Structure and assembly of the central hub of the baseplate of bacteriophage T4

2013 Fiscal Year Final Research Report

• Project/Area Number: 23570190
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Biophysics
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: ARISAKA Fumio 東京工業大学, 生命理工学研究科, 教授 (80133768)
• Co-Investigator(Kenkyū-buntansha): KANAMARU Shuji 東京大学, 大学院生命理工学研究科, 助教 (50376951)
• Project Period (FY): 2011 – 2013
• Keywords: バクテリオファージ / 分子集合 / 立体構造 / 蛋白質間相互作用 / 感染機構 / 溶菌 / 溶菌阻止 / 尾繊維

Research Abstract

1. Tube initiator protein, gp48, which were fused with SlyD at the N-terminus was expressed in a soluble fraction and crystallized. 2. The C-terminal domain of gp37 from phage PP01 which constitutes the tail fiber together with gp38 were co-expressed and the complex with 3:1 stoichiometry was isolated and crystallized. It was shown that the C-terminal 13 kDa polypeptide was self-cleaved. 3. The complex of the soluble domain of the holin and the rapid lysis protein gp rI was crystallized and the structure has been successfully determined, which is expected to contribute to understanding the mechanisma of lysis inhibition.

Research Products

• [Journal Article] Crystal structure of YidC reveals a membrane protein insertion mechanism (2014)
  • Author(s): K. Kumazaki, S. Chiba, M. Takemoto, A. Furukawa, K. Nishiyama, Y. Sugano, T. Mori, N. Dohmae, K. Hirata, Y. Nakada-Nakura, A.D. Maturana, Y. Tanaka, H. Mori, Y. Sugita, F. Arisaka, K. Ito, R. Ishitani, T. Tsukazaki and O. Nureki.
  • Journal Title: Nature Volume: 509 (7501) Pages: 516-20
  • DOI: 10.1038/nature13167
  • Peer Reviewed
• [Journal Article] Role of positions e and g in the fibrous assembly formation of an amphipathicα-helix-forming polypeptide (2014)
  • Author(s): Takei T, Tsumoto K, Yoshino M, Kojima S, Yazaki K, Ueda T, Takei T, Arisaka F, Miura K.
  • Journal Title: Biopolymers Volume: 102(3) Pages: 260-72
  • DOI: 10.1002/bip.22479
  • Peer Reviewed
• [Journal Article] Structure and properties of the C-terminalβ-helical domain of VgrG protein from Escherichia coli O157 (2014)
  • Author(s): Uchida K, Leiman PG, Arisaka F, Kanamaru S.
  • Journal Title: J.Biochem Volume: 155(3) Pages: 173-82
  • DOI: 10.1093/jb/mvt109
  • Peer Reviewed
• [Journal Article] Intermolecular interactions and conformation of antibody dimers present in IgG1 biopharmaceuticals (2014)
  • Author(s): Iwura T, Fukuda J, Yamazaki K, Kanamaru S, Arisaka F.
  • Journal Title: J.Biochem Volume: 155(1) Pages: 63-71
  • DOI: 10.1093
  • Peer Reviewed
• [Journal Article] Assembly of pyrene-modified DNA/RNA duplexes incorporating a G-rich single strand region (2013)
  • Author(s): Kohji Seio, Munefumi Tokugawa, Hirosuke Tsunoda, Akihiro Ohkubo, Fumio Arisaka, Mitsuo Sekine.
  • Journal Title: Bioorg Med Chem Lett Volume: 23(24) Pages: 6822-4
  • DOI: 10.1016/j.bmcl.2013.10.012
  • Peer Reviewed
• [Journal Article] Atg38 is required for autophagy-specific phosphatidylinositol 3-kinase complex integrity (2013)
  • Author(s): Araki Y, Ku W-C, Akioka M, May AI, Hayashi Y, Arisaka F, Ishihama Y, Ohsumi Y.
  • Journal Title: J. Cell Biol Volume: 203(2) Pages: 299-313
  • DOI: 10.1083/jcb.201304123
  • Peer Reviewed
• [Journal Article] Protein interactions in the assembly of the tail of bacteriophage T4 (2013)
  • Author(s): F. Arisaka and S. Kanamaru.
  • Journal Title: Biophys Rev Volume: 5 Pages: 79-84
  • Peer Reviewed
• [Journal Article] The molecular architecture of the bacteriophage T4 neck (2013)
  • Author(s): Fokine A, Zhang Z, Kanamaru S, Bowman VD, Aksyuk AA, Arisaka F, Rao VB, Rossmann MG.
  • Journal Title: J Mol Biol Volume: 425(10) Pages: 1731-44
  • DOI: 10.1016/j.jmb.2013.02.012
  • Peer Reviewed
• [Journal Article] Crystal structure of Cex1p reveals the mechanism of tRNA trafficking between nucleus and cytoplasm (2013)
  • Author(s): Nozawa K, Ishitani R, Yoshihisa T, Sato M, Arisaka F, Kanamaru S, Dohmae N, Mangroo D, Senger B, Becker HD, Nureki O.
  • Journal Title: Nucleic Acids Res Volume: 41(6) Pages: 3901-14
  • DOI: 10.1093/nar/gkt010
  • Peer Reviewed
• [Journal Article] Semi-synthesis of an artificial scandium(iii) enzyme with aβ-helical bio-nanotube (2012)
  • Author(s): Inaba H, Kanamaru S, Arisaka F, Kitagawa S, Ueno T.
  • Journal Title: Dalton Trans Volume: 41(37) Pages: 11424-7
  • Peer Reviewed
• [Journal Article] Stoichiometry of Protein Interactions in Bacteriophage T4 Tail Assembly in "Stoichiometry and Research --- The Importance of Quantity in Biomedicine" Edited by Alessio Innocenti (2012)
  • Author(s): Fumio Arisaka.
  • Journal Title: INTECH, Rijeka, Croatia Pages: 243-258
  • Peer Reviewed
• [Journal Article] Indolepyruvate ferredoxin oxidoreductase : An oxygen- sensitive ironesulfur enzyme from the hyperthermophilic archaeon Thermococcus profundus (2012)
  • Author(s): Yukiko Ozawa, Masood Ahmed Siddiqui, Yasufumi Takahashi, Akio Urushiyama, Daijiro Ohmori, Fumiyuki Yamakura, Fumio Arisaka, and Takeo Imai.
  • Journal Title: Journal of Bioscience and Bioengineering Volume: 114(1) Pages: 23-7
  • DOI: 10.1016/j.jbiosc.2012.02.014.
  • Peer Reviewed
• [Journal Article] Structure of a dominant-negative helix-loop-helix tran- scriptional regulator suggests mechanisms of autoinhibition (2012)
  • Author(s): Ishii R, Isogaya K, Seto A, Koinuma D, Watanabe Y, Arisaka F, Yaguchi SI, Ikushima H, Dohmae N, Miyazono K, Miyazawa K, Ishitani R, Nureki O.
  • Journal Title: EMBO J Volume: 31(11) Pages: 2541- 52
  • DOI: 10.1038/emboj.2012.77
  • Peer Reviewed
• [Journal Article] Archaeal ribosomal stalk protein interacts with translation factors in a nucleotide- independent manner via its conserved C terminus (2012)
  • Author(s): Nomura N, Honda T, Baba K, Naganuma T, Tanzawa T, Arisaka F, Noda M, Uchiyama S, Tanaka I, Yao M, Uchiumi T.
  • Journal Title: Proc Natl Acad Sci U S A Volume: 109(10) Pages: 3748-53
  • DOI: 10.1073/pnas.1112934109
  • Peer Reviewed
• [Journal Article] Accumulation ofβ-conglycinin in soybean cotyledon through formation of disulfide bonds betweenα' andαsubunits (2012)
  • Author(s): Wadahama H, Iwasaki K, Matsusaki M, Nishizawa K, Ishimoto M, Arisaka F, Takagi K, Urade R.
  • Journal Title: Plant Physiology Volume: 158 Pages: 1395-1405
  • DOI: 10.1104/pp.111.189621
  • Peer Reviewed
• [Journal Article] Crystallographic analysis reveals octamerization of viroplasm matrix protein P9-1 of Rice black streaked dwarf virus (2012)
  • Author(s): Fusamichi Akita, Akifumi Higashiura, Takumi Shimizu, Yingying Pu, Mamoru Suzuki, Tamaki Uehara-Ichiki, Takahide Sasaya, Shuji Kanamaru, Fumio Arisaka, Tomitake Tsukihara, Atsushi Nakagawa and Toshihiro Omura.
  • Journal Title: J Virol Volume: 86(2) Pages: 746-56
  • DOI: 10.1128/JVI.00826-11
  • Peer Reviewed
• [Journal Article] Screw motion regulates multiple functions of T4 phage protein gene product 5 during cell puncturing (2011)
  • Author(s): Nishima W, Kanamaru S, Arisaka F, Kitao A.
  • Journal Title: J Am Chem Soc Volume: 133(34) Pages: 13571- 6
  • DOI: 10.1021/ja204451g
  • Peer Reviewed
• [Journal Article] Genomic and proteomic characterization of the large Myoviridae bacteriophage TMA of the extreme thermophile Thermus thermophilus (2011)
  • Author(s): Tamakoshi M, Murakami A, Sugisawa M, Tsuneizumi K, Takeda S, Saheki T, Izumi T, Akiba T, Mitsuoka K, Toh H, Yamashita A, Arisaka F, Hattori M, Oshima T, Yamagishi A.
  • Journal Title: Bacteriophage Volume: 1(3) Pages: 152-164
  • Peer Reviewed
• [Journal Article] Biochemical analysis and kinetic modeling of the thermal inactivation of MBP-fused heparinase I : Implications for a comprehensive thermostabilization strategy (2011)
  • Author(s): Chen S, Ye F, Chen Y, Chen Y, Zhao H, Yatsunami R, Nakamura S, Arisaka F, Xing XH.
  • Journal Title: Biotechnol Bioeng Volume: 108(8) Pages: 1841-51
  • DOI: 10.1002/bit.23144
  • Peer Reviewed
• [Journal Article] Dimer-tetramer association equilibraia of human adult hemoglobin and its Mutants as observed by analytical ultracentrifugation Methods (2011)
  • Author(s): Fumio Arisaka, Yukifumi Nagai, Masako Nagai.
  • Volume: 54(1)
  • Pages: 175-80
  • DOI: 10.1016/j.ymeth.2011.01.003
  • Peer Reviewed
• [Journal Article] Dual modification of a triple-strandedβ-helix nanotube with Ru and Re metal complexes to promote photocatalytic reduction of CO(2) (2011)
  • Author(s): Yokoi N, Miura Y, Huang CY, Takatani N, Inaba H, Koshiyama T, Kanamaru S, Arisaka F, Watanabe Y, Kitagawa S, Ueno T.
  • Journal Title: Chem Commun (Camb) Volume: 47(7) Pages: 2074-6
  • DOI: 10.1039/c0cc03015e
  • Peer Reviewed