, S. Fujiwara, T. Imanaka, H. Atomi, J. Bacteriol., 195(9):1940-1948, 2013.

  • “Effective chiral discrimination of tetravalent polyamines on single-DNA compaction.” Y. Yoshikawa, N. Umezawa, Y. Imamura, T. Kanbe, N. Kato, K. Yoshikawa, T. Imanaka, T. Higuchi, Angew. Chem., 52(13), 3712-3716, 2013.

  • “Thermostable alcohol dehydrogenase from Thermococcus kodakarensis KOD1 for enantioselecyive bioconversion of aromatic secondary alcohols.” X. Wu, C. Zhang, I. Orita, T. Imanaka, T. Fukui, X.-H. Xing, Appl. Environment. Microbiol., 79(7), 2209-2217, 2013.

  • “Genetic studies on the virus-like regions in the genomeof hyperthermophilic archaeon, Thermococcus kodakarensis.” K. Tagashira, W. Fukuda, M. Matsubara, T. Kanai, H. Atomi, T. Imanaka, Extremophiles, 17(1), 153-160, 2013.


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2012

  • “Crystal structures of the HypCD complex and the HypCDE ternary complex: Transient intermediate complexes during [NiFe] hydrogenasematuration.” , S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, K. Miki, Structure, 20, 1-14, Dec.5, 2012.

  • “Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway” R. Aono, T. Sato, A. Yano, S. Yoshida, Y. Nishitani, K. Miki, T. Imanaka, H.Atomi, J. Bacteriol., 2012 [Epub ahead of print]

  • “Structure of the [NiFe]-hydrogenase maturation protein HypF from Thermococcus kodakarensis KOD1.” T. Tominaga, S. Watanabe, R. Matsumi, H. Atomi, T. Imanaka, K. Miki, Acta Crystallogr. Sec. F Struc. Biol. Cryst. Commun., 68(Pt 10), 1153-1157, 2012.

  • “A detailed biochemical characterization of phosphopantothenate synthetase, a novel enzyme involved in coenzyme A biosynthesis in the Archaea.” T. Ishibashi, H. Tomita, Y. Yokooji, T. Morikita, B. Watanabe, J. Hiratake, A. Kishimoto, A. Kita, K. Miki, T. Imanaka, H. Atomi, Extremophiles, 16(6), 819-828, 2012.

  • “Overview of the genetic tools in the Archaea.” H. Atomi, T. Imanaka, T. Fukui, Frontiers in Microbiol, 3, Article 337, 1-13, 2012.

  • “Biochemical characterization of pantoate kinase, a novel enzyme necessary for coenzyme A biosynthesis in the Archaea.” H. Tomita, Y. Yokooji, T. Ishibashi, T. Imanaka, and H. Atomi, J. Bacteriol., 194 (19), 5434- 5443, 2012.

  • “Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1.” A. Nakamura, M. Fujihashi, R. Aono, T. Sato, Y. Nishiba, S. Yoshida, A. Yano, H. Atomi, T. Imanaka, K. Miki, J. Biol. Chem., 287 (25), 20784-20796, 2012.

  • “A new thermostable β-glucosidase mined from Dictyoglomus thermophilum: Properties and performance in octyl glucoside synthesis at high temperatures.” Z.Z. Zou, H.L. Yu, C.X. Li, X.W. Zhou, C. Hayashi, J. Sun, B.H. Liu, T. Imanaka, J.-H. Xu, Bioresource Technology, 118, 425-430, 2012.

  • “油分解細菌の分離とバイオオーグメンテーションへの利用” 高松邦明、山津敦史、宮北憲治、今中忠行、 環境バイオテクノロジー学会誌、12, 47-57, 2012.

  • “Indole-3-glycerol-phosphate synthase is recognized by a cold-inducible group II chaperonin in Thermococcus kodakarensis.”　L. Gao, A. Danno, S. Fujii, W. Fukuda, T. Imanaka, and S. Fujiwara, Appl. Environ. Microbiol., 78(11), 3806-3815, 2012.

  • “Characterization and in vitro interaction study of a [NiFe] hydrogenase large subunit from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1.” D. Sasaki, S. Watanabe, T. Kanai, H. Atomi, T. Imanaka, K. Miki, Biochem. Biophys. Res. Comm., 417, 192-196, 2012.

  • “Rhodoligotrophos appendicifer gen. nov., sp. nov., an appendaged bacterium isolated from a freshwater Antarctic lake.” W. Fukuda, K. Yamada, Y. Miyoshi, H. Atomi, and T. Imanaka, Int. J. Syst. Evol. Microbiol., 62, 1945-1950, 2012.

  • “Characterization and in vitro interaction study of a [NiFe] hydrogenase large subunit from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1.” D. Sasaki, S. Watanabe, T. Kanai, H. Atomi, T. Imanaka, K. Miki, Biochem. Biophys. Res. Commun., 417(1), 192-196, 2012.



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2011

  • “Crosslinking of enzyme coaggregate with polyethyleneimine: A simple and promising method for preparating stable biocatalyst of Serratia marcescens lipase.” J. Pan, X.-D. Kong, C.-X. Li, Q. Ye, J.-H. Xu, T. Imanaka, J. Mol. Catalysis B: Enzymatic, 68, 256-261, 2011

  • “Critical behavior of megabase-size DNA toward the transition into a compact state.” Y. Yosikawa, Y. Suzuki, K. Yamada, W. Fukuda, K. Yoshikawa, K. Takeyasu, T. Imanaka, J. Chem. Phys., 135, 225101-225107, 2011

  • “ Molecular bases of thermophily in hyperthermophiles. ” T. Imanaka, Proc. Jpn. Acad., Ser.B,, 87, 587-602, 2011

  • “ Highly efficient DNA compaction mediated by in vivo antitumor-active tetrazolato-bridged dinuclear platinum(II) complex. ” Y. Yoshikawa, S. Komeda, M. Uemura, T. Kanbe, M. Chikuma, K. Yoshikawa, T. Imanaka, Inorganic Chem., 50, 11729-11735, 2011

  • “ Application of a novel thermostable NAD(P)H oxidase from hyperthermophilic archaeon for the regeneration of both NAD(+) and NADP(+). ” X. Wu, H. Kobori, I. Orita, C. Zhang, T. Imanaka, XH. Xing, T. Fukui, Biotechnol Bioeng., 2011 Aug 9. doi: 10.1002/bit.23294. [Epub ahead of print]

  • “ Biochemical and genetic characterization of the three metabolic routes in Thermococcus
    kodakarensis     linking glyceraldehyde-3-phosphate and 3-phosphoglycerate. ” K. Matsubara, Y. Yokooji, H. Atomi, T. Imanaka, Mol. Microbiol., 81(5), 1300-1312, 2011

  • “ Family B DNA polymerase from a hyperthermophilic archaeon Pyrobaculum calidifontis: Cloning, characterization and PCR application.” S. F. Ali, N. Rashid, T. Imanaka, M. Akhtar J. Biosci. Bioeng., 112(2), 118-123, 2011

  • “ Binding ability of chitinase onto cellulose: An atomic force microscopic studuy.” Y. Kikkawa, M. Fukuda, A. Kashiwada, K. Matsuda, M. Kanesato, M. Wada, T. Imanaka, T. Tanaka Polymer J., 43, 742-744, 2011

  • “ Distinct physiological roles of the three [NiFe]-hydrogenase orthologs in the hyperthermophilic archaeon Thermococcus kodakarensis.” T. Kanai, R. Matsuoka, H. Beppu, A. Nakajima, Y. Okada, H. Atomi, T. Imanaka, J. Bacteriol., 193(12), 3109-3116, 2011 .

  • “ Salt Has a Biphasic Effect on the Higher-Order Structure of a DNA-Protamine Complex .” N. Makita, Y. Yoshikawa, Y. Takenaka, T. Sakaue, M. Suzuki, C. Watanabe, T. Kanai, T. Kanbe, T. Imanaka, K. Yoshikawa J. Phys. Chem., 115, 4453-4459, 2011

  • “Histon and TK0471/TrmBL2 form a novel heterogeneous architecture in the hyperthermophilic archaeon Thermococcus kodakarensis.” Maruyama, H., Shin, M., Oda, T., Matsumi, R., Ohniwa, R. L., Itoh, T., Shirahige, K., Imanaka, T., Atomi, H., Yoshimura, S. H., Takeyasu, K. Mol. Biol. Cell, 22, 386-398, 2011

  • “Application ofThermococcus kodakarensis as a host for geneexpression and protein secretion. ” R. Takemasa, Y. Yokooji, A. Yamatsu, H. Atomi, T. Imanaka Appl. Environ. Microbiol., 77(7), 2392-2398, 2011

  • “Structural basis for branching-enzyme activity of glycoside hydrolase family 57: Structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.” Murakami, M., Takata, H., Imanaka, T. Proteins, 79(2), 547-557, 2011

  • “Constrictibacter antarcticus gen. nov., sp. nov., a cryptoendolithic microorganism in Antarctic white rock.”　 Yamada K., Fukuda W., Kondo Y., Miyoshi Y., Atomi H., Imanaka T. Int. J. Syst. Evol. Microbiol.,　61, 1973-1980, 2011

  • “Synthesis of optically pure S-sulfoxide by Escherichia coli transformant cells coexpressing the P450 monooxygenase and glucose dehydrogenase genes.” 　Zhang J.D., Li A.T., Yu H.L., Imanaka T., Xu J.H. 　J. Ind. Microbiol. Biotechnol. 38(5), 633-641, 2011



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2010

  • “Efficient production of active form recombinant cassava hydroxynitrile lyase using Escherichia coli in low-temperature culture. ” H. Semba, E. Ichige, T. Imanaka, H. Atomi, H. Aoyagi Methods Mol. Biol., 643, 133-144, 2010

  • “Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile.” Y. Nishitani, S. Yoshida, M. Fujihashi, K. Kitagawa, T. Doi, H. Atomi, T. Imanaka, K. Miki J. Biol. Chem., 285(50), 39339-39347, 2010

  • “Comparative study of kinetics on DNA double-strand break induced by photo- and gamma-irradiation: Protective effect of water-soluble flavonoids.” Yoshikawa, Y., Mori, T., Suzuki, M., Imanaka, T., Yoshikawa, K. Chem. Phys. Lett., 501:146-151, 2010

  • “Formate-driven growth coupled with H2 production.” 　Kim Y.J., Lee H.S., Kim E.S., Bae S.S., Lim J.K., Matsumi R., Lebedinsky A.V., Sokolova T.G., Kozhevnikova D.A., Cha S.S., Kim S.J., Kwon K.K., Imanaka T., Atomi H., Bonch-Osmolovskaya E.A., Lee J.H., Kang S.G. Nature　467(7313):352-355 (2010) PMID: 20844539

  • “Dual biosynthesis pathway for longer chain polyamines in hyperthermophilic archaeon Thermococcus kodakarensis.”　Morimoto N., Fukuda W., Nakajima N., Masuda T., Terui Y., Kanai T., Oshima T., Imanaka T., Fujiwara, S.　 J. Bacteriol. 　 192(19):4991-5001 (2010). PMID: 20675472

  • “Characterization of NADH Oxidase/NADPH Polysulfide Oxidoreductase and Its Unexpected Participation in Oxygen Sensitivity in an Anaerobic Hyperthermophilic Archaeon”   Kobori H., Ogino M., Orita I., Nakamura S., Imanaka T., Fukui T.  J. Bacteriol.　192(19):5192-5202 (2010) PMID: 20675490

  • “Characteristic effect of an anticancer dinuclear platinum(II) complex on the higher-order structure of DNA.”  Kida N., Katsuda Y., Yoshikawa Y., Komeda S., Sato T., Saito Y., Chikuma M., Suzuki M., Imanaka T., Yoshikawa K.  J. Biol. Inorg. Chem. 15(5):701-707 (2010)　 PMID:20237813

  • “Identification of the Phr-dependent heat shock regulon in the hyperthermophilic archaeon, Thermococcus kodakaraensis.”  Kanai T., Takedomi S., Fujiwara S., Atomi H., Imanaka T.  J. Biochem.  147(3):361-370 (2010)　 PMID:19887527

  • “Thermococcus kodakaraensis mutants deficient in di-myo-inositol phosphate use aspartate to cope with heat stress.”  Borges N., Matsumi R., Imanaka T., Atomi H., Santos H.  J. Bacteriol. 192(1):191-197 (2010)　PMID: 19880594


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2009

  • “Protein synthesis in giant liposomes using the in vitro translation system of Thermococcus kodakaraensis.”  Yamaji K., Kanai T.,Nomura S.M., Akiyoshi K., Negishi M., Chen Y., Atomi H., Yoshikawa K., Imanaka T.  IEEE Trans. NanoBioscience 8(4):325-331, (2009)　PMID: 19884103

  • “Crystal structure of HypA, a nickel-binding metallochaperone for [NiFe] hydrogenase maturation.”  Watanabe S., Arai T., Matsumi R., Atomi H., Imanaka T., Miki K.  J. Mol. Biol.  394(3):448-459 (2009)　PMID: 19769985

  • “Property of cold inducible DEAD-box RNA helicase in hyperthermophilic archaea.”  Shimada Y., Fukuda W., Akada Y., Ishida M., Nakayama J., Imanaka T., Fujiwara. S.  Biochem. Biophys. Res. Commun.  389(4):622-7 (2009)　PMID: 19755115

  • “Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea.”  Yokooji Y., Tomita H., Atomi H., Imanaka T.  J. Biol. Chem.  284(41):28137-28145  (2009)　PMID: 19666462

  • “Efficient in vitro synthesis of cis-polyisoprenes using a thermostable cis-prenyltransferase from a hyperthermophilic archaeon Thermococcus kodakaraensis.”  Yamada Y., Fukuda W., Hirooka K., Hiromoto T., Nakayama J., Imanaka T., Fukusaki E., Fujiwara S.  J. Biotechnol.  143(2):151-6. (2009)　PMID: 19583987

  • “Highly thermostable L-threonine dehydrogenase from the hyperthermophilic archaeon Thermococcus kodakaraensis,”  Bashir Q., Rashid N., Jamil F., Imanaka T., Akhtar M. J. Biochem.  146(1), 95-102. (2009)　PMID:19307254

  • "Effect of growth temperature and growth phase on lipid composition of archaeal membrane　from Thermococcus kodakaraensis." Matsuno Y., Sugai A., Higashibata H., Fukuda W., Ueda K., Uda I., Sato I., Itoh T.,　Imanaka T., Fujiwara S.  Biosci. Biotechnol. Biochem.  73(1):104-108 (2009)　 PMID:19129645


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