PUBLICATIONS

  • Takada, H.#, Fujiwara, K., Atkinson, G. C., Chiba, S., Hauryliuk, V.# (2024) Resolution of ribosomal stalling by EF-P and ABCF ATPases YfmR and YkpA/YbiT. Nucleic Acids Res. gkae556. doi: 10.1093/nar/gkae556.
    (# corresnpoinding authors,)

    Takada, H.#*, Paternoga, H.#*, Fujiwara, K., Nakamoto, J. A., Park, E. N., Dimitrova-Paternoga, L., Beckert, B., Saarma, M., Tenson, T., Buskirk, A. R., Atkinson, G. C., Chiba, S., Wilson, D. N., Hauryliuk, V. (2024) A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis. Nucleic Acids Res. gkae399. doi: 10.1093/nar/gkae399.
    (# corresnpoinding authors, * contributed equally)

  • Fujiwara, K.#, Tsuji, N., Yoshida, M., Takada, H., Chiba, S.# (2024) Patchy and widespread distribution of bacterial translation arrest peptides associated with the protein localization machinery. Nat Commun. 15, 2711. doi: 10.1038/s41467-024-46993-3.
    (# corresponding authors)

  • Gersteuer, F.*, Morici, M.*, Gabrielli, S., Fujiwara, K., Safdari, H. A., Paternoga, H., Bock, L. V., Chiba, S., Wilson, D. N. (2024) The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome. Nat Commun. 15, 2431. doi: 10.1038/s41467-024-46762-2.
    (* contributed equally)

  • Morici, M., Gabrielli, S., Fujiwara, K., Paternoga, H., Beckert, B., Bock, L. V., Chiba, S.#, Wilson, D. N.# (2024) RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity. Nat Commun. 15, 2432. doi: 10.1038/s41467-024-46761-3.
    (# corresponding authors)

  • Ugajin, N., Imami, K., Takada, H., Ishihama, Y., Chiba, S., Mishima, Y. (2023) Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development. RNA. 29, 1910-1927. doi: 10.1261/rna.079633.123.

  • Shiota, N., Shimokawa-Chiba, N., Fujiwara, K., Chiba, S. (2023) Identification of Bacillus subtilis YidC Substrates Using a MifM-instructed Translation Arrest-based Reporter. J. Mol. Biol. 435, 168172. doi: 10.1016/j.jmb.2023.168172.
  • Obana, N., Takada, H., Crowe-McAuliffe, C., Iwamoto, M., Egorov, A.A., Wu, K.J.Y., Chiba, S., Murina, V., Paternoga, H., Tresco, B.I.C., Nomura, N., Myers, A.G., Atkinson, G.C., Wilson, D.N., Hauryliuk, V. (2023) Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR. Nucleic Acids Res. 51, 4536-4554. doi: 10.1093/nar/gkad193.

  • Chiba, S., Fujiwara, K., Chadani, Y., Taguchi, H. (2023) Nascent chain-mediated translation regulation in bacteria: translation arrest and intrinsic ribosome destabilization. J Biochem. 173, 227-236.
    doi: 10.1093/jb/mvad007.

  • Takada, H., Mandell, Z. F., Yakhnin, H., Glazyrina, A., Chiba, S., Kurata, T., Wu, K. J. Y., Tresco, B. I. C., Myers, A. G., Aktinson, G. C., Babitzke, P., Hauryliuk, V. (2022) Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp. Nucleic Acids Res. 50, 6174-89.
    doi: 10.1093/nar/gkac497.

  • Sakiyama, K., Shimokawa-Chiba, N., Fujiwara, K., Chiba, S. (2021) Search for translation arrest peptides encoded upstream of genes for components of protein localization pathways. Nucleic Acids Res. 49, 1550-1566.
    doi: 10.1093/nar/gkab024.
  • Fujiwara, K., Katagi, Y., Ito, K. and Chiba, S. (2020) Proteome-wide Capture of Co-translational Protein Dynamics in Bacillus subtilis Using TnDR, a Transposable Protein-Dynamics Reporter. Cell Rep. 33, 108250.
    doi: 10.1016/j.celrep.2020.108250.

  • Ito, K., Shimokawa-Chiba, N., Chiba, S. (2019) Sec translocon has an insertase-like function in addition to polypeptide conduction through the channel. F1000Res. 8:F1000 Faculty Rev-2126. (review)
    doi: 10.12688/f1000research.21065.1. eCollection 2019.

  • Shimokawa-Chiba, N.*, Müller, C.*, Fujiwara, K., Beckert, B., Ito, K., Wilson, D. N.#, Chiba, S.# (2019) Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis. Nat Commun 10, 5397.
    doi:10.1038/s41467-019-13408-7
    (* equally contributed; # corresponding authors)

  • Yura, T., Miyazaki, R., Fujiwara, K., Ito, K., Chiba, S., Mori, H. and Akiyama, Y. (2018) Heat shock transcription factor σ(32) defective in membrane transport can be suppressed by transposon insertion into genes encoding a restriction enzyme subunit or a putative autotransporter in Escherichia coli. Genes Genet Syst. 93, 229-235.
    doi: 10.1266/ggs.18-00040.

  • Fujiwara, K., Ito, K. and Chiba, S. (2018) MifM-instructed translation arrest involves nascent chain interactions with the exterior as well as the interior of the ribosome. Sci Rep. 8, 10311.
    doi: 10.1038/s41598-018-28628-y.

  • Ito, K., Mori, H. and Chiba, S. (2018) Monitoring substrate enables real-time regulation of a protein localization pathway. FEMS Microbiology Letters, 365, 11. (review)
    doi: 10.1093/femsle/fny109

  • Chadani, Y., Niwa, T., Izumi, T., Sugata, N., Nagao, A., Suzuki, T.,Chiba, S., Ito, K. and Taguchi, H. (2017) Intrinsic ribosome destabilization underlies translation and provides an organism with a strategy of environmental sensing. Mol Cell. 68, 528-539.e5.
    doi: 10.1016/j.molcel.2017.10.020.

  • Chadani, Y,, Niwa, T., Chiba, S., Taguchi, H. and Ito, K. (2016) Integrated in vivo and in vitro nascent chain profiling reveals widespread translational pausing. Proc. Natl. Acad. Sci. USA. 113, E829-E838.
    doi: 10.1073/pnas.1520560113
  • 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. Proc. Natl. Acad. Sci. USA. 112, E5513-E5522.
    doi: 10.1073/pnas.1513001112.
  • Sohmen, D., Chiba, S., Shimokawa-Chiba, N., Innis, A., Berninghausen, O., Beckmann, R., Ito, K. and Wilson, D. (2015) Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling. Nat. Commun. 6, 6941.
    doi: 10.1038/ncomms7941.

  • Shimokawa-Chiba, N., Kumazaki, K., Tsukazaki, T., Nureki, O., Ito, K. and Chiba, S. (2015) Hydrophilic microenvironment required for the channel-independent insertase function of YidC protein. Proc. Natl. Acad. Sci. USA. 112, 5063-5068.
    doi: 10.1073/pnas.1423817112.
  • *Chiba, S. and Ito, K. (2015) MifM monitors total YidC activities of Bacillus subtilis including that of YidC2, the target of regulation. J Bacteriol. 197, 99-107.
    doi: 10.1128/JB.02074-14.
    (* corresponding author)
  • Nakamori, K., Chiba, S. and Ito, K. (2014) Identification of a SecM segment required for export-coupled release from elongation arrest. FEBS Lett. 588, 3098-3103.
    doi: 10.1016/j.febslet.2014.06.038.
  • Kumazaki, K*., Chiba, S*., Takemoto, M., Furukawa, A., Nishiyama, K.I., Sugano, Y., Mori, T., Dohmae, N., Hirata, K., Nakada-Nakura, Y., Maturana, A.D., Tanaka, Y., Mori, H., Sugita, Y., Arisaka, F., Ito, K., Ishitani, R., Tsukazaki, T. and Nureki, O. (2014) Structural basis of Sec-independent membrane protein insertion by YidC. Nature, 509, 516-520.
    doi: 10.1038/nature13167.
    (*These authors contributed equally to this work)
  • Ito, K. and Chiba, S. (2013) Arrest peptides: cis-acting modulators of translation. Annu. Rev. Biochem. 82, 171-202. (review)
    doi: 10.1146/annurev-biochem-080211-105026.
  • Chiba, S. and Ito, K. (2012) Multisite ribosomal stalling: A unique mode of regulatory nascent chain action revealed for MifM. Mol. Cell 47, 863-872.
    doi: 10.1016/j.molcel.2012.06.034.
  • 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(12): e28413.
    doi: 10.1371/journal.pone.0028413.
  • 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.
    doi: 10.1073/pnas.1108376108.
  • 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.
    doi: 10.1073/pnas.1018343108.
  • White, R., Chiba, S., Pang, T., Dewey, J. S., Savva, C. G., Holzenburg, A., Pogliano, K. and Young, R. (2011) Holin triggering in real time. Proc. Natl. Acad. Sci. USA. 108, 798-803.
    doi: 10.1073/pnas.1011921108.
  • Ito, K., Chiba, S. and Pogliano, K. (2010) Divergent stalling sequences sense and control cellular physiology.  Biochem. Biophys. Res. Commun. 393, 1-5. (review)
    doi: 10.1016/j.bbrc.2010.01.073.
  • Chiba, S., Lamsa, A. and Pogliano, K. (2009) A ribosome-nascent chain sensor of membrane protein biogenesis in Bacillus subtilis. EMBO J. 18, 3461-3475.
    doi: 10.1038/emboj.2009.280.
  • Aung, S., Shum, J., Abanes-De, Mello, A., Broder, D. H., Fredlund-Gutierrez, J., Chiba, S. and Pogliano, K. (2007) Dual localization pathways for the engulfment proteins during Bacillus subtilis sporulation. Mol. Microbiol. 65, 1534-1546.
  • Chiba, S., Coleman, K. and Pogliano, K. (2007) Impact of membrane fusion and proteolysis on SpoIIQ dynamics and interaction with SpoIIIAH. J. Biol. Chem. 282, 2576-2586.
  • Chiba, S., Ito, K. and Akiyama, Y. (2006)  The Escherichia coli plasma membrane contains two PHB (prohibitin homology) domain protein complexes of opposite orientations.  Mol. Microbiol. 60, 448-457.
  • Jiang, X., Rubio, A., Chiba, S. and Pogliano, K. (2005) Engulfment-regulated proteolysis of SpoIIQ: evidence that dual checkpoints control sigma activity. Mol. Microbiol. 58, 102-115.
  • Chiba, S., Akiyama, Y. and Ito, K. (2002)  Membrane protein degradation by FtsH can be initiated from either end.  J. Bacteriol. 184, 4775-4782.
  • Shimohata, N., Chiba, S., Saikawa, N., Ito, K. and Akiyama, Y. (2002)  The Cpx stress response system of Escherichia coli senses plasma membrane proteins and controls HtpX, a membrane protease with cytosolic active site.  Genes Cells 7, 653-662.
  • Chiba, S., Akiyama, Y., Mori, H., Matsuo, E. and Ito, K. (2000)  Length recognition at the N-terminal tail for the initiation of FtsH-mediated proteolysis.  EMBO Reports 1, 47-52.