Division of Developmental Regulation
Department of Molecular Cell Biology
Publications

Yamamoto, D., Uchihashi, T., Kodera, N., Yamashita, H., Nishikori, S., Ogura, T., Mikihiro Shibata, M. and Ando, T. High-speed atomic force microscopy techniques for observing dynamic biomolecular processes. Methods Enzymol., in press.

 

Esaki, M. and Ogura, T. ATP-bound form of the D1 AAA domain inhibits an essential function of Cdc48p/p97. Biochem. Cell Biol., in press.

 

Sasagawa, Y., Otani, M., Higashitani, N., Higashitani, A., Sato, K., Ogura, T., and Yamanaka, K. Caenorhabditis elegans p97 controls germline-specific sex determination by controlling TRA-1 level in a CUL-2-dependent manner. J. Cell Sci. 122, 3663-3672, 2009.

 

Matsushita-Ishiodori, Y., Yamanaka, K., Hashimoto, H., Esaki, M., and Ogura, T. Conserved aromatic and basic amino acid residues in the pore region of C. elegansspastin play critical roles in microtubule-severing. Genes Cells 14, 925-940, 2009.

 

Nishikori, S., Yamanaka, K., Sakurai, T., Esaki, M. and Ogura, T. p97 homologs from C. elegans , CDC-48.1 and CDC-48.2, suppress the aggregate formation of huntingtin exon1 containing expanded polyQ repeat. Genes Cells 13, 827-838, 2008.

 

Yamauchi, S., Higashitani, N., Otani, M., Higashitani, A., Ogura, T. and Yamanaka, K. Involvement of HMG-12 and CAR-1 in the cdc-48.1 expression of Caenorhabditis elegans . Dev. Biol. 318, 348-359, 2008.

 

Okuno, T. and Ogura, T. FtsH protease, a eubacterial membrane-bound AAA protease. In ATP-dependent proteases (Research Signport, ed. E. Kutejova) pp.87-114, 2008.

 

Ogura, T., Matsushita-Ishiodori, Y., Johjima, A., Nishizono, M., Nishikori, S., Esaki M. and Yamanaka. K. From the common molecular basis of the AAA protein to various energy-dependent and -independent activities of AAA proteins. Biochem. Soc. Trans. 36, 68-71, 2008.

 

Sasagawa, Y., Yamanaka, K. and Ogura, T. ER E3 ubiquitin ligase HRD-1 and its specific partner chaperone BiP play important roles in ERAD and developmental growth in C. elegans . Genes Cells 12, 1063-1073, 2007.

 

Matsushita-Ishiodori, Y., Yamanaka, K. and Ogura, T. The C. elegans homologue of the spastic paraplegia protein, spastin, disassembles microtubules. Biochem. Biophys. Res. Commun. 359,157-162, 2007.

 

Sasagawa, Y., Yamanaka, K., Nishikori, S. and Ogura, T. Caenorhabditis elegansp97/CDC-48 is crucial for progression of meiosis I. Biochem. Biophys. Res. Commun. 358, 920-924, 2007.

 

Yamauchi, S., Sasagawa, Y., Ogura, T. and Yamanaka, K. Differential expression pattern of UBX family genes in Caenorhabditis elegans . Biochem. Biophys. Res. Commun. 358, 545-552, 2007.

 

Sasagawa, Y., Sato, S., Ogura, T. and Higashitani, A. C. elegans RBX-2-CUL-5- and RBX-1-CUL-2-based complexes are redundant for oogenesis and activation of the MAP kinase MPK-1. FEBS Lett. 581, 145-150, 2007.

 

Yakushiji, Y., Nishikori, S., Yamanaka, K., and Ogura, T. Mutational analysis of the functional motifs in the ATPase domain of C. elegans fidgetin homologue FIGL-1: Firm evidence for an intersubunit catalysis mechanism of ATP hydrolysis by AAA ATPases. J. Struct. Biol. 156, 93-100, 2006.

 

Okuno, T., Yamanaka, K., and Ogura, T. Characterization of mutants of the Escherichia coli AAA protease, FtsH, carrying a mutation in the central pore region. J. Struct. Biol. 156, 109-114, 2006.

 

Okuno, T., Yamanaka, K., and Ogura, T. Flavodoxin, a new fluorescent substrate for monitoring proteolytic activity of FtsH lacking a robust unfolding activity. J. Struct. Biol. 156, 115-119, 2006.

 

Yamauchi, S., Yamanaka, K., and Ogura, T. Comparative analysis of expression of two p97 homologues in Caenorhabditis elegans. Biochem. Biophys. Res. Commun. 345, 746-753, 2006

 

Okuno, T., Yamanaka, K., and Ogura, T. An AAA protease FtsH can initiate proteolysis from internal sites of a model substrate, apo-flavodoxin. Genes Cells 11, 261-268, 2006.

 

Sakamoto, W., Miura, E., Kaji, Y., Okuno, T., Nishizono, M., and Ogura, T. Allelic characterization of the leaf-variegated mutation var2 identifies the conserved amino acid residues of FtsH that are important for ATP hydrolysis and proteolysis. Plant Mol. Biol. 56, 705-716, 2004.

 

Yakushiji, Y., Yamanaka, K., and Ogura, T. Identification of a cysteine residue important for the ATPase activity of C. elegans fidgetin homologue.FEBS Lett. 578, 191-197, 2004.

 

Akiyama, Y., Ito, K., and Ogura, T. FtsH protease. In Handbook of Proteolytic Enzymes, 2nd edition, A. J. Barrett, N. D. Rawlings and J. F. Woessner (ed.) Academic Press, pp. 794-798, 2004.

 

Yamanaka, K., Okubo, Y., Suzaki, T., and Ogura, T. Analysis of the two p97/VCP/Cdc48p proteins of Caenorhabditis elegans and their suppression of polyglutamine-induced protein aggregation. J. Struct. Biol. 146, 242-250, 2004.

 

Okuno, T., Yamada-Inagawa, T., Karata, K., Yamanaka, K., and Ogura, T. Spectrometric analysis of degradation of a physiological substrate s32 by Escherichia coli AAA protease FtsH. J. Struct. Biol. 146, 148-154, 2004.

 

Ogura, T., Whiteheart, S. W., and Wilkinson, A. J. Conserved arginine residues implicated in ATP hydrolysis, nucleotide-sensing, and inter-subunit interactions in AAA and AAA+ ATPases. J. Struct. Biol. 146, 106-112, 2004.

 

Yamada-Inagawa, T., Okuno, T., Karata, K., Yamanaka, K., and Ogura, T. Conserved pore residues in the AAA protease FtsH are important for proteolysis and its coupling to ATP hydrolysis. J. Biol. Chem. 278, 50182-50187, 2003.

 

Ogura, T., and Tanaka, K. Dissecting various ATP-dependent steps involved in proteasomal degradation. Mol. Cell 11, 3-5, 2003.

 

Krzywda, S., Brzozowski, A. M., Verma, C., Karata, K., Ogura, T., and Wilkinson, A. J. The crystal structure of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli at 1.5 A resolution. Structure 10, 1073-1083, 2002.

 

Krzywda, S., Brzozowski, A. M., Karata, K., Ogura, T., and Wilkinson, A. J. Crystallization of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 58, 1066-1067, 2002.

 

Yamanaka, K., Shimamoto, T., Inouye, S., and Inouye, M. Retrons. In Mobile DNA II, N. Craig, R. Craigie, M. Gellert and A. Lambowitz (ed.) ASM Press, pp. 784-795, 2002.

 

Ogura, T., and Wilkinson, A. J. AAA+ superfamily ATPases: common structure-diverse function. Genes Cells 6, 575-597, 2001.

 

Karata, K., Verma, C. S., Wilkinson, A. J., and Ogura, T. Probing the mechanism of ATP hydrolysis and substrate translocation in the AAA protease FtsH by modelling and mutagenesis. Mol. Microbiol. 39, 890-903, 2001.

 

Inagawa, T., Kato, J., Niki, H., Karata, K., and Ogura, T. Defective plasmid partition in ftsH mutants of Escherichia coli. Mol. Genet. Genomics 265, 755-762, 2001.

 

Phadtare, S., Yamanaka, K., Kato, I., and Inouye, M. Antibacterial activity of 4,5-dihydroxy-2-cyclopentan-1-one (DHCP) and cloning of a gene conferring DHCP resistance in Escherichia coli. J. Mol. Microbiol. Biotechnol. 3, 461-465, 2001.

 

Tomoyasu, T., Arsene, F., Ogura, T., and Bukau, B. The C terminus of s32 is not essential for degradation by FtsH. J. Bacteriol. 183, 5911-5917, 2001.

 

Yamanaka, K., and Inouye, M. Induction of CspA, an E. coli major cold-shock protein, upon nutritional upshift at 37°C. Genes Cells 6, 279-290, 2001.

 

Yamanaka, K., and Inouye, M. Selective mRNA degradation by polynucleotide phosphorylase in cold shock adaptation in Escherichia coli. J. Bacteriol. 183, 2808-2816, 2001.

 

Yamanaka, K., Zheng, W., Crooke, E., Wang, Y. H., and Inouye, M. CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli. Mol. Microbiol. 39, 1572-1584, 2001.

 

Tatsuta, T., Joo, D. M., Calendar, R., Akiyama, Y., and Ogura, T. Evidence for an active role of the DnaK chaperone system in the degradation of s32. FEBS Lett. 478, 271-275, 2000.

 

Prajapati, R. S., Ogura, T., and Cutting, S. M. Structural and functional studies on an FtsH inhibitor from Bacillus subtilis. Biochim. Biophys. Acta 1475, 353-359, 2000.

 

Teff, D., Koby, S., Shotland, Y., Ogura, T., and Oppenheim, A. B. A colicin-tolerant Escherichia coli mutant that confers Hfl phenotype carries two mutations in the region coding for the C-terminal domain of FtsH (HflB). FEMS Microbiol. Lett. 183, 115-117, 2000.

 

Iwasaki, H., Han, Y.-W., Okamoto, T., Ohnishi, T., Yoshikawa, M., Yamada, K., Toh, H., Daiyasu, H., Ogura, T., and Shinagawa, H. Mutational analysis of the functional motifs of RuvB, an AAA+ class helicase and motor protein for Holliday junction branch migration. Mol. Microbiol. 36, 528-538, 2000.

 

Inouye, M., and Yamanaka, K. Cold shock response in Escherichia coli. Horizon Press, 2000.

 

Phadtare, S., Yamanaka, K., and Inouye, M. The cold-shock response. In Bacterial Stress Response, G. Storz and R. Hengge-Aronis, eds. ASM Press, pp. 33-45, 2000.

 

Wang, N., Yamanaka, K., and Inouye, M. Acquisition of double-stranded DNA-binding ability in a hybrid protein between Escherichia coli CspA and the cold shock domain of human YB-1. Mol. Microbiol. 38, 526-534, 2000.

 

Yamanaka, K., Hwang, J., and Inouye, M. Characterization of GTPase activity of TrmE, a member of a novel GTPase superfamily, from Thermotoga maritima. J. Bacteriol. 182, 7078-7082, 2000.