Publication

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Articles

1.     Levy, M., Falkovich, R., Vonshak, O., Bracha, D., Tayar, A. M., Shimizu, Y., Daube, S. S., *Bar-Ziv, R. H. (2021) Boundary-Free Ribosome Compartmentalization by Gene Expression on a Surface. ACS Synth. Biol. 10: 609-619.

2.     Demeiry, M. E., Ali, A., Abouleila, Y., Zarad, W., El-Gendy, H, Salam, R. A., Hadad, G., Shimizu, Y., Masujima, T., *Emara, S. (2021) Direct infusion nano-electrospray ionization mass spectrometry for therapeutic drug monitoring of ciprofloxacin and its metabolites in human saliva. J. Pharm. Biomed. Anal. 195: 113866.

3.     Kawaguchi, D., Kodama, A., Abe, N., Takebuchi, K., Hashiya, F., Tomoike, F., Nakamoto, K., Kimura, Y., *Shimizu, Y., *Abe, H. (2020) Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis. Angew. Chem. Int. Ed. Engl. 59: 17403-17407.

4.     Hibi, K., Amikura, K., Sugiura, N., Masuda, K., Ohno, S., Yokogawa, T., Ueda, T., *Shimizu, Y. (2020) Reconstituted cell-free protein synthesis using in vitro transcribed tRNAs. Commun. Biol. 3: 350.

5.     Ogawa, M., Shintani-Domoto, Y., Nagashima, Y., Ode, K. L., Sato, A., Shimizu, Y., Ohashi, K., Roehrl, M. H. A., Ushiku, T., Ueda, H. R., *Fukayama, M. (2020) Mass spectrometry-based absolute quantification of amyloid proteins in pathology tissue specimens: Merits and limitations. PLoS One 15: e0235143.

6.     Aoki, M., Shoji, H., Kashiro, A., Takeuchi, K., Shimizu, Y., Honda, K. (2020) Prospects for Comprehensive Analyses of Circulating Tumor Cells in Tumor Biology. Cancers 12:1135.

7.     Nakamoto, K., Abe, N., Tsuji, G., Kimura, Y., Tomoike, F., Shimizu, Y., Abe, H. (2020) Chemically synthesized circular RNAs with phosphoramidate linkages enable rolling circle translation. Chem. Commun. 56: 6217-6220.

8.     Susaki, E. A., Shimizu, C., Kuno, A., Tainaka, K., Li, X., Nishi, K., Morishima, K., Ono, H., Ode, K. L., Saeki, Y., Miyamichi, K., Isa, K., Yokoyama, C., Kitaura, H., Ikemura, M., Ushiku, T., Shimizu, Y., Saito, T., Saido, T. C., Fukayama, M., Onoe, H., Touhara, K., Isa, T., Kakita, A., Shibayama, M., Ueda, H. R. (2020) Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues. Nat. Commun. 11: 1982.

9.     Shimojo, M., Amikura, K., Masuda, K., Kanamori, T., Ueda, T., *Shimizu, Y. (2020) In vitro reconstitution of functional small ribosomal subunit assembly for comprehensive analysis of ribosomal elements in E. coli. Commun. Biol. 3: 142.

10.  Demeiry, M. E., Ali, A., Abouleila, Y., Shimizu, Y., Masujima, T., Salam, R. A., Hadad, G., Emara, S. (2020) Quantification and targeted detection of ciprofloxacin in dosage form and human urine by direct injection nano-electrospray ionization multi-stage mass spectrometry. Microchem. J. 153: 104534.

11.  Ali, A., Abouleila, Y., Shimizu, Y., Hiyama, E., Emara, S., *Mashaghi, A., *Hankemeier, T. (2019) Single-cell metabolomics by mass spectrometry: Advances, challenges, and future applications. Trends Analyt. Chem. 120: 115436.

12.  Karimiavargania, M., Tada, S., Minagawa, N., Shimizu, Y., Hirose, T., Ito, Y., *Uzawa, T. (2019) Phosphorogenic and spontaneous formation of tris(bipyridine)ruthenium in peptide scaffolds. J. Pept. Sci., 25: e3158.

13.  Ali, A., Abouleila, Y., Shimizu, Y., Hiyama, E., Watanabe, T. M., Yanagida, T., *Germond, A. (2019) Single-cell screening of tamoxifen abundance and effect using mass spectrometry and Raman-spectroscopy. Anal. Chem., 91: 2710-2718.

14.  Matsumoto, A., Uehara, Y., Shimizu, Y., Ueda, T., Uchiumi, T., *Ito, K. (2019) High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus. Proteins, 87: 226-235.

15.  Abouleila, Y., Onidani, K., Ali, A., Shoji, H., Kawai, T., Lim, C. T., Kumar, V., Okaya, S., Kato, K., Hiyama, E., Yanagida, T., Masujima, T., *Shimizu, Y., *Honda, K. (2019) Live single cell mass spectrometry reveals cancer-specific metabolic profiles of circulating tumor cells. Cancer Sci., 110: 697-706.

16.  Gessesse, B., Nagaike, T., Nagata, K., Shimizu, Y., *Ueda, T. (2018) G-Protein Coupled Receptor Protein Synthesis on a Lipid Bilayer Using a Reconstituted Cell-Free Protein Synthesis System. Life (Basel), 8: E54.

17.  Tamaru, D., *Amikura, K., Shimizu, Y., Nierhaus, K. H., Ueda, T. (2018) Reconstitution of 30S ribosomal subunits in vitro using ribosome biogenesis factors. RNA, 24: 1512-1519.

18.  Tainaka, K., Murakami, T. C., Susaki, E. A., Shimizu, C., Saito, R., Takahashi, K., Hayashi-Takagi, A., Sekiya, H., Arima, Y., Nojima, S., Ikemura, M., Ushiku, T., Shimizu, Y., Murakami, M., Tanaka, K. F., Iino, M., Kasai, H., Sasaoka, T., Kobayashi, K., Miyazono, K., Morii, E., Isa, T., Fukayama, M., Kakita, A., *Ueda, H. R. (2018) Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents. Cell Rep., 24: 2196-2210.e9.

19.  *Matsuura, T., Hosoda, K., Shimizu, Y. (2018) Robustness of a reconstituted Escherichia coli protein translation system analyzed by computational modeling. ACS Synth. Biol., 7: 1964-1972.

20.  Narumi, R., Masuda, K., Tomonaga, T., Adachi, J., Ueda, H. R., *Shimizu, Y. (2018) Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics. Synth. Syst. Biotechnol. 3: 97-104.

21.  Senoussi, A., Lee Tin Wah, J., Shimizu, Y., Robert, J., Jaramillo, A., Findeiss, S., Axmann, I. M., Estevez-Torres, A. (2018) Quantitative Characterization of Translational Riboregulators Using an in Vitro Transcription-Translation System. ACS Synth. Biol. 7:1269-1278.

22.  Murakami, T. C., Mano, T., Saikawa, S., Horiguchi, S. A., Shigeta, D., Baba, K., Sekiya, H., Shimizu, Y., Tanaka, K. F., Kiyonari, H., Iino, M., Mochizuki, H., Tainaka, K., Ueda, H. R. (2018) A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing. Nat. Neurosci. 21: 625-637.

23.  *Matsuura, T., Tanimura, N., Hosoda, K., Yomo, T., *Shimizu, Y. (2017) Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling. Proc. Natl. Acad. Sci. U. S. A. 114: E1336-E1344 (*corresponding author).

24.  #Narumi, R., #*Shimizu, Y., Ukai-Tadenuma, M., Ode, K. L., Kanda, G. N., Shinohara, Y., Sato, A., Matsumoto, K., *Ueda, H. R. (2016) Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins. Proc. Natl. Acad. Sci. U. S. A. 113: E3461-E3467 (#equally contributed, *corresponding author).

25.  Sunagawa, G. A., Sumiyama, K., Ukai-Tadenuma, M., Perrin, D., Fujishima, H., Ukai, H., Nishimura, O., Shi, S., Ohno, R., Narumi, R., Shimizu, Y., Tone, D., Ode, K. L., Kuraku, S., Ueda, H. R. (2016) Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene. Cell Rep. 14: 662-677.

26.  *Tanaka, Y. *Shimizu, Y. (2015) Integration of a reconstituted cell-free protein-synthesis system on a glass microchip. Anal. Sci. 31: 67-71. (*equally contributed & corresponding author)

27.  Susaki, E. A., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., Watanabe, T. M., Yokoyama, C., Onoe, H., Eguchi, M., Yamaguchi, S., Abe, T., Kiyonari, H., Shimizu, Y., Miyawaki, A., Yokota, H., Ueda, H. R. (2014) Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell 157: 726-739.

28.  Shimizu, Y. (2014) Biochemical aspects of bacterial strategies for handling the incomplete translation processes. Front. Microbiol. 5: 170.

29.  Shimizu, Y., Kuruma, Y., Kanamori, T., Ueda, T. (2014) The PURE System for Protein Production. Methods Mol. Biol. 1118: 275-284.

30.  Matsumoto, A., Shimizu, Y., Takemoto, C., Ueda, T., Uchiumi, T., Ito, K. (2013) Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Thermus thermophilus HB8. Acta. Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. 69: 332-335.

31.  Fujino, Y., Fujita, R., Wada K., Fujishige, K., Kanamori, T., Hunt, L., Shimizu, Y., Ueda, T. (2012) Robust in vitro affinity maturation strategy based on interface-focused high-throughtput mutational scanning. Biochem. Biophys. Res. Commun. 428: 395-400.

32.  Kihira, K. Shimizu, Y., Shomura, Y., Shibata, N., Kitamura, M., Nakagawa, A, Ueda, T., Ochi, K., Higuchi, Y. (2012) Crystal structure analysis of the translation factor RF3 (release factor 3). FEBS Lett. 586: 3705-3709.

33.  Shimizu, Y. (2012) ArfA recruits RF2 into stalled ribosomes. J. Mol. Biol. 423: 624-631.

34.  Ito, K., Murakami, R., Mochizuki, M., Qi, H., Shimizu, Y., Miura, K. I., Ueda, T., Uchiumi, T. (2012) Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase. Nucleic Acids Res. 40: 10521-10531.

35.  Ito, K., Qi, H., Shimizu, Y., Murakami, R., Miura, K. I., Ueda, T., Uchiumi, T. (2011) Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Escherichia coli in complex with the acceptor-TYC domain of tRNA. Acta. Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. 67: 1566-1569.

36.  Yamamoto, T., Shimizu, Y., Ueda, T., Shiro, Y., Suematsu, M. (2011) Application of micro-reactor chip technique for millisecond quenching of deuterium incorporation into 70S ribosomal protein complex. Int. J. Mass Spectrom. 302: 132-138.

37.  Zhou Z. P., Shimizu, Y., Tadakuma, T., Taguchi, H., Ito, K., Ueda, T. (2011) Single molecule imaging of the trans-translation entry process via anchoring of the tagged ribosome. J. Biochem. 149: 609-618.

38.  Ohashi, H., Kanamori, T., Shimizu, Y., Ueda, T. (2010) A highly controllable reconstituted cell-free system -- a breakthrough in protein synthesis research. Curr. Pharm. Biotechnol.11: 267-271.

39.  Shimizu, Y., Ueda, T. (2010) PURE technology. Methods Mol. Biol. 607: 11-21.

40.  Yamamoto, T., Shimizu, Y., Ueda, T., Shiro, Y. (2010) Mg2+ dependence of 70 S ribosomal protein flexibility revealed by hydrogen/deuterium exchange and mass spectrometry. J. Biol. Chem. 285: 5646-5652.

41.  Takahashi, S., Iida, M., Furusawa, H., Shimizu, Y., Ueda, T., Okahata, Y. (2009) Real-time monitoring of cell-free translation on a quartz-crystal microbalance. J. Am. Chem. Soc.131: 9326-9332.

42.  Osada, E., *Shimizu, Y., Akbar, B. K., Kanamori, T., Ueda, T. (2009) Epitope mapping using ribosome display in a reconstituted cell-free protein synthesis system. J. Biochem. 145: 593-700. (*corresponding author)

43.  Uemura, S., Iizuka, R., Ueno, T., Shimizu, Y., Taguchi, H., Ueda, T., Puglisi, J. D., Funatsu, T. (2008) Single molecule imaging of full protein synthesis by immobilized ribosomes. Nucleic Acids Res. 36: e70.

44.  Takahashi, S., Akita, R., Matsuno, H., Furusawa, H., Shimizu, Y., Ueda, T., Okahata, Y. (2008) 70S ribosomes bind to Shine-Dalgarno sequences without required dissociations. Chembiochem 9: 870-873.

45.  Takahashi, S., Furusawa, H., Shimizu, Y., Ueda, T., Okahata, Y. (2007) Kinetic analysis of the effects of translation enhancers in translation initiation. Nucleic Acids Symp. Ser. (Oxf). 51: 45-46.

46.  Doi, Y., Ohtsuki, T., Shimizu, Y., Ueda, T., Sisido, M. (2007) EF-Tu mutants expand amino acid tolerance of protein biosynthesis system. J. Am. Chem. Soc. 129: 14458-14462.

47.  Watanabe, K., Toh, Y., Suto, K., Shimizu, Y., Oka, N., Wada, T., Tomita, K. (2007) Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase. Nature 449: 867-871.

48.  Qi, H., *Shimizu, Y., Ueda, T. (2007) Ribosomal protein S1 is not essential for the trans-translation machinery. J. Mol. Biol. 368: 845-852. (*corresponding author)

49.  Ohashi, H., *Shimizu, Y., Ying, B. W., Ueda, T. (2007) Efficient protein selection based on ribosome display system with purified components. Biochem. Biophys. Res. Commun.352: 270-276. (*corresponding author)

50.  **Suto, K., **Shimizu, Y., Watanabe, K., Ueda, T., Fukai, S., Nureki, O. Tomita, K. (2006) Crystal structures of leucyl/phenylalanyl-tRNA-protein transferase and its complex with an aminoacyl-tRNA analog. EMBO J., 25: 5942-5950. (**equally contributed).

51.  Takahashi, S., Akita, R., Furusawa, H., Shimizu, Y., Ueda, T., Okahata, Y. (2006) Kinetic analysis of ribosome binding process onto mRNA using a quartz-crystal microbalance. Nucleic Acids Symp. Ser. (Oxf). 50: 49-50. 

52.  Shimizu, Y., Kuruma, Y., Ying, B. W., Umekage, S., Ueda, T. (2006) Cell-free translation systems for protein engineering. FEBS J. 273: 4133-4140.

53.  Shimizu, Y., Ueda, T. (2006) SmpB triggers GTP hydrolysis of elongation factor Tu on ribosomes by compensating for the lack of codon-anticodon interaction during trans-translation initiation. J. Biol. Chem. 281: 15987-15996.

54.  Kuruma, Y., Nishiyama, K., Shimizu, Y., Muller, M., Ueda, T. (2005) Development of a minimal cell-free translation system for the synthesis of presecretory and integral membrane proteins. Biotechnol. Prog. 21: 1243-1251.

55.  Shimizu, Y., Kanamori, T., Ueda, T. (2005) Protein synthesis by pure translation systems. Methods 36: 299-304.

56.  Takayama, T., Ogawa, T., Hidaka, M., Shimizu, Y., Ueda, T., Masaki, H. (2005) Esterification of Escherichia coli tRNAs with D-histidine and D-lysine by aminoacyl-tRNA synthetases. Biosci. Biotechnol. Biochem. 69: 1040-1041.

57.  Udagawa, T., Shimizu, Y., Ueda, T. (2004) Evidence for the translation initiation of leaderless mRNAs by the intact 70 S ribosome without its dissociation into subunits in eubacteria. J. Biol. Chem. 279: 8539-8546.

58.  Ying, B. W., Suzuki, T., Shimizu, Y., Ueda, T. (2003) A novel screening system for self-mRNA targeting proteins. J. Biochem. 133: 485-491.

59.  Nomura, T., Mochizuki, R., Dabbs, E. R., Shimizu, Y., Ueda, T., Hachimori, A., Uchiumi, T. (2003) A point mutation in ribosomal protein L7/L12 reduces its ability to form a compact dimer structure and to assemble into the GTPase center. Biochemistry 42: 4691-4698.

60.  Shimizu, Y., Ueda, T. (2002) The role of SmpB protein in trans-translation. FEBS Lett. 514: 74-77.

61.  Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., Ueda, T. (2001) Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19: 751-755.

日本語総説

1.     清水義宏, 松浦友亮 (2019) タンパク質合成と数理モデル. 生物工学 97: 492-495.

2.     清水義宏, Yasmine Abouleila, Ahmed Ali, 鬼谷薫, 渡邉朋信, Arno Germond, 本田一文 (2019) 一細胞質量分析によるメタボローム解析. Proteome Letters 4: 1-7.

3.     鳴海良平, 清水義宏, 上田泰己 (2017) 無細胞合成ペプチドを利用したタンパク質絶対定量. Proteome Letters 2: 75-82.

4.     安達仁朗, 清水義宏 (2017) 第一章 2節 人工細胞と無細胞タンパク質合成システム. 人工細胞の創製とその応用 (シーエムシー出版 植田充美 監修) 8-14.

5.     清水義宏, 木賀大介 (2015) 無細胞タンパク質合成システム. 生物工学 93: 603-606.

6.     清水義宏 (2014) 生命動態システム科学 III. 合成生物学 1. 人工細胞 (4) 生命の部分再構成としてのPURE system. 生体の科学 65(5): 498-499.

7.     清水義宏 (2013) 第一章2節 無細胞タンパク質合成. タンパク質結晶の最前線 (シーエムシー出版 杉山成 監修) 18-24.

8.     清水義宏, 上田卓也 (2012) 4章 タンパク質合成システムの再構成. 生命システム工学 (化学同人 田口精一 編) 45-70.

9.     清水義宏 (2011) 自己複製可能な無細胞翻訳系の構築に向けて. 実験医学 29: 1078-1083.

10.  清水義宏 (2008) 試験管の中でタンパク質をつくる 東京大学アイソトープ総合センターニュース, 39(3): 2-4.

11.  清水義宏, 上田卓也 (2008) 再構築型無細胞タンパク質合成系. やさしい原理からはいるタンパク質科学実験法 １ タンパク質をつくる (化学同人): 148-156.

12.  清水義宏, 上田卓也 (2008) 大腸菌由来酵素, 因子群を用いた翻訳. RNA実験ノート上巻 (羊土社): 128-130.

13.  清水義宏, 上田卓也 (2007) 翻訳伸長段階におけるリボソームおよびtRNAのダイナミクスと分子擬態. 実験医学, 25: 5-12.

14.  上田卓也, 清水義宏 (2004) 再構成蛋白質合成系: PURESYSTEM. 和光純薬時報, 72: 2-4.

15.  清水義宏, 上田卓也 (2004) 無細胞蛋白質合成系: 大腸菌由来完全再構成系PURESYSTEM. 蛋白質核酸酵素 49: 1520-1526.

16.  清水義宏, 上田卓也 (2004) 無細胞タンパク質合成系. タンパク質実験ノート (羊土社): 195-201.

17.  上田卓也, 清水義宏 (2003) 無細胞タンパク質合成系のピュアアプローチ. 生物物理 43: 9-14.

18.  清水義宏, 上田卓也 (2002) 無細胞タンパク質合成システム. 実験医学 20: 2020-2025.

19.  清水義宏, 上田卓也 (2002) 無細胞タンパク質合成系の新展開. 遺伝子医学 6: 266-270.

Book Chapters

1.  Ying, B. W., Shimizu, Y., Ueda, T. (2007) The PURE system: a minimal cell-free translation system. Cell-Free Expression (ed. Kudlicki, W., Katzen, F., and Bennett, R.) Eurekah Bioscience Collection.

2.  Ueda, T., Inoue, A., Shimizu, Y. (2004) Cell-free translation systems. Encyclopedia of Molecular Cell Biology and Molecular Medicine (ed. Meyer, R.A.) Wiley-VCH Verlag GmbH & Co, KGaA, Weinheim: 451-461.

3.  Ueda, T., Inoue, A., Kaida, M., Baba, R., Shimizu, Y. (2002) PURE system - New cell-free translation system reconstituted with purified components. Cell-free translation systems (ed. A. S. Spirin) Springer Verlag, Heidelberg: 53-60.