Laboratory of Protein Biogenesis

千葉志信　論文リスト

【原著論文および英文総説】

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.
ライフサイエンス新着レビューの記事（日本語）はこちら
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)
ライフサイエンス新着論文レビューで紹介記事を書きました（こちら）。
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.
ライフサイエンス新着論文レビューで紹介記事を書きました（こちら）。
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.

【日本語総説・Web記事・書籍など】

千葉志信、藤原圭吾 (2022) 新生ポリペプチド鎖が制御する翻訳動態．実験医学増刊 Vol.40 No.12 セントラルドグマの新常識〜転写・翻訳の驚きの新機構と再定義されるDNA・RNA・タンパク質の世界
千葉志信、茶谷悠平 (2021) 翻訳途上で機能する新生ポリペプチド鎖. 月刊細胞 53巻9号（2021年8月号）, 525-528.
千葉志信、田口英樹 (2019) 翻訳途上で機能する新生ポリペプチド鎖. 実験医学 Vol.37, No.18 (11月号), 3048-3054.
田口英樹、茶谷悠平、千葉志信、伊藤維昭 (2018) 終止コドンに依らず翻訳を途中終了させる酸性アミノ酸の連続配列. バイオサイエンスとインダストリー (B&I) 76, 239-241.
千葉志信 (2018) 調節性翻訳アレストペプチドによる細胞機能の制御. 生化学　第90巻第2号, 147-157.
茶谷悠平、千葉志信、伊藤維昭、田口英樹 (2018) 翻訳途上の新生ポリペプチド鎖が引き起こすリボソームの不安定化とその生理的意義.　実験医学 Vol. 36, No. 8 (5月号) 1364-1367.
茶谷悠平、千葉志信、伊藤維昭、田口英樹 (2017) 翻訳の途上の新生ポリペプチド鎖がひき起こすリボソームの不安定化および環境のセンサーとしての利用. ライフサイエンス新着レビュー　DOI: 10.7875/first.author.2017.130
伊藤維昭、茶谷悠平、千葉志信、田口英樹 (2016) タンパク質の翻訳伸長には個性（緩急リズム）がある. バイオサイエンスとインダストリー (B&I) 74, 428-430
Koreaki Ito (Editor) "Regulatory Nascent Polypeptides" Springer. ISBN 978-4-431-55051-8. DOI 10.1007/978-4-431-55052-5
- Ito, K. and Chiba, S (2014) Biological significance of nascent polypeptides that stall the ribosome. pp 3-20, Regulatory Nascent Polypeptides (Ed. Ito, K.), Springer Japan
- Chiba, S (2014) MifM, a regulatory nascent chain that monitors membrane protein integration. pp 257-277, Regulatory Nascent Polypeptides (Ed. Ito, K.), Springer Japan
熊崎薫、千葉志信、塚崎智也、濡木理「膜組み込み酵素YidCによるタンパク質の細胞膜への組み込みの分子機構」ライフサイエンス新着論文レビュー（原著論文「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, 509, 516-520.」に関しての紹介記事です）（掲載サイトはこちら）
千葉志信、伊藤維昭　「枯草菌MifMの解析から明らかにされた翻訳の途上にあるポリペプチド鎖によるユニークな翻訳伸長の停止」ライフサイエンス新着論文レビュー（原著論文「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.」に関しての紹介記事です）（掲載サイトはこちら）
小椋光、唐田清伸、千葉志信、秋山芳展　「AAAプロテアーゼ」蛋白質核酸酵素（増刊「新世紀における蛋白質科学の進展」（中村春木，森川耿右，鈴木紘一，三浦謹一郎（編）） 46, 1679-1685, 2001

千葉志信 論文リスト

千葉志信　論文リスト