September 28 (Fri) - 29 (Sat), 2012
Public Relations Center
http://www.thermus.org

The 2nd Annual Meeting for Whole-Organism Science Society
Joint Meeting withThe 11th Annual Meeting of Structural-Biological Whole Cell Project
ProgramFriday, September 28<Symposium> Model Organisms (1)Abstract No.

Chair Persons: Gota Kawai and Seiki Kuramitsu
13:30 – 14:00

14:00 – 14:30

Disruption of Drosophila serine palmitoyl transferase and acetyl-coA
carboxylase cause tissue overgrowth associated with altered Notch andWnt signaling
11
2○Takeshi Sasamura , Kenji Matsuno , Mark E. Fortini12( Osaka Univ., Thomas Jefferson Univ.)
Halocynthia roretzi, a Japanese ascidian species, as a model animal forthe study of chordate embryogenesis○Gaku Kumano, Naohito Takatori, Hiroki Nishida(Dep. of Biol. Sci., Grad. Sch. of Sci., Osaka Univ.)

14:30 – 15:00

Reverse proteomics in fission yeast○Akihisa Matsuyama, Minoru Yoshida(Chem. Genet. Lab., RIKEN Adv. Sci. Instit.)

15:00 – 15:30

Functional profiling of the E.coli genes in long-term stationary phase- Application of new single gene deletion library with bar code tag 112○Hirotada Mori , Yuta Otsuka and Barry L. Wanner(1Grad. Sch. of Biol. Sci., Nara Inst. of Sci. and Technol.,2
Dep. of Biol. Sci., Purdue Univ.)

15:30 – 16:00

Coffee Break,

【1】

【4】

【5】

【6】

Taking Photographs of All Members<Symposium> Imagings of SACLA and SPring-8

Abstract No.

Chair Persons: Masaki Yamamoto and Noritake Yasuoka
16:00 – 16:30

Molecular imaging of whole cells with coherent X-rays
Changyong Song(RIKEN SPring-8 Center)

16:30 – 17:00

Protein crystallography free from radiation damage at SACLA【8】11
1
11○Hideo Ago , Go Ueno , Kunio Hirata , Takaaki, Hikima , Hironori Murakami , Eiki
Yamashita2, and Masaki Yamamoto1(1RIKEN SPring-8 Center, 2Osaka Univ.)

17:00 – 17:30

Achieved protein micro-crystallography at the micro-focus beamline BL32XU 【9】111
1○Kunio Hirata , Yoshiaki Kawano , Koichi Hashimoto , Go Ueno ,
1,2
2
1,2
Kazuya Hasegawa , Hideo Okumura , Takashi Kumasaka , and Masaki Yamamoto1(1RIKEN/SPring-8 Center, 2JASRI/SPring-8)【7】

17:30 – 18:00

SAXS & MD simulation to investigate protein flexibility in solution
112○Mamoru Sato , Mitsunori Ikeguchi , Tomotaka Oroguchi
12( Yokohama City Univ., Keio Univ.)

18:00 – 19:30

Seminar Banquet (in Cafeteria)

19:30 – 21:15

Oral Presentation【10】

Chair Persons: Keiko Sakamoto, Hitoshi Iino, and Kenji Fukui
Quantification of mechanical force driving the left-handed twisting of the gut epithelial tube inDrosophila
【2】
1, 3
12
23
○Naotaka Nakazawa , Reo Maeda , Shukei Sugita , Takeo Matsumoto , and Kenji Matsuno(1Dept. Biol. Sci./Tec., Tokyo Univ. Sci., 2Dept. Mech. Eng., Nagoya Inst. Tech.,3
Dept. Biol. Sci., Osaka Univ.)
Control of cell number mediated by a Drosophila RhoGEF, Pebble, is required for left-rightasymmetric development of the embryonic hindgut
【3】
1,2
1,2
1,2
1
○Mitsutoshi Nakamura , Kenjiroo Matsumoto , Yuta Iwamoto , Takeshi Muguruma ,Naotaka Nakazawa1,2, Ryo Hatori1,2, Kiichiro Taniguchi1, Reo Maeda1, and Kenji Matsuno2(1Dep. Biol. Sci. and Technol., Tokyo Univ. Sci., 2Dep. Biol. Sci., Grad. Sch. of Sci., Osaka Univ.)
Functional profiling of the E. coli genes in long-term stationary phase- Application of new single gene deletion library with bar code tag 【6】Hirotada Mori1, ○Yuta Otsuka1 and Barry L. Wanner2 (1Grad. Sch. Biol. Sci., Nara Inst. Sci. andTechnol., 2Dep. Biol. Sci., Purdue University)
Substrate tRNA recognition mechanism of tRNA (m5U54) methyltransferase (TrmFO) based on
biochemical analysis
【13】
12
1
1
○Ryota Yamagami1, Koki Yamashita , Hiroshi Nishimasu , Chikako Iwashita , Akira Hirata ,Osamu Nureki2, and Hiroyuki Hori1,3 (1Dept. Materials Sci. Biotechnol., Grad. Sch. ofSci. and Eng., Ehime Univ.,2 Dept. of Basic Biophysic. and Biochem. Grad. Sch. of Sci., Univ. ofTokyo,3 VBL, Ehime Univ.)
Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI)from Thermus thermophilus
【14】
111
1
1
○Hiroyuki Takuma , Masayuki Minoji , Natumi Ushio , Chie Tomikawa , Akira Hirata ,Chikako Iwashita1, Ochi Anna1, and Hiroyuki Hori1,2 (1Dept. of Materials Sci. and Biotechnol.,Grad. Sch. of Sci. and Eng., Ehime Univ., 2VBL, Ehime Univ.)
Functional analysis of Yeast tRNA (m2G10) methyltransferase (Trm11-Trm112)○Yu Nishida, Kazuki Okada, Akira Hirata, and Hiroyuki Hori (Dept. of Materials Sci. andBiotechnol., Grad. Sch. of Sci. and Eng., Ehime Univ.)【15】

Whole-cell research of Thermus thermophilus HB8: N-terminomics using MS/MS database
【21】
11223
○Kwang Kim , Hiroki Okanishi , Kiyoshi Yamazaki , Teruo Yasunaga , Yoshitaka Bessho , Ryoji
Masui1,3, and Seiki Kuramitsu1,3 (1Dept. Biol. Sci., Grad. Sch. Sci., Osaka Univ., 2Dept of GenomeInformatics, Research Institute for Microbial Diseases, Osaka Univ, and 3RIKEN SPring-8 Center,Harima Institute.)
Whole-cell research of Thermus thermophilus HB8: role of RNases
1221,22○Hiromasa Ohyama , Yoshihiro Agari , Kenji Fukui , Noriko Nakagawa , Akeo Shinkai ,
1,2
1,2 1
Seiki Kuramitsu , and Ryoji Masui ( Dept. Biol. Sci., Grad. Sch. Sci., Osaka Univ.,
2RIKEN SPring-8 Center, Harima Inst.)【22】

Whole cell research of Thermus thermophilus HB8: protein phosphorylation
121133○Yota Iio , Yoshio Takahata , Masao Inoue , Kwang Kim , Kenji Fukui , Yoshihiro Agari ,31, 31,2,3 1
Akeo Shinkai , Ryoji Masui and Seiki Kuramitsu( Dept. Biol. Sci., Grad. Sch. Sci.,
Osaka Univ., 2 Grad. Sch. Frontier Biosci., Osaka Univ., and 3 RIKEN SPring-8 Center,Harima Inst.)【23】

Nucleotide binding extremely stabilizes a protein kinase from Thermus thermophilus HB8
12,31,2,3 1○Takero Miyagawa , Ryoji Masui and Seiki Kuramitsu( Grad. Sch. Frontier Biosci.,
23Osaka Univ., Grad. Sch. Sci., Osaka Univ., and RIKEN SPring-8 Center, Harima Inst.)【24】

Whole-cell research of Thermus thermophilus HB8: protein acetylation
111, 21, 2 1○Hiroki Okanishi , Kwang Kim , Ryoji Masui , and Seiki Kuramitsu ( Dept. Biol. Sci.,
2Grad. Sch. Sci., Osaka Univ.; RIKEN SPring-8 Center)【25】

RIKEN SPring-8 Center Protein Crystallography Database【27】○Naoki Kunishima1, Michihiro Sugahara1, Tomoyuki Tanaka1, Hisashi Naitow1, Yoshihiro Agari1,Akeo Shinkai1, Seiki Kuramitsu1, Koro Nishikata2, Tetsuro Toyoda2, Yukuhiko Asada1 (1RIKEN
SPring-8 Center, 2RIKEN Bioinformatics and Systems Engineering Division)
Functional analysis of TTC1871 LysR-type transcriptional regulator
1111, 2
○Matsushita Hajime , Takeo Tomita , Tomohisa Kuzuyama , Makoto Nishiyama
12( Biotechnology Research Center, The University of Tokyo, RIKEN SPring-8 center)
Analysis of structure-function relationships of homoisocitrate dehydrogenase homologs fromSulfolobus acidocaldarius
1
111,2○Kento Takahashi , Takeo Tomita , Tomohisa Kuzuyama , Makoto Nishiyama
12( Biotechnology Research Center, The University of Tokyo, RIKEN Spring-8)

【30】

【31】

Analyses of interacting proteins with PilF and PilT from Thermus thermophilus
11 1○Takuto Yasuda , Ayumi koike ( Dept. Appl. Biosci., Grad. Sch. Eng., Kanagawa Inst. ofTech.)【33】

Developing a new disulfide formation assay using superfolder GFP○Yuma Mori, Takashi Tamura, Akio Ebihara, Seiki Kuramitsu, and Kenji Inagaki (Dept ofBioscience, Grad. Sch. Nat. Sci. & Tech., Okayama Univ.)【19】

Regulatory mechanism for endonuclease activity of the DNA mismatch repair
endonuclease MutL1123
3○Kenji Fukui , Hitoshi Iino , Tatsuya Yamamoto , Kwang Kim , Atsuhiro Shimada ,Seiki
1,3 1
2
3Kuramitsu ( RIKEN Harima Inst., Keio Univ., Osaka Univ.)【35】

Small-angle X-ray scattering analysis of the DNA mismatch repair endonuclease
1
1
1,2
1
○Hitoshi Iino , Takaaki Hikima , Seiki Kuramitsu , and Kenji Fukui(1RIKEN SPring-8
2
Center, Grad. Sch. of Sci. Osaka Univ.)【36】

MutS stimulates the endonuclease activity of MutL in an ATP hydrolysis-dependent manner
1
1,2
1,22○Atsuhiro Shimada , Ryoji Masui , Seiki Kuramitsu , and Kenji Fukui(1Grad. Sch. of2Sci. Osaka Univ., RIKEN SPring-8 Center, Harima Inst.)【37】

Kinetic analysis of interactions between MutS and MutL involved in DNA mismatch repair【38】
111,221,2 1○Yoshito Hata , Atsuhiro Shimada , Ryoji Masui , Kenji Fukui , and Seiki Kuramitsu ( Dept.
Biol. Sci., Grad. Sch. Sci., Osaka Univ., 2RIKEN SPring-8 Center, Harima Inst.)
Molecular functional analysis of RadA/Sms protein, a bacterial RecA paralog
121,21,21,2○Masao Inoue , Kenji Fukui , Noriko Nakagawa , Ryoji Masui , and Seiki Kuramitsu
12( Dept. Biol. Sci., Grad. Sch. Sci., Osaka Univ., RIKEN SPring-8 Center, Harima Inst.)【39】

Genetic analysis of putative nucleases and helicases involved in double-strand break repair
in Thermus thermophilus HB8【40】1232,31,2,3 1○Yuki Fujii , Masao Inoue , Kenji Fukui , Ryoji Masui , and Seiki Kuramitsu( Grad. Sch.
Frontier Biosci., Osaka Univ., 2Grad. Sch. Sci., Osaka Univ., and 3RIKEN SPring-8 Center,Harima Inst.)
Analysis of unique catalytic mechanism of exonuclease TTHA0118 fromThermus thermophilus HB8【41】1122,31,2,3○Yuri Uemura , Taisuke Wakamatsu , Atsuhiro Shimada , Ryoji Masui and Seiki Kuramitsu(1Grad. Sch. Frontier Biosci., Osaka Univ., 2Grad. Sch. Sci., Osaka Univ., 3RIKEN SPring-8Center, Harima Inst.)
Nucleoid-associated histone-like protein HU may act on RNA
12,32,31,2,3 1○Yuya Nishida , Noriko Nakagawa , Ryoji Masui and Seiki Kuramitsu( Grad. Sch.
23Frontier Biosci., Osaka Univ., RIKEN SPring-8 Center, Harima Inst., Grad. Sch. Sci., OsakaUniv.)【42】

Identification of various types of post-translational modifications of the bacterial histone-likeprotein HU in Thermus thermophilus HB8【43】1122,31,2,3○Yoshiyuki Tochizawa , Yuya Nishida , Kwang Kim , Ryoji Masui , and Seiki Kuramitsu(1Grad. Sch. Frontier Biosci., Osaka Univ., 2Grad. Sch. Sci., Osaka Univ., and 3RIKEN SPring-8Center, Harima Inst.)
Structural analysis of the heterodimer structure of the T. thermophiles tRNA modification
enzymes, MnmE/MnmG using SAXS
【48】
11111○Aya Kitamura , Takaaki Hikima , Masaki Yamamoto , Kayoko Matsumoto , Toshi Arima ,Kwang Kim2, Seiki Kuramitsu1,2, Yoshitaka Bessho1 (1RIKEN Spring-8 Center, Harima Inst., 2Dep.
Biol. Sci., Grad. Sch. Sci., Osaka Univ.)
Crystal structure of PurC from Sulfolobus tokodaii【50】
122,32,41,2○Ryosuke Umebayashi , Mayumi Kanagawa , Seiki Baba , Gota Kawai , and Gen-ichi Sampei
1234( Univ. Electro-Commun., RIKEN SPring-8 Center, SPring-8/JASRI, Chiba Inst. Tech.)
Crystal structure of PurU from Thermus thermophilus HB811233○Yuki Yanagida , Naoki Ogata , Mayumi Kusano , Mayumi Kanagawa , Yumiko Inoue , Seiki
3,42,31,3 1
2Baba , Gota Kawai , and Gen-ichi Sampei ( Univ. Electro-Commun. , Chiba Inst. Tech.,
3RIKEN SPring-8 Center, 4SPring-8/JASRI)【51】

Reaction mechanisms of the two related enzymes, PurN and PurU
Mayumi Kusano1, Toshiaki Shimasaki1, Gen-ichi Sampei2,3 and ○Gota Kawai1,3 (1Chiba Inst.
Tech., 2Univ. Electro-Commun., 3RIKEN SPring-8 Center)【52】

Nucleoside salvage pathway in Thermus thermophilus HB8【53】
12,31,2,3○Fumiaki Tomoike , Noriko Nakagawa , Seiki Kuramitsu, and Ryoji Masui2,3 (1Grad. Sch.
Frontier Biosci., Osaka Univ., 2Grad. Sch. Sci., Osaka Univ., 3RIKEN SPring-8 Center.)
Mn-catalase as a primary scavenger of intracellular hydrogen peroxide inThermus thermophilus
1,2111,3 1○Akio Ebihara , Miho Manzoku , Kenji Fukui , Seiki Kuramitsu ( RIKEN SPring-823Center, Gifu Univ., Osaka Univ.)
Whole-cell research of Thermus thermophilus HB8: metabolism via whole-cell proteomics
111,21,2 1○Kwang Kim , Hiroki Okanishi , Ryoji Masui , and Seiki Kuramitsu ( Dept. Biol.
2Sci., Grad. Sch. Sci., Osaka Univ., and RIKEN SPring-8 Center, Harima Inst.)

21:15 – 22:00

Poster Discussion and Mixer

【54】

【55】

Saturday, September 29
8:30 – 9:00

Morning Poster Discussion<Symposium> Model Organisms (2) : Thermophiles etc.

Abstract No.

Chair Persons: Hiroyuki Hori and Ken Hirotsu
9:00 – 9:10

Visiting Yellowstone National Park, the place of discovery of thermophiles
Hiroyuki Hori
(Ehime Univ.)

9:10 – 9:30

Adaptation of Thermus thermophilus to environmental temperature via tRNA
modification enzymes-modified nucleotides network in tRNA
【12】
Chie Tomikawa1, Kazuo Ishida1, Takashi Kunibayashi1, Anna Ochi1, Tamotsu Kanai2,Akira Hirata1, Chikako Iwashita1, and ○Hiroyuki Hori1,3(1Grad. Sch. of Sci. and Eng., Ehime Univ., 2Grad. Sch. of Eng., Kyoto Univ., 3VBL,
Ehime Univ.)

9:30 – 10:00

Studies on molecular recognition by tylosin-resistance methyltransferase
enzymeSatoko Yoshizawa(Centre de Génétique Moléculaire UPR 3404, CNRS,Université Paris-Sud)

【11】

【16】

10:00 – 10:30

Functions of Genes Involved in Polyamine Biosynthesis inThermus thermophilus
【17】
11
2
2
○Tairo Oshima , Toshiyuki Moriya , Yumiko Takeda , Toshihiro Ohta ,Yuka Niiya3, Toshiro Iwaki3, and Masami Ishida3(1Inst of Envir. Microbiol., Kyowa-kako Co., 2The Dep. of Envir. Genomics, TokyoUniv. of Pharm. and Life Sci., 3The Grad. Sch. of Marine and Technol., Tokyo Univ. ofMarine Sci. and Technol.)

10:30 – 11:00

A trial to predict DNA-binding residues and their target sequences oftranscription factors
Ayumi Numazawa, ○Kei Yura (Ochanomizu Univ.)

11:00 – 11:30

Poster Discussion

11:30 – 12:15

Lunch Break

12:15 – 12:30

General Assembly（学会総会）【18】<Symposium> Model Organisms (3) : Extreme Thermophiles etc. Abstract No.
Chair Persons: Tairo Oshima and Takashi Tamura
12:30 – 12:45

Curation of genome annotation of Thermus thermophilus HB8
1,2
1,2○Ryoji Masui and Seiki Kuramitsu(1Grad. Sch. Sci., Osaka Univ., 2RIKEN SPring-8 Center)

12:45 – 13:00

Thermophiles resources, fission yeast resources and other genetic materials
at RIKEN BioResource Center【26】○Takehide Murata, Masato Okubo, Shotaro Kishikawa, Yukari Kujime, Chitose
Kurihara, Megumi Sakayori, Koji Nakade, Satoko Masuzaki, Takahito Yamasaki, andYuichi Obata (Gene Engineering Division, RIKEN BioResource Center)

13:00 – 13:15

An L-glucose catabolic pathway in Paracoccus sp. 43P
Tetsu Shimizu, Naoki Takaya, and ○Akira Nakamura(Faculty of Life Environ. Sci., University of Tsukuba)

13:15 – 13:30

Substrate recognition mechanism of a homolog of homoisocitrate
dehydrogenase from Thermococcus kodakarensis, TK0280
【29】
1112
○Takeo Tomita , Yin Lu Lu , Kento Takahashi , Haruyuki Atomi , Tomohisa
Kuzuyama1, Makoto Nishiyama1,3(1Biotechnology Research Center, The University of Tokyo, 2Grad. Sch. of Eng., Kyoto
Univ., 3RIKEN SPring-8 Center)

13:30 – 13:45

Type IV pilus structural protein of Thermus thermophilus HB8 and HB27
【32】
1,211
1○Masatada Tamakoshi , Hibiki Itoga , Satoshi Akanuma , Akihiko Yamagishi(1Dept. Mol. Biol., Tokyo Univ. of Pharm. Life Sci., 2RIKEN SPring-8 Center, HarimaInstitute)

13:45– 14:00

A comparative study on homologous recombination mediators fromT. thermophilus
【34】
1,23
3
3○Takeshi Shinohara , Tatsuhiko Inoue , Ryouji Masui , Seiki Kuramitsu , TakehikoShibata1,2, Tsutomu Mikawa2(1Grad. Sch. Nanobiosci., Yokohama City Univ., 2RIKEN Adv. Sci. Inst., 3Departmentof Biological Sciences, Graduate School of Science, Osaka University)

14:00 – 14:15

Coffee Break

【20】

【28】

Chair Persons: Yoshinori Koyama and Tsutomu Mikawa
14:15 – 14:30

14:30 – 14:45

14:45 – 15:00

Functional identification of transcriptional regulators fromT. thermophilus HB8Akeo Shinkai (RIKEN SPring-8 Center, Harima Inst.)
Structural and functional analysis of TetR family transcriptional regulator
PfmR from Thermus thermophilus HB8○Yoshihiro Agari, Keiko Sakamoto, Akeo Shinkai(RIKEN SPring-8 Center, Harima Inst.)
Structural and functional analysis of TetR family transcriptional regulator
TTHA0167 from T. thermophilus HB8○Keiko Sakamoto, Yoshihiro Agari, Akeo Shinkai(RIKEN SPring-8 Center, Harima Inst.)

【44】

【45】

【46】

15:00 – 15:15

Research and development of bio-molecular imaging technology atSPring-8/SACLA【47】
123
1○Yoshitaka Bessho , Yasumasa Joti , Takashi Kimura , Aya Kitamura , Akemi
Shibuya1, Masami Ueta4, Akira Wada4, Shoji Takeuchi5, Toshifumi Sakaguchi6,
Tamakoshi Masatada7, Shota Nitahara7, Toshiyuki Moriya8, Tairo Oshima8, Yoshinori
Nishino3(1RIKEN Spring-8 Center., 2XFEL division, JASRI, 3RIES, Hokkaido Univ., 4Yoshida
Biol. Lab. 5Tokyo Univ., 6Pref. Univ. Hiroshima, 7Tokyo Univ. of Pharm. and Life Sci.,
8Kyowa-kako Co. Ltd.)

15:15 – 15:30Origin and evolution of the enzymes in the purine biosynthetic pathway:
an analysis in view of protein structures【49】
1,22,322,4○Gen-ichi Sampei , Seiki Baba , Mayumi Kanagawa , Gota Kawai(1Univ. Electro-Commun., 2RIKEN SPring-8 Center, 3SPring8/JASRI, 4Chiba Inst.
Tech.)

15:30 – 15:45

Example of genome-based identification of novel enzymatic activity andmetabolic pathway【56】
Yutaka Kawarabayashi (Lab. for Func. Genomics of Extremophiles, Kyushu Univ.)

15:45 – 16:00

Award Ceremony
Tairo Oshima (President)

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