Sugimoto S., Yamanaka K., Niwa T., Terasawa Y., Kinjo Y., Mizunoe Y. and Ogura T. Hierarchical model for the role of J-domain proteins in distinct cellular functions. J. Mol. Biol. 433: 166750, 2021.
Mojumder S., Sawamura R., Murayama Y., Ogura T., and Yamanaka K.* Functional characterization of UBXN-6, a C-terminal cofactor of CDC-48, in C. elegans. Biochem. Biophys. Res. Commun. 509: 462-468, 2019.
Sugimoto S., Arita-Morioka K., Terao A., Yamanaka K., Ogura T. and Mizunoe Y. Multitasking of Hsp70 chaperone in the biogenesis of bacterial functional amyloids. Commun. Biol. 1: 52, 2018.
Arita-Morioka K., Yamanaka K., Mizunoe Y., Tanaka Y., Ogura T., and Sugimoto S. Inhibitory effects of Myricetin derivatives on curli-dependent biofilm formation in Escherichia coli. Sci. Rep. 8: 8452, 2018.
Tsuda Y., Yamanaka K.,* Toyoshima R., Ueda M., Masuda T., Misumi Y., Ogura T., and Ando Y. Development of transgenic Caenorhabditis elegans expressing human transthyretin as a model for drug screening. Sci. Rep. 8: 17884, 2018.
Sugimoto S., Okuda K., Miyakawa R., Sato M., Arita-Morioka K., Chiba A., Yamanaka K., Ogura T., Mizunoe Y., and Sato C. Imaging of bacterial multicellular behavior in biofilms in liquid by atmospheric scanning electron microscopy. Sci. Rep. 6: 25889, 2016.
Murayama Y., Ogura T., and Yamanaka K.* Characterization of C-terminal adaptors, UFD-2 and UFD-3, of CDC-48 on the polyglutamine aggregation in C. elegans. Biochem. Biophys. Res. Commun. 459: 154-160, 2015.
Sugimoto S., Arita-Morioka K., Mizunoe Y., Yamanaka K., and Ogura T. Thioflavin T as a fluorescence probe for monitoring RNA metabolism at molecular and cellular levels. Nucleic Acids Res. 43: e92, 2015.
Arita-Morioka K., Yamanaka K., Mizunoe Y., Ogura T., and Sugimoto S. Novel strategy for biofilm inhibition by using small molecules targeting molecular chaperone DnaK. Antimicrob. Agents Chemother. 59: 633-641, 2015.
Matsuyama S., Moriuchi M., Siuco M.A., Yano S., Morino-Koga S., Shuto T., Yamanaka K., Kondo T., Araki E., and Kai H. Mild electrical stimulation increases stress resistance and suppresses fat accumulation via activation of LKB1-AMPK signaling pathway in C. elegans. PLoS ONE 9: e114690, 2014.
Yamanaka K., Sasagawa Y., and Ogura T. Recent advances in p97/VCP/Cdc48 cellular function. Biochim. Biophys. Acta 1823: 130-137, 2012. (Review)
Onitake A., Yamanaka K.* Esaki M., and Ogura T. C. elegans fidgetin homologue FIGL-1, a nuclear-localized AAA ATPase, binds to SUMO. J. Struct. Biol. 179: 143-151, 2012.
Onitake A., Matsushita-Ishiodori Y., Johjima A., Esaki M., Ogura T., and Yamanaka K.* The C-terminal a-helix of SPAS-1, a C. elegans spastin homologue, is crucial for microtubule severing. J. Struct. Biol. 179: 138-142, 2012.
Sasagawa Y., Higashitani A., Urano T., Ogura T., and Yamanaka K.* CDC-48/p97 is required for proper meiotic chromosome segregation via controlling AIR-2/Aurora B kinase localization in Caenorhabditis elegans. J. Struct. Biol. 179: 104-111, 2012.
Nishikori S., Esaki M., Yamanaka K., Sugimoto S., and Ogura T. Positive cooperativity of the p97 AAA ATPase is critical for essential functions. J. Biol. Chem. 286: 15815-15820, 2011.
Sasagawa Y., Yamanaka K.,* Saito-Sasagawa Y., and Ogura T. C. elegans UBX cofactors for CDC-48/p97 control spermatogenesis. Genes Cells 15: 1201-1215, 2010.
Sugimoto S., Yamanaka K., Nishikori S., Miyagi A., Ando T., and Ogura T. AAA+ chaperone ClpX regulates dynamics of prokaryotic cytoskeletal protein FtsZ. J. Biol. Chem. 285: 6648-6657, 2010.
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. elegans spastin 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.
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 elegans p97/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.
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. Flavodoxin, a new fluorescent substrate for monitoring proteolytic activity of FtsH lacking a robust unfolding activity. J. Struct. Biol. 156: 115-119, 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. An AAA protease FtsH can initiate proteolysis from internal sites of a model substrate, apo-flavodoxin. Genes Cells 11: 261-268, 2006.
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.
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.
Inouye M., Ke H., Yashio A., Yamanaka K., Nariya H., Shimamoto T., and Inouye S. Complex formation between a putative 66-residue thumb domain of bacterial reverse transcriptase RT-Ec86 and the primer recognition RNA. J. Biol. Chem. 279: 50735-50742, 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.
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.
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.
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.
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., 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.
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.
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.
Phadtare S., Yamanaka K., and Inouye M. Cold-shock response. pp33-45, In Bacterial Stress Response (G. Storz and R. Hengge-Aronis ed.), ASM Press, 2000.
Wang N., Yamanaka K., and Inouye M. CspI, the ninth member of the CspA family of Escherichia coli, is induced upon cold shock. J. Bacteriol. 181: 1603-1609, 1999.
Yamanaka K., Inouye M., and Inouye S. Identification and characterization of five cspA homologous genes from Myxococcus xanthus. Biochem. Biophys. Acta 1447: 357-365, 1999.
Yamanaka K., Mitta M., and Inouye M. Mutation analysis of the 5′ untranslated region of the cold shock cspA mRNA of Escherichia coli. J. Bacteriol. 181: 6284-6291, 1999.
Yamazoe M., Onogi T., Sunako Y., Niki H., Ichimura T., Yamanaka K., and Hiraga S. Complex formation of MukB, MukE, and MukF proteins involved in chromosome partitioning in E. coli. EMBO J. 18: 5873-5884, 1999.
Yamanaka K.* Cold shock response in Escherichia coli. J. Mol. Microbiol. Biotechnol. 1: 193-202, 1999. (Review)
Yamanaka K., Fang L., and Inouye M. The CspA family in Escherichia coli: multiple gene duplication for stress adaptation. Mol. Microbiol. 27: 247-255, 1998. (Review)
Yamanaka K., and Inouye M. Growth-phase-dependent expression of cspD, encoding a member of the CspA family in Escherichia coli. J. Bacteriol. 179: 5126-5130, 1997.
Imamura R., Yamanaka K., Ogura T., Hiraga S., Fujita N., Ishihama A., and Niki H. Identification of the cpdA gene encoding cyclic 3′,5′-adenosine monophosphate phosphodiesterase in Escherichia coli. J. Biol. Chem. 271: 25423-25429, 1996.
Kido M., Yamanaka K., Mitani T., Niki H., Ogura T., and Hiraga S. RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli. J. Bacteriol. 178: 3917-3925, 1996.
Saleh A.Z.M., Yamanaka K., Niki H., Ogura T., Yamazoe M., and Hiraga S. Carboxyl terminal region of the MukB protein in Escherichia coli is essential for DNA binding activity. FEMS Microbiol. Lett. 143: 211-216, 1996.
Yamanaka K.,* Ogura T., Niki H., and Hiraga S. Identification of two new genes, mukE and mukF, involved in chromosome partitioning in Escherichia coli. Mol. Gen. Genet. 250: 241-251, 1996.
Tomoyasu T., Gamer J., Bukau B., Kanemori M., Mori H., Rutman A.J., Oppenheim A.B., Yura T., Yamanaka K., Niki H., Hiraga S., and Ogura T. Escherichia coli FtsH is a membrane-bound, ATP-dependent protease which degrades the heat-shock transcription factorσ32. EMBO J. 14: 2551-2560, 1995.
Yamanaka K.,* Ogura T., Niki H., and Hiraga S. Characterization of the smtA gene encoding an S-adenosylmethionine-dependent methyltransferase of Escherichia coli. FEMS Microbiol. Lett. 133: 59-63, 1995.
Yamanaka K.,* Ogura T., Koonin E.V., Niki H., and Hiraga S. Multicopy suppressors, mssA and mssB, of an smbA mutation of Escherichia coli. Mol. Gen. Genet. 243: 9-16, 1994.
Yamanaka K.,* Ogura T., Murata K., Suzaki T., Niki H., and Hiraga S. Characterization of translucent segments observed in an smbA mutant of Escherichia coli. FEMS Microbiol. Lett. 116: 61-66, 1994.
Yamanaka K.,* Mitani T., Ogura T., Niki H., and Hiraga S. Cloning, sequencing, and characterization of multicopy suppressors of a mukB mutation in Escherichia coli. Mol. Microbiol. 13: 301-312, 1994.
Yamanaka K.,* Mitani T., Ogura T., Niki H., and Hiraga S. Two mutant alleles of mukB, a gene essential for chromosome partition in Escherichia coli. FEMS Microbiol. Lett. 123: 27-32, 1994.
Tomoyasu T., Yuki T., Morimura S., Mori H., Yamanaka K., Niki H., Hiraga S., and Ogura T. The Escherichia coli FtsH protein is a prokaryotic member of a protein family of putative ATPases involved in membrane functions, cell cycle control and gene expression. J. Bacteriol. 175: 1344-1351, 1993.
Tomoyasu T., Yamanaka K., Murata K., Suzaki T., Bouloc P., Kato A., Niki H., Hiraga S., and Ogura T. Topology and subcellular localization of FtsH protein in Escherichia coli. J. Bacteriol. 175: 1352-1357, 1993.
Begg K.J., Tomoyasu T., Donachie W.D., Khattar M., Niki H., Yamanaka K., Hiraga S., and Ogura T. Escherichia coli mutant Y16 is a double mutant carrying thermosensitive ftsH and ftsI mutations. J. Bacteriol. 174: 2416-2417, 1992.
Imamura R., Niki H., Kitaoka M., Yamanaka K., Ogura T., and Hiraga S. Characterization of high molecular weights of complexes and polymers of cytoplasmic proteins in Escherichia coli. Res. Microbiol. 143: 743-753, 1992.
Niki H., Imamura R., Kitaoka M., Yamanaka K., Ogura T., and Hiraga S. E. coli MukB protein involved in chromosome partition forms a homodimer with a rod-and-hinge structure having DNA binding and ATP/GTP binding activities. EMBO J. 11: 5101-5109, 1992.
Yamanaka K., Ogura T., Niki H., and Hiraga S. Identification and characterization of the smbA gene, a suppressor of the mukB null mutant in Escherichia coli. J. Bacteriol. 174: 7517-7526, 1992.
Yamanaka K., Nagata K., and Ishihama A. Temporal control for translation of influenza virus mRNAs. Arch. Virol. 120: 33-42, 1991.
Yamanaka K., Ogasawara N., Yoshikawa H., Ishihama A., and Nagata K. In vivo analysis of the promoter structure of the influenza virus RNA genome using a transfection system with an engineered RNA. Proc. Natl. Acad. Sci. USA 88: 5369-5373, 1991.
Hiraga S., Niki H., Imamura R., Ogura T., Yamanaka K., Feng J., Ezaki B., and Jaffé A. Mutants defective in chromosome partitioning in E. coli. Res. Microbiol. 142: 189-194, 1991.
Yamanaka K., Ogasawara N., Ueda M., Yoshikawa M., Ishihama A., and Nagata K. Characterization of a temperature-sensitive mutant in the RNA polymerase PB2 subunit gene of influenza A/WSN/33 virus. Arch. Virol. 144: 65-73, 1990.
Yamanaka K., Ishihama A., and Nagata K. Reconstitution of influenza virus RNA-nucleoprotein complexes structurally resembling native viral ribonucleoprotein cores. J. Biol. Chem. 265: 11151-11155, 1990.
