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.
