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SHIMIZU Yoshihiro

Academic OrganizationTEL
Education and Research OrganizationGraduate School of Medicine, Science and TechnologyFAX
PositionProfessorMail Address
Address3-1-1, Asahi, Matsumoto City 390-8621Web site

Profile

Academic Background
Degree
博士(工学) , Tokyo University

Research

Books, Articles, etc.
Articles
Ebola virus-like particles reprogram cellular metabolism.
J. Mol. Med.,101:557-568 2023
Author:Tang, H., Abouleila, Y., Saris, A., Shimizu, Y., Ottenhoff, T. H. M., *Mashaghi, A.


ePURE_JSBML: A tool for constructing a deterministic model of a reconstituted Escherichia coli protein translation system with a user-specified nucleic acid sequence.
Adv. Biol.,7:e2200177-e2200177 2023
Author:*Shimizu, Y., Tanimura, N., Matsuura, T.


A large-scale targeted proteomics of plasma extracellular vesicles shows utility for prognosis prediction subtyping in colorectal cancer.
Cancer Med.,12:7616-7626 2023
Author:Kasahara, K., Narumi, R., Nagayama, S., Masuda, K., Esaki, T., Obama, K., *Tomonaga, T., Sakai, Y., *Shimizu, Y., *Adachi, J.


Transfer RNA Synthesis-Coupled Translation and DNA Replication in a Reconstituted Transcription/Translation System.
ACS Synth. Biol.,11:2791-2799 2022
Author:Miyachi, R., Shimizu, Y., *Ichihashi, N.


A red light-responsive photoswitch for deep tissue optogenetics.
Nat. Biotechnol.,40:1672-1679 2022
Author:Kuwasaki, Y., Suzuki, K., Yu, G., Yamamoto, S., Otabe, T., Kakihara, Y., Nishiwaki, M., Miyake, K., Fushimi, K., Bekdash, R., Shimizu, Y., Narikawa, R., Nakajima, T., Yazawa, M., *Sato, M.


Capillary microsampling-based single-cell metabolomics by mass spectrometry and its applications in medicine and drug discovery.
Cancer Biomark.,33:437-447 2022
Author:Abouleila Y., Ali, A., Masuda, K., Mashaghi, A., *Shimizu, Y.


Tracking metabolites at single-cell resolution reveals metabolic dynamics during plant mitosis.
Plant Physiol.,189:459-464 2022
Author:Okubo-Kurihara, E., Ali, A., Hiramoto, M., Kurihara, Y., Abouleila, Y., Abdelazem, E. M., Kawai, T., Makita, Y., Kawashima, M., Esaki, T., Shimada, H., Mori, T., Hirai, M. Y., Higaki, T., Hasezawa, S., Shimizu, Y., Masujima, T., *Matsui, M.


Cell-Free Synthesis of Human Endothelin Receptors and Its Application to Ribosome Display.
Anal. Chem.,(94):3831-3839 2022
Author:Nakai, H., Isshiki, K., Hattori, M., Maehira, H., Yamaguchi, T., Masuda, K., Shimizu, Y., Watanabe, T., Hohsaka, T., Shihoya, W., Nureki, O., Kato, Y., Watanabe, H., *Matsuura, T.


Efficient and precise protein synthesis in a cell-free system using a set of in vitro transcribed tRNAs with nucleotide modifications.
Methods Mol.,2433:151-168 2022
Author:Amikura, K., Hibi, K., *Shimizu, Y.


In vitro reconstitution of the Escherichia coli 70S ribosome with a full set of recombinant ribosomal proteins.
J. Biochem.,171:227-237 2022
Author:Aoyama, R., Masuda, K., Shimojo, M., Kanamori, T., Ueda, T., *Shimizu, Y.


Versatile and multiplexed mass spectrometry-based absolute quantification with cell-free-synthesized internal standard peptides.
J. Proteomics,251:104393 2022
Author:Masuda, K., Kasahara, K., Narumi, R., Shimojo, M., *Shimizu, Y.


Antisense Oligonucleotide Modified with Disulfide Units Induces Efficient Exon Skipping in mdx Myotubes through Enhanced Membrane Permeability and Nucleus Internalization.
Chembiochem,22:3437-3442 2021
Author:Hiraoka, H., Shu, Z., Tri Le, B., Masuda, K., Nakamoto, K., Fangjie, L., Abe, N., Hashiya, F., Kimura, Y., Shimizu, Y., Veedu, R. N., *Abe, H.


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


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) 2021
Author:Demeiry, M. E., Ali, A., Abouleila, Y., Zarad, W., El-Gendy, H, Salam, R. A., Hadad, G., Shimizu, Y., Masujima, T., *Emara, S.


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


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


Mass spectrometry-based absolute quantification of amyloid proteins in pathology tissue specimens: Merits and limitations.
PLoS One,15:e0235143 2020
Author: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.


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


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


Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues.
Nat. Commun.,11:1982 2020
Author:*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.


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


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 2020
Author:Demeiry, M. E., Ali, A., Abouleila, Y., Shimizu, Y., Masujima, T., Salam, R. A., Hadad, G., *Emara, S.


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


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


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


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


Live single cell mass spectrometry reveals cancer-specific metabolic profiles of circulating tumor cells.
Cancer Sci.,110:697-706 2019
Author: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.


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


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


Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents.
Cell Rep.,24:2196-2210. e9 2018
Author: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.


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


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


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


A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing.
Nat. Neurosci.,21:625-637 2018
Author: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.


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


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


Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene.
Cell Rep.,14:662-677 2016
Author: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.


Integration of a reconstituted cell-free protein-synthesis system on a glass microchip.
Anal. Sci.,31:67-71 2015
Author:#*Tanaka, Y. #*Shimizu, Y.


Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis.
Cell,157:726-739 2014
Author: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.


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


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


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 2013
Author:Matsumoto, A., Shimizu, Y., Takemoto, C., Ueda, T., Uchiumi, T., *Ito, K.


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


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


ArfA recruits RF2 into stalled ribosomes.
J. Mol. Biol.,423:624-631 2012
Author:*Shimizu, Y.


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


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 2011
Author:*Ito, K., Qi, H., Shimizu, Y., Murakami, R., Miura, K. I., Ueda, T., Uchiumi, T.


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


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


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


PURE technology.
Methods Mol. Biol.,607:11-21 2010
Author:Shimizu, Y., *Ueda, T.


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


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


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


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


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


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


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


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


Ribosomal protein S1 is not essential for the trans-translation machinery.
J. Mol. Biol.,386:845-852 2007
Author:Qi, H., *Shimizu, Y., Ueda, T.


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


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


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


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


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 2006
Author:Shimizu, Y., *Ueda, T.


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


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


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


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 2004
Author:Udagawa, T., Shimizu, Y., *Ueda, T.


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


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 2003
Author:Nomura, T., Mochizuki, R., Dabbs, E. R., Shimizu, Y., Ueda, T., Hachimori, A., *Uchiumi, T.


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


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