Recent Publications


  • Yoshitani, K., Hizukuri, Y., and Akiyama, Y. (2019).
    An in vivo protease activity assay for investigating the functions of the Escherichia coli membrane protease HtpX. FEBS Lett., 593, 843-851.
  • Yoshitani, K.a, Ishii, E.a, Taniguchi, K., Sugimoto, H., Shiro, Y., Akiyama, Y., Kato, A., Utsumi, R., Eguchi, Y. (2019). aequally contributed
    Identification of an internal cavity in the PhoQ sensor domain for PhoQ activity and SafA-mediated control. Biosci. Biotechnol. Biochem., 11. 1-11.

  • Shahrizal, M., Daimon, Y., Tanaka, Y., Hayashi, Y., Nakayama, S., Iwaki, S., Narita, S.-i., Kamikubo, H., Akiyama, Y., Tsukazaki, T. (2019).
    Structural basis of the function of the β-barrel assembly-enhancing protease BepA. J. Mol. Biol., 431. 625-635.


  • Yura, T., Miyazaki, R., Fujiwara, K., Ito, K., Chiba, S., Mori, H., Akiyama, Y. (2018).
    Heat shock transcription factor σ32 defective in membrane transport can be suppressed by transposon insertion into the genes for a restriction enzyme subunit or a putative autotransporter in E. coli. Genes Genet. Syst., 93. 229-235.
  • Yamano, K., Wang, C., Sarraf, SA., Münch, C., Kikuchi, R., Noda, NN., Hizukuri, Y., Kanemaki, MT., Harper, W., Tanaka, K., Matsuda, N., Youle, RJ. (2018).
    Endosomal Rab cycles regulate Parkin-mediated mitophagy. eLife, 7, e31326.
  • Mori, H., Sakashita, S., Ito, J., Ishii, E., Akiyama, Y. (2018).
    Identification and characterization of a translation arrest motif in VemP by systematic mutational analysis. J. Biol. Chem., 293(8), 2915-2926.
  • Miyazaki, R., Myougo, N., Mori, H., Akiyama, Y. (2018).
    A photo-cross-linking approach to monitor folding and assembly of newly synthesized proteins in a living cell. J. Biol. Chem., 293(2), 677-686.


  • Daimon, Y., Iwama-Masui, C., Tanaka, Y., Shiota, T., Suzuki, T., Miyazaki, R., Sakurada, H., Lithgow, T., Dohmae, N., Mori, H., Tsukazaki, T., Narita, S.-i., Akiyama, Y. (2017).
    The tetratricopeptide repeat (TPR) domain of BepA is required for productive interaction with substrate proteins and the β-barrel assembly machinery (BAM) complex. Mol. Microbiol., 106(5), 760-776.
  • Furukawa, A., Yoshikaie, K., Mori, T., Mori, H., Morimoto, Y.V., Sugano, Y., Iwaki, S., Minamino, T., Sugita, Y., Tanaka, Y., Tsukazaki, T. (2017).
    Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF. Cell Rep., 19(5), 895-901.
  • Akiyama, K., Hizukuri, Y., Akiyama, Y. (2017).
    Involvement of a conserved GFG motif region in substrate binding by RseP, an Escherichia coli S2P protease. Mol. Microbiol., 104(5), 737-751.


  • Miyazaki, R., Yura, T., Suzuki, T., Dohmae, N., Mori, H., and Akiyama, Y. (2016).
    A Novel SRP Recognition Sequence in the Homeostatic Control Region of Heat Shock Transcription Factor σ32. Scientific reports, 6, 24147.


  • Akiyama, K., Mizuno, S., Hizukuri, Y., Mori, H., Nogi, T., and Akiyama, Y. (2015).
    Roles of the membrane-reentrant β-hairpin-like loop of RseP protease in selective substrate cleavage. eLife, 4, e08928.
  • Ishii, E., Chiba, S., Hashimoto, N., Kojima, S., Homma, M., Ito, K., Akiyama Y., and Mori, H. (2015).
    Nascent chain-monitored remodeling of the Sec machinery for salinity adaptation of marine bacteria.
    Proceedings of the National Academy of Sciences, 112(40), E5513-E5522.
  • Daimon, Y., Narita, S.-i.* and Akiyama, Y.* (2015)
    Activation of TA system toxins suppresses lethality caused by the loss of σE in Escherichia coli. J. Bacteriol., 197, 2316-2324.


  • Kumazaki, K., Kishimoto, T., Furukawa, A., Mori, H., Tanaka, Y., Dohmae, N., Ishitani, R., Tsukazaki, T.*, and Nureki, O.* (2014)
    Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase. Sci. Rep. 4, 7299.
  • Kumazaki, K., Chiba, S., Takemoto, M., Furukawa, A., Nishiyama, KI., Sugano, Y., Mori, T., Dohmae, N., Hirata, K., Nakada-Nakura, Y., Maturana, AD., Tanaka, Y., Mori, H., Sugita, Y., Arisaka, F., Ito, K., Ishitani, R., Tsukazaki, T., Nureki, O.(2014)
    Structural basis of Sec-independent membrane protein insertion by YidC. Nature.
  • Mio, M.*, Tsukazaki, T., Mori, H., Kawata, M., Moriya, T., Sasaki, Y., Ishitani, R., Ito, K., Nureki, O.* and Sato, C.* (2014)
    Conformational variation of the translocon enhancing chaperone SecDF. J. Struct. Funct. Genomics 15, 107-115
  • Arolas, JL., García-Castellanos, R., Goulas, T., Akiyama, Y., Gomis-Rüth, FX.,(2014)
    Expression and purification of integral membrane metallopeptidase HtpX. Protein Expr. Purif . 99C. 113-118.
  • Hizukuri, Y., Oda, T., Tabata, S., Tamura-Kawakami, K., Oi, R., Sato, M., Takagi, J., Akiyama, Y., Nogi, T.(2014)
    A structure-based model of substrate discrimination by a noncanonical PDZ tandem in the intramembrane-cleaving protease RseP. Structure 22, 326-336.


  • Lim, B., Miyazaki, R., Neher, S., Siegele, D. A., Ito, K., Walter, P., Akiyama, Y., Yura, T. and Gross, C. A., (2013) Heat shock transcription factor σ32 co-opts the signal recognition particle to regulate protein homeostasis in E. coli. PLoS Biol. 11, e1001735.
  • Narita, S., Masui, C., Suzuki, T., Dohmae, N., Akiyama, Y. (2013)
    Protease homolog BepA (YfgC) promotes assembly and degradation of β-barrel membrane proteins in Escherichia coli. Proc. Natl. Acad. Sci. USA. 110, E3612-3621.


  • Hizukuri, Y. and Akiyama, Y. (2012)
    PDZ domains of RseP are not essential for sequential cleavage of RseA or stress-induced σE activation in vivo. Mol. Microbiol. 86, 1232-1245.
  • Suno, R., Shimoyama, Abe, A., Shimodate, N., Watanabe, Y.-h., Akiyama, Y., and Yoshida, M. (2012)
    Conformational transition of the lid helix covering the protease active site is essential for the ATP-dependent protease activity of FtsH. FEBS Lett. 586, 3117-3121.
  • Xue, Y., Chowdhury, S., Liu, X., Akiyama, Y., Ellman, J. and Ha, Y. (2012)
    Conformational change in rhomboid protease GlpG induced by inhibitor binding to its S’ subsites. Biochemistry 51, 3723-3731.


  • Ito, K., Chadani, Y., Nakamori, K., Chiba, S., Akiyama, Y., and Abo, T. (2011)
    Nascentome analysis uncovers futile protein synthesis in Escherichia coli. PLoS ONE 6, e28413.
  • Saito, A., Hizukuri, Y., Matsuo, E. -i., Chiba, S., Mori, H., Nishimura, O., Ito, K. and Akiyama, Y. (2011)
    Post-liberation cleavage of signal peptides is catalyzed by the site-2 protease (S2P) in bacteria. Proc. Natl. Acad. Sci. USA. 108, 13740-13745.
  • Tsukazaki, T.a), Mori, H.a), Echizen, Y., Ishitani, R., Fukai, S., Tanaka, T., Perederina, A., Vassylyev, D. G., Kohno, T., Maturana, A. D., Ito, K. and Nureki, O. (2011)
    Structure and function of a membrane component SecDF that enhances protein export. Nature 474, 235-238.
    a) equally contributed.
  • Chiba, S., Kanamori, T., Ueda, T., Akiyama, Y., Pogliano, K. and Ito, K. (2011)
    Recruitment of a species-specific translational arrest module to monitor different cellular processes. Proc. Natl. Acad. Sci. USA. 108, 6073-6078.