ACHIEVEMENT

Papers

2017

  • Honda T, Imai H, Suzuki T, Miyoshi T, Ito K, *Uchiumi T. (2017) Binding of translation elongation factors to individual copies of the archaeal ribosomal stalk protein aP1 assembled onto aP0. Biochem Biophys Res Commun. 483(1):153-158.

2016

  • *Miyoshi T, *Ito K, Murakami R, Uchiumi T. (2016) Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute. Nature Commun. 7, 11846
  • Shigeno Y, Uchiumi T, *Nomura T. (2016) Involvement of ribosomal protein L6 in assembly of functional 50S ribosomal subunit in Escherichia coli cells. Biochem Biophys Res Commun. 473(1):237-42.
  • Murakami R, Miyoshi T, *Uchiumi T, *Ito K. (2016) Crystal structure of translation initiation factor 5B from the crenarchaeon Aeropyrum pernix. Proteins. 84(5):712-7.
  • *Nomura T, Ito M, Kanamori M, Shigeno Y, Uchiumi T, Arai R, Tsukada M, Hirabayashi K, Ohkawa K. (2016) Characterization of silk gland ribosomes from a bivoltine caddisfly, Stenopsyche marmorata: translational suppression of a silk protein in cold conditions. Biochem Biophys Res Commun. 469(2):210-5.

2015

  • Imai H, Miyoshi T, Murakami R, Ito K, Ishino Y, *Uchiumi T. (2015) Functional role of the C-terminal tail of the archaeal ribosomal stalk in recruitment of two elongation factors to the sarcin/ricin loop of 23S rRNA. Genes to Cells 20(7):613-24.
  • Sato H, Onozuka M, Hagiya A, Hoshino S, Narita I, *Uchiumi T. (2015) Characterization of anti-P monoclonal antibodies directed against the ribosomal protein-RNA complex antigen and produced using Murphy Roths large autoimmune-prone mice. Clin Exp Immunol. 179, 236-44

2014

  • *Ito,K., Honda,T., Suzuki,T., Miyoshi,T., Murakami,R., Yao,M., *Uchiumi,T. (2014) Molecular insights into the interaction of the ribosomal stalk protein with elongation factor 1α. Nucleic Acids Res. 42, 14042-52
  • *Ochiai,A., Sugai,H., Harada,K., Tanaka,S., Ishiyama,Y., Ito,K., Tanaka,T., Uchiumi,T., Taniguchi,M., *Mitsui,T. (2014) Crystal structure of α-amylase from Oryza sativa: molecular insights into enzyme activity and thermostability. Biosci Biotechnol Biochem. 78, 989-97
  • Hino,M., Zhang,J., Takagi,H., Miyoshi,T., Uchiumi,T., Nakashima,T., Kakuta,Y., *Kimura,M. (2014) Characterization of putative toxin/antitoxin systems in Vibrio parahaemolyticus. J Appl Microbiol. 117, 185-95
  • *Uchiumi,T., Baba,K., Onozuka,M. (2014) The dynamic functional structure of the ribosome discovered by the analysis of the autoimmune target. 生化学 85, 924-931

2013

  • Lee,KM., Yusa,K., Chu,LO., Yu,CW., Oono,M., Miyoshi,T., Ito,K., Shaw,PC., *Wong,KB., *Uchiumi,T. (2013) Solution structure of human P1?P2 heterodimer provides insights into the role of eukaryotic stalk in recruiting the ribosome-inactivating protein trichosanthin to the ribosome. Nucleic Acids Res. 41, 8776-87
  • Matsumoto,A., Shimizu,Y., Takemoto,C., Ueda,T., Uchiumi,T. and *Ito,K. (2013) Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Thermus thermophilus HB8. Acta Crystallogr Sect F Struct Biol Cryst Commun. 69 (Pt3), 332-335
  • Nishida,K., Miyoshi,K., Ogino, A., Miyoshi,T., Siomi,H. and *Siomi,M. (2013) Role of R2D2, a Cytoplasmic D2 Body Component, in the Endogenous siRNA Pathway in Drosophila. Molecular Cell, 49, 680-91.
  • Baba,K., Tumuraya,K., Tanaka,I., Yao,M. and *Uchiumi,T. (2013) Molecular dissection of the silkworm ribosomal stalk complex: the role of multiple copies of the stalk proteins. Nucleic Acids Res. 41, 3635-43

2012

  • *Ito, K., Murakami, R., Mochizuki, M., Qi, H., Shimizu, Y., Miura, K., Ueda, T., Uchiumi, T. (2012) Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase. Nucleic Acids Res. 40, 10521-10531.
  • *Odani, S., Ito, N., Hasegawa, M., Uchiumi, T., Hase, S. (2012) Identification of L-3-hydroxykynurenine O-sulfate in the buccal gland secretion of the parasitic lamprey, Lethenteron japonicum. Amino Acids 43, 2505-2512.
  • Nomura, N., Honda, T., Baba, K., Naganuma, T., Tanzawa, T., Arisaka, F., Noda, M., Uchiyama, S., Tanaka, I., *Yao, M., and *Uchiumi, T. (2012) Archaeal ribosomal stalk protein interacts with translation factors in a nucleotide-independent manner via its conserved C terminus. Proc. Natl. Acad. Sci. U S A, 109, 3748-3753.
  • Mochizuki, M., Kitamyo, M., Miyoshi, T., Ito, K., and *Uchiumi, T. (2012) Analysis of Chimeric Ribosomal Stalk Complexes from Eukaryotic and Bacterial Sources: Structural Features Responsible for Specificity of Translation Factors. Genes to Cells 17, 273?284.

2011

  • *Ito, K., Qi, H., Shimizu, Y., Murakami, R., Miura, K., Ueda, T., and Uchiumi, T. (2011) Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Escherichia coli in complex with the acceptor-TΨC domain of tRNA. Acta Crystallogr Sect F Struct Biol Cryst Commun. 67(Pt 12), 1566-1569.
  • Muhs, M., Yamamoto, H., Ismer, J., Takaku, H., Nashimoto, M., Uchiumi, T., Nakashima, N., Mielke, T., Hildebrand, P. W., Nierhaus, K. H., and *Spahn, C. M. (2011) Structural basis for the binding of IRES RNAs to the head of the ribosomal 40S subunit. Nucleic Acids Res. 39, 5264-5275.

2010

  • Saito, K., Kobayashi, K., Wada, M., Kikuno, I., Takusagawa, A, Mochizuki, M., Uchiumi, T., Ishitani, R., *Nureki, O., and *Ito, K. (2010) An omnipotent role of archaeal EF1α in translational elongation and termination, and quality control of protein synthesis. Proc. Natl. Acad. Sci. U S A 107, 19242-19247.
  • Kimura, K., Wada, A., Ueta, M., Ogata, A., Tanaka, S., Sakai, A., Yoshida, H., Fushitani, H., Miyamoto, A., Fukushima, M., Uchiumi, T., and *Tanigawa, N. (2010) Comparative proteomic analysis of the ribosomes in 5-fluorouracil resistance of a human colon cancer cell line using the radical-free and highly reducing method of two-dimensional polyacrylamide gel electrophoresis. Int. J. Oncol., 37, 1271-1278.
  • *Siomi, M. C., Miyoshi, T., and Siomi, H. (2010) piRNA-mediated silencing in Drosophila germlines. Semin. Cell. Dev. Biol. 21, 754-759.
  • Miyoshi, T., Takeuchi, A., Siomi, H., and *Siomi, M. C. (2010) A direct role for Hsp90 in pre-RISC formation in Drosophila. Nat Struct Mol Biol. 17, 1024-1026.
  • Miyoshi, K., Miyoshi, T., and *Siomi, H. (2010) Many ways to generate microRNA-like small RNAs: non-canonical pathways for microRNA production. Mol. Genet. Genomics. 284, 95-103.
  • Miyoshi, K., Miyoshi, T., Hartig, J. V., Siomi, H., and *Siomi, M. C. (2010) Molecular mechanisms that funnel RNA precursors into endogenous small-interfering RNA and microRNA biogenesis pathways in Drosophila. RNA 16, 506-515.
  • Hasegawa, M., Ikeda, Y., Kanzawa, H., Sakamoto, M., Goto, M., Tsunasawa, S., Uchiumi, T., and *Odani, S. (2010) Multiple gamma-glutamylation: a novel type of post-translational modification in a diapausing Artemia cyst protein. Biochem. Biophys. Res. Commun., 394, 36-41.
  • Naganuma, T., Nomura, N., Yao, M., Mochizuki, M., *Uchiumi, T., and *Tanaka, I. (2010) Structural basis for translation factor recruitment to the eukaryotic/archaeal ribosomes. J. Biol. Chem. 285, 4747-4756.

2009

  • Hattori, M., Jin, Y., Nishimasu, H., Tanaka, Y., Mochizuki, M., Uchiumi, T., Ishitani, R., Ito, K., and *Nureki, O. (2009) Structural basis of novel interactions between the small-GTPase and GDI-like domains in prokaryotic FeoB iron transporter. Structure, 17, 1345-1355.
  • *Nakashima, N., and Uchiumi, T. (2009) Functional analysis of structural motifs in dicistroviruses. Virus Res. 139, 137-147.
  • Miyoshi, T., Nomura, T., and *Uchiumi, T. (2009) Engineering and characterization of the ribosomal L10/L12 stalk complex: a structural element responsible for high turnover of the EF-G-dependent GTPase. J. Biol Chem. 284, 85-92.

2008

  • Nomura, T., Nakatsuchi, M., Sugita, D., Nomura, M., Kaminishi, T., Takemoto, C., Shirouzu, M., Miyoshi, T., Yokoyama, S., Hachimori, A., and *Uchiumi, T. (2008) Biochemical evidence for the heptameric complex L10(L12)6 in the Thermus thermophilus ribosome: in vitro analysis of its molecular assembly and functional properties. J Biochem. 144, 665-673.
  • Ito, K., Nakanishi, M., Lee, W. C., Zhi, Y., Sasaki, H., Zenno, S., Saigo, K., Kitade, Y., and *Tanokura, M. (2008) Expansion of substrate specificity and catalytic mechanism of azoreductase by x-ray crystallography and site-directed mutagenesis. J. Biol. Chem. 283, 13889-13896.
  • Miyoshi, T., and *Uchiumi, T. (2008) Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes. Nucleic Acids Res. 36, 1783-1791.

2007

  • Maki, Y., Hashimoto, T., Zhou, M., Naganuma, T., Ohta, J., Nomura, T., Robinson, C. V., and *Uchiumi, T. (2007) Three binding sites for stalk protein dimers are generally present in ribosomes from archaeal organism. J. Biol Chem. 282, 32827-32833.
  • Ming, H., Kato, Y., Miyazono, K., Ito, K., Kamo, M., Nagata, K., and *Tanokura, M. (2007) Crystal structure of thioredoxin domain of ST2123 from thermophilic archaea sulfolobus tokodaii strain7. Proteins 69, 204-208.
  • Naganuma, T., Shiogama, K., and *Uchiumi, T. (2007) The N-terminal regions of eukaryotic acidic phosphoproteins P1 and P2 are crucial for heterodimerization and assembly into the ribosomal GTPase-associated center. Genes to Cells 12, 501-510.
  • Yamamoto, H., Nakashima, N., Ikeda, Y., and *Uchiumi, T. (2007) Binding mode of the first aminoacyl-tRNA in translation initiation mediated by Plautia stali intestine virus IRES. J Biol Chem. 282, 7770-7776.
  • Nishiyama, T., Yamamoto, H., Uchiumi, T., and *Nakashima, N. (2007) A eukaryotic ribosomal protein interacts with the conserved loop region in a dicistroviral intergenic internal ribosome entry site. Nucleic Acids Res. 35, 1514-1521.