2024

A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis. 

#Miyauchi, K., #Kimura, S., #Akiyama, N., Inoue, K., Ishiguro K., Vu TS., Srisuknimit V., Koyama K., Hayashi G., Soma A., Nagao A., Shirouzu M., Okamoto A., Waldor M. K., Suzuki T. (#co-first authors)

Nat Chem Biol https://doi.org/10.1038/s41589-024-01726-x (2024)

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2023

A tRNA modification in Mycobacterium tuberculosis facilitates optimal intracellular growth.

#Tomasi F. G., #*Kimura S., Rubin E. J., Waldor M. K., (#co-first authors, *corresponding author)

eLife, https://doi.org/10.7554/eLife.87146.1 (2023)

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Peptidyl tRNA hydrolase is required for robust prolyl-tRNA turnover in Mycobacterium tuberculosis.

#Tomasi F. G., #Schweber J. T. P., #Kimura S., Zhu J., Cleghorn L., A., T., Davis S. H., Green S. R., Waldor M. K., Rubin E. J., (#co-first authors),

mBio, e03469-22 (2023)

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2022

Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine.

*Kimura S., Srisuknimit V., McCarty K., Dedon P. C., Kranzusch P., J., *Waldor M. K. (*co-corresponding authors),

Nat. Commun., 13, 5994 (2022)

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2021

Distinct evolutionary pathways for the synthesis and function of tRNA modifications.

Kimura S.,

Briefings in Functional Genomics, 20;2, 125-134 (2021) Review article

 

2020

Probing the diversity and regulation of tRNA modifications.

*Kimura S., Srisuknimit V., and *Waldor M. K. (*co-corresponding authors),

Curr. Opin. Microbiol., 57; 41-48 (2020) Review article

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Growth-optimized aminoacyl-tRNA synthetase levels prevent maximal tRNA charging.

Parker D. J., Lalanne J. B., Kimura S., Johnson G. E., Waldor M. K., and Li G. W.,

Cell Syst., 11, 121-130.e6 (2020)

 

Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications.

*Kimura S., Dedon P. C., and *Waldor M. K. (*co-corresponding authors),

Nat. Chem. Biol, 16, 964-972 (2020)

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2019

Dual pathways of tRNA hydroxylation ensure efficient translation by expanding decoding capability.

#Sakai Y., #Kimura S., and Suzuki T. (#co-first authors),

Nat. Commun., 10: 2858-2873 (2019)

 

The RNA degradosome promotes tRNA quality control through clearance of hypomodified tRNAs.

*Kimura S., and *Waldor M. K. (*co-corresponding authors)

Proc. NatI. Acad Sci USA, 116 (4): 1394-1403 (2019)

 

2017

Biogenesis and iron-dependency of ribosomal RNA hydroxylation.

Kimura S., Sakai Y, Ishiguro K, and Suzuki T.,

Nucleic Acids Res, 45(22):12974-12986 (2017)
 

2016

The nucleoid binding protein H-NS biases genome-wide transposon insertion landscapes.

Kimura S., Hubbard T. P., Davis B. M. and Waldor M. K.,

mBio, 1(10):16125 (2016)

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Biogenesis and growth phase-dependent alteration of 5-methoxycarbonyl methoxyuridine in tRNA anticodons.

Sakai Y., Miyauchi K., Kimura S., and Suzuki T.,

Nucleic Acids Res, 44(2):509-23 (2016)

 

2015

A cytosine methyltransferase modulates the cell envelope stress response in the cholera pathogen.

Chao M. C., Zhu S., Kimura S., Davis B. M., Schadt E. E., Fang G., and Waldor M. K.,

PLoS Genet., 11: e1005666 (2015)

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RlmCD-mediated U747 methylation promotes efficient G748 methylation by methyltransferase RlmAII in 23S rRNA in Streptococcus pneumoniae; interplay between two rRNA methylations responsible for telithromycin susceptibility.

Shoji T., Takaya A., Sato Y., Kimura S., Suzuki T., and Yamamoto T.,

Nucleic Acids Res, 43, 8964-8972 (2015)

 

Single methylation of 23S rRNA triggers late steps of 50S ribosomal subunit assembly.

Arai T., Ishiguro K., Kimura S., Sakaguchi Y., Suzuki T., and Suzuki T.,

Proc. NatI. Acad. Sci. USA 112: E4707-4716 (2015)

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Ribosomal RNA methyltransferases contribute to Staphylococcus aureus virulence.

Kyuma T., Kimura S., Hanada Y., Suzuki T., Sekimizu K., and Kaito C.,

FEBS J., 282:2570-2584 (2015)

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Iron-sulfur proteins responsible for RNA modifications.

Kimura S. and Suzuki T.,

Biochim Biophys Acta. 1853: 1272-1283 (2015) Review article [OA]

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2014

A single acetylation of 18S rRNA is essential for biogenesis of the small ribosomal subunit in Saccharomyces cerevisiae.

Ito S., Akamatsu Y., Noma A., Kimura S., Miyauchi K., Ikeuchi Y., Suzuki T., and Suzuki T.,

J. Biol. Chem., 289: 26201-26212 (2014)

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Discovery of the beta-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs.

Kimura S., Miyauchi K., Ikeuchi Y., Thiaville P. C., Crécy-Lagard V., and Suzuki T.,

Nucleic Acids Res, 42: 9350-9365 (2014)

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2012

A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification.

Miyauchi K., Kimura S., and Suzuki T.,

Nat. Chem. Biol., 9, 105-111 (2012)

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Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity.

Kimura S., Ikeuchi Y., Kitahara K., Sakaguchi Y., Suzuki T., and Suzuki T.,

Nucleic Acids Res, 40, 4071-4085 (2012)

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2011

Structural basis of tRNA agmatinylation essential for AUA codon decoding.

Osawa T., Kimura S., Terasaka N., Inanaga H., Suzuki T., and Numata T.,

Nat. Struct. & Mol. Biol., 18, 1275-1280 (2011)

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Biogenesis of 2-agmatinylcytidine catalyzed by the dual protein and RNA kinase TiaS.

#Terasaka N., #Kimura S., Osawa T., Numata T., and Suzuki T. (#co-first authors),

Nat. Struct. & Mol. Biol., 18, 1268-1274 (2011)

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Deficit of tRNALys modification by Cdkal1 causes the development of type 2 diabetes in mice.

Wei F. Y., Suzuki T., Watanabe S., Kimura S., Kaitsuka T., Fujimura A., Matsui H., Atta M., Michiue H., Fontecave M., Yamagata K., Suzuki T., Tomizawa K.,

J. Clin. Invest. 121(9); 3598-3608 (2011)

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2010

Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea.
Ikeuchi Y., Kimura S., Numata T., Nakamura D., Yokogawa T., Ogata T., Wada T., Suzuki T., and Suzuki T.,
Nat. Chem. Biol., 6, 277-282 (2010)

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Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA.

Kimura S., and Suzuki T.,

Nucleic Acids Res., 38, 1341-52 (2010)

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2009

Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase.

Nakanishi K., Bonnefond L., Kimura S., Suzuki T., Ishitani R., and Nureki O.,

Nature, 461, 1144-1148 (2009)

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Aquifex aeolicus tRNA (N2, N2-guanine)-dimethyltransferase (Trm1) catalyzes transfer of methyl groups not only to guanine 26 but also to guanine 27 in tRNA.

Awai T., Kimura S., Tomikawa C., Ochi A., Ihasanawati, Bessho Y., Yokoyama S., Ohno S., Nishikawa K., Yokogawa T., Suzuki T., and Hori H.,

J. Biol. Chem., 284, 20467-20478 (2009)