理研セミナー高度好熱菌 丸ごと一匹 プロジェクト
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はじめに |
1～10.Progress in the whole-cell project of an extreme thermophile,Thermus thermophilus HB8Synchrotron-Radiation System Biology Research Group |
11.Publication of experimental data in crystallographic analysis of bacterial proteins by integrated database projectNaoki Kunishima, Akina Ozawa, Michihiro Sugahara, Akeo Shinkai, Seiki Kuramitsu,Yukuhiko Asada |
12.Integrated database resources in Kyoto Encyclopedia of Genes and Genomes (KEGG) and Database Center for Life Science (DBCLS)Toshiaki Katayama |
13.Biological resources of thermophiles Thermus thermophilus, Aeropyrum pernix and Sulfolobus tokodaii in the Gene Engineering Division, RIKEN BioResource CenterTakehide Murata, Masato Okubo, Shotaro Kishikawa, Yukari Kujime, Chitose Kurihara,Koji Nakade, Megumi Hirose, Satoko Masuzaki, Yuichi Obata |
14.Identification of small non-coding RNAs in Thermus thermophilusGota Kawai1,2, Nobuharu Ito1, Akito Shimada1,Seiki Kuramitsu2,3, Gen-ichi Sampei2,4, Yoshitaka Bessho2 |
15.Possible missing genes of Thermus thermophilus HB8 genomeShin-ichi Yokobori1, Tairo Oshima2, Yoshitaka Bessho3 |
16.Mobile genetic elements of Thermus thermophilus: a functional insertion sequence and novel phagesMasatada Tamakoshi1,2, Momoko Okuda1, Motoki Sugisawa1, Akihiko Yamagishi1 |
17.Strategies for Expression of Foreign Genes in Thermus thermophilus : The Case Study of the Deinococcal Tryptophan Synthase GeneYoshinori Koyama |
18.Building a Database for Deinococcus and Thermus Comparative Genomic AnalysesKei Yura |
19.Proteogenomics of bacteria: from genome annotation to physiologyJean Armengaud |
20.New era for network biology of Escherichia coliHirotada Mori1,2 |
21.Nucleic Acids (DNA and RNA) are not boring long polymers composed of only four types of nucleotides: evolutionary implicationsHenri GROSJEAN |
22.New micro-beam beamline at SPring-8, targeting at protein micro-crystallographyMasaki Yamamoto1, Kunio Hirata1, Go Ueno1, Yoshiaki Kawano1, Takaaki Hikima1, Atsushi Nisawa1, Hironori Murakami1, Nobutaka Shimizu1,2, Takashi Kumasaka1,2 |
23.Development of Coherent Imaging Methods Using Synchrotron Radiation and FELY. Nishino1, Y. Tanaka2, Y. Takahashi3, K. Maeshima4, M. Guizar-Sicairos5, Y. Bessho2, T. Oroguchi6, Y. Joti7, M. Okada8, M. Okaya9, K. Nozaki10, R. Tsutsumi3, M. Yabashi7, M. Nagasono7, S. Matsui8, J. Fienup5, K. Yamauchi3, E. Matsubara9, and T. Ishikawa2,7 |
24.Recent activity of neutron diffractometers for biological crystallography at JAEATaro Tamada, Kazuo Kurihara, Takashi Ohhara, Ryota Kuroki |
25.Integration of Imagings Using Electrons and PhotonsKuniaki Nagayama |
26.The X-Ray Free Electron Laser in JapanTetsuya Ishikawa |
27.Challenges regarding the 3D imaging of biological macromolecules in the gas phase - Preparing for x-ray free electron laser experimentsJ. Günter Grossmann1, Takaaki Hikima2, James A. Austin1, Andrew Entwistle3, Masaki Yamamoto2, Richard W. Strange1, Naoto Yagi2, Ikuo Konishi3, Tetsuya Ishikawa2, S. Samar Hasnain1 |
28.The System-Biological Project of a Model Organism, Thermus thermophilus HB8: Frontier Light for the Central Dogma of LifeYoshitaka Bessho1, Akeo Shinkai1, Seiki Kuramitsu1,2 |
29.Study of transcriptional regulatory system of T. thermophilus HB8: Regulatory mechanism of CRISPR/cas systemAkeo Shinkai |
30.Structural and functional analysis of the global transcriptional regulator SdrP from Thermus thermophilus HB8Yoshihiro Agari1,2, Seiki Kuramitsu1,2,3, Akeo Shinkai1 |
31.Structure and function of the transcriptional repressor CsoR from Thermus thermophilus HB8Keiko Sakamoto1, Yoshihiro Agari1, Kazuko Agari1, Seiki Kuramitsu1,2, Akeo Shinkai1 |
32.“Intracellular thermosensor” function of a cold shock protein from Thermus thermophilus HB8Ryosuke Mega1, Akeo Shinkai2, Noriko Nakagawa1,2, Ryoji Masui1,2, and Seiki Kuramitsu1,2 |
33.Global analysis of RNases from Thermus thermophilus HB8Hiromasa Ohyama1, Noriko Nakagawa1,2, Seiki Kuramitsu1,2, and Ryoji Masui1,2 |
34.Structural comparison of β-CASP nucleases: RNase J and CPSF groupsHirohito Ishikawa1, Hiromasa Ohyama1, Yuya Nishida2, Noriko Nakagawa1,3, Seiki Kuramitsu1,2,3, Ryoji Masui1,3 |
35.Network of modified nucleosides and modification enzymes in Thermus thermophilus tRNAChie Tomikawa1, Kazuo Ishida1, Takashi Kunibayashi1, Anna Ochi1, Tamotsu Kanai2, Takashi Yokogawa3, Akira Hirata1, Chikako Iwashita1, Hiroyuki Hori1,4,5 |
36.Establishment of in vitro assay system for folate-dependent tRNA U54 methyltransferase TrmFORyota Yamagami1, Koki Yamashita1, Hiroshi Nishimasu2, Chikako Iwashita1,Akira Hirata1,Osamu Nureki2, Hiroyuki Hori1,3 |
37.Functional analysis of dihydrouridine synthetase from Thermus thremophilusTakeshi Yoshida1, Eri Iwasaki1,Takako Awai1,Chie Tomikawa1, Akira Hirata1,2, Hiroyuki Hori1,2 |
38.The importance of a modified nucleoside m7G46 in 3D-core of tRNA in Thermus thermophilusChie Tomikawa1, Tamotsu Kanai2, Takashi Yokogawa3, Hiroyuki Hori1,4,5 |
39.Biosynthesis of tRNA thiouridine in Thermus thermophilus and its evolutionary relationship with eukaryotic ubiquitin systemNaoki Shigi1, Yuriko Sakaguchi2, Shin-ichi Asai3, Tsutomu Suzuki2, Kimitsuna Watanabe4 |
40.Whole-cell proteome analysis of T. thermophilus HB8 by using nano-LC and Q-TOFKwang KIM1, Yoshio TAKAHATA2, Ryoji MASUI1,3, and Seiki KURAMITSU1,2,3 |
41.Analysis of protein phosphorylation in prokaryotes –Identification of phosphorylated protein by mass spectrometry–Yoshio Takahata1, Kwang Kim2, Ryoji Masui2,3, Seiki Kuramitsu1,2,3 |
42.Genetic analysis of the gcp gene, an unknown-essential gene common to living organismsKazumasa Kitahara1, Takefumi Onodera2, Takayuki Hoshino1, Issay Narumi2, Akira Nakamura1 |
43.Structural and functional analysis of a highly conserved hypothetical protein, TTHA1606Fumiaki Tomoike1, Taisuke Wakamatsu1, Noriko Nakagawa2,3, Ryoji Masui2,3, and Seiki Kuramitsu1,2,3 |
44.Structural and functional analysis of a putative novel nucleotide-metabolizing enzyme, TTHA1091Akiko Tsunetou1, Fumiaki Tomoike2, Noriko Nakagawa1,3, Ryoji Masui1,3, Seiki Kuramitsu1,2,3 |
45.Thermus thermophilus HB8 periplasmic proteins TthA0610, TthA1422 and their redoxmediated disulfide bond formationTakashi Tamura, Takamasa Yoshida, Asako Kiyoto, Akio Ebihara, Seiki Kuramitsu, and Kenji Inagaki |
46.The thermodynamic effect of a designed disulphide bond on the molecular surface of cold shock protein from Thermus thermophilus HB8Shn-ichi Kidokoro, Aoi Hasegawa, Naoto Hirose,Takashi Miyamoto,Rena Sato |
47.Crystal structure of a novel goose-type lysozyme with chitinase activity from Ralstonia sp. A-471Takao Arimori1, Nobuo Okazaki1, Mitsuhiro Ueda2, Masami Nakazawa2, Kazutaka Miyatake2, Ryota Kuroki1, Taro Tamada1 |
48.Photoresponse of Thermus thermophilus HB27Hideaki Takano1, Ryuta Yamazaki1, Wataru Hakamada1, Akira Nakamura2, Takayuki Hoshino2, Teruhiko Beppu1, Kenji Ueda1 |
49.Responses of Cell to Stress –Analysis of Heat Shock Protein from System Biology-Nakayama Hiroko1, Hosono Kiyoshi1，Isozaki Kenji1， Akio Ito2，Akira Yanou3，Meisou To3，Yusuke Murase4，Kazuhiko Yamamoto1,2 |
50.Structural Studies on General Stress Response Mechanism in Bacillus subtilisLen Ito, Masatomo Makino, Takeshi Hoshino, Nobutaka Shimizu, Takashi Kumasaka |
51.Formation of semiconductor nano-particles by bacteria isolated from natural oil-producing environmentsToshifumi Sakaguchi, Ryosuke Shimizu |
52.Enigmas of Polyamine Metabolisms of Thermus thermophilus HB8: Is sym-Homospermidine Synthesized by a Unique Enzyme?Tairo Oshima |
53.Lysine and arginine biosynthesis in SulfolobusTakuya Ouchi1, Takeo Tomita1, Akira Horie1, Tomohisa Kuzuyama1, Makoto Nishiyama1,2 |
54.Molecular mechanism for allosteric regulation of glutamate dehydrogenase from Thermus thermophilusTakeo Tomita1, Makoto Nishiyama1,2 |
55.Mechanism of Feedback Inhibition of Homocitrate Synthase from Thermus thermophilusTakuya Okada1, Takeo Tomita1, Tomohisa Kuzuyama1, Makoto Nishiyama1,2 |
56.The crystal structures of amino acid kinase LysZ and carrier protein LysW involved in lysine biosynthesis of Thermus thermophilusAyako Yoshida, Takeo Tomita, Tomohisa Kuzuyama, Makoto Nishiyama |
57.Multilateral analysis of purine and pyrimidine nucleotides biosynthetic pathwayGen-ichi Sampei1,2, Ryota Miyazawa1，Hideya Yamamoto1, Sakiko Suzuki3,Seiki Baba2,4, Noriko Nakagawa2,5, Akio Ebihara2, and Gota Kawai2,3 |
58.Crystal structure of PurK from Thermotoga maritimaRyota Miyazawa1, Mayumi Kanagawa2, Seiki Baba2,3, Noriko Nakagawa2,4, Akio Ebihara2, Gota Kawai2,5, Gen-ichi Sampei1,2 |
59.An unique metabolism of pyrimidine nucleosides in Thermus thermophilus HB8Fumiaki Tomoike1, Noriko Nakagawa2,3, Ryoji Masui2,3, and Seiki Kuramitsu1,2,3 |
60.Neutron Diffraction Study of ADP-ribose pyrophosphatase from Thermus thermophilus HB8Motoyasu Adachi1, Takao Arimori1, Taro Tamada1, Kazuo Kurihara1, Takushi Ooga2, Seiki Kuramitsu2, Nobuo Kamiya3,Ryota Kuroki1 |
61.DNA repair subsystems of Thermus thermophilus HB8Kenji Fukui1, Ryoji Masui1,2, Noriko Nakagawa1,2, Taisuke Wakamatsu3, Hitoshi Iino1, Rihito Morita2, Masao Inoue2, Atsuhiro Shimada2, Shuhei Nakane2, Kyoko Majima2, Yuya Nishida2, Ryuichi Asano2, Seiki Kuramitsu1,2,3 |
62.A general mechanism for SSB displacement from ssDNA upon SSB–protein interactionJin Inoue1,2, Takayuki Nagae3, Masaki Mishima3, Yutaka Ito3, Takehiko Shibata1,2,Tsutomu Mikawa1,2,4 |
63.Direct interaction of RecO with RecA is involved in regulation of RecA functionTakeshi Shinohara1, Jin Inoue1,2, Takehiko Shibata1,2, Tsutomu Mikawa2,3 |
64.Analysis of the inhibition mechanism of extension of RecA filament by RecXSaya Okui1,2, Jin Inoue1,2, Kunitake Iju1, Kaori Habu3, Yutaka Ito3, Takehiko Shibata1,2,Tsutomu Mikawa1,2,4 |
65.Cellular and molecular functional analysis of a bacterial Rad52_Rad22 family protein from Thermus thermophilus HB8Tatsuhiko Inoue1, Atsuhiro Shimada2, Noriko Nakagawa2,3, Ryoji Masui2,3, Seiki Kuramitsu1,2,3 |
66.Inactivation of DNA repair genes leads to activation of vitamin B1 biosynthesis in Thermus thermophilus HB8Kenji Fukui1, Taisuke Wakamatsu1,2, Yoshihiro Agari1,2, Ryoji Masui1,3, Seiki Kuramitsu1,2,3 |
67.Structural and functional analyses of ATP-dependent regulation of MutLHitoshi Iino1,2, Kwang Kim2, Tatsuya Yamamoto3, Atsuhiro Shimada2, Ryoji Masui1,2, Seiki Kuramitsu1,2, Kenji Fukui1 |
68.Structure of RecJ exonuclease definces its specificity for single-stranded DNATaisuke Wakamatsu1, Yutaro Kotera2, Noriko Nakagawa2,3, Seiki Kuramitsu1,2,3, Ryoji Masui2,3 |
69.Role of RecJ-like 5'-3' exonuclease in oligo(deoxy)nucleotide degradationTaisuke Wakamatsu1, Kwang Kim2, Noriko Nakagawa2,3, Seiki Kuramitsu1,2,3, Ryoji Masui2,3 |
70.The partial reconstitution of DNA mismatch repair in Thermus thermophilus HB8Atsuhiro Shimada1, Kenji Fukui2, Noriko Nakagawa1,2, Ryoji Masui1,2, Seiki Kuramitsu1,2 |
71.Molecular functional analysis of RadA/Sms: A RecA-like proteinMasao Inoue1, Kenji Fukui2, Noriko Nakagawa1,2, Ryoji Masui1,2, and Seiki Kuramitsu1,2 |
72.Functional analysis of an alkyltransferase-like protein by DNA microarrayHisahiro Hishinuma1, Rihito Morita1, Noriko Nakagawa1,2, Ryoji Masui1,2, Seiki Kuramitsu1,2 |
73.Functional analysis of an alkyltransferase-like protein that involved in a novel nucleotide excision repair systemRihito Morita1, Nakagawa Noriko1,2, Seiki Kuramitsu1,2, Ryoji Masui1,2 |
74.DNA-Protein Binding Studies: Investigating an ATL Protein from T.thermophilus HB8Oliver Wilkinson1, David M. Williams1, Ryoji Masui2, Seiki Kuramitsu2 |
75.Molecular functional analysis of DNA polymerase I in base excision repairKyoko Majima1, Shuhei Nakane1, Noriko Nakagawa1,2, Ryoji Masui1,2, Seiki Kuramitsu1,2 |
76.Structural and functional analysis of bacterial DNA polymerase X involved in DNA repair processesShuhei Nakane1, Hirohito Ishikawa1, Noriko Nakagawa1,2, Ryoji Masui1,2, Seiki Kuramitsu1,2 |
77.Functional analysis of nucleoid associated protein HU from Thermus thermophilus HB8Yuya Nishida1, Noriko Nakagawa2,3, Ryoji Masui2,3, Seiki Kuramitsu1,2,3 |
78.An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNARyuichi Asano1, Hirohito Ishikawa1, Shuhei Nakane1, Noriko Nakagawa1,2, Seiki Kuramitsu1,2, Ryoji Masui1,2 |