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.