Publications

1. Structural basis of substrate diversity and functional evolution of archaeal RNA-splicing endonucleases.
   Yuna Miyata, Ryota Yamagami, Takuya Kawamura, Hiroyuki Hori, Akira Hirata
   Nucleic acids research 53(16) 2025年8月27日査

2. Transfer RNA Recognition Mechanism of Thermoplasma acidophilum Trm56, a SPOUT tRNA Methyltransferase that Possesses an Unusually Long C-terminal Region.
   Soichiro Hidetaka, Shuhei Fukumoto, Takahiro Hasegawa, Takuya Kawamura, Mami Ototake, Shizuka Moriguchi, Miyu Namba, Chie Tomikawa, Ryota Yamagami, Akira Hirata …
   Journal of molecular biology 437(19) 169328-169328 2025年7月14日  査読有り

3. A transfer RNA methyltransferase with an unusual domain composition catalyzes 2'-O-methylation at position 6 in tRNA. 

Teppei Matsuda, Ryota Yamagami, Aoi Ihara, Takeo Suzuki, Akira Hirata, Hiroyuki Hori

Nucleic acids research 53(13) 2025年7月8日

4. Recombinant expression and purification of wheat aminoacyl-tRNA synthetases and IRES-dependent polypeptide synthesis with homogeneously derived purified factors 

Haruyuki Furukawa, Ryota Yamagami, Yuto Nagashio, Kensuke Tsutsumi, Kazuki Goto, Takumi Nishioka, Takumi Kondo, Keigo Hisamatsu, Takeru Aga, Ryunosuke Watanabe …

Biochimie 2025年6月  

5. tRNA pseudouridine synthase D (TruD) fromThermus thermophilusmodifies U13 in tRNAAsp, tRNAGlu, and tRNAGlnand U35 in tRNATyr
   Ryota Yamagami, Kojiro Takahashi, Shogo Shingu, Miyu Namba, Kohsuke Kamizaki, Hiroyuki Hori
   RNA (New York, N.Y.) 31(6) 850-867 2025年5月16日

6. A transfer RNA methyltransferase with an unusual domain composition catalyzes 2′-O-methylation at position 6 in tRNA 

Teppei Matsuda, Ryota Yamagami, Aoi Ihara, Takeo Suzuki, Akira Hirata, Hiroyuki Hori

BioRxiv: the preprint server for biology 2025年4月4日

7. ArcS from Thermococcus kodakarensis transfers L-lysine to preQ0 nucleoside derivatives as minimum substrate RNAs.
   Shu Fujita, Yuzuru Sugio, Takuya Kawamura, Ryota Yamagami, Natsuhisa Oka, Akira Hirata, Takashi Yokogawa, Hiroyuki Hori
   The Journal of biological chemistry 300(8) 107505-107505 2024年6月27日

8. High-throughput mutational analysis of a methyltransferase ribozyme.
   Ryota Yamagami, Hina Kubota, Emi Kohno, Hiroyuki Hori
   Frontiers in RNA Research 2 2024年6月

9. Rational design of oligonucleotides for enhanced in vitro transcription of small RNA.
   Teppei Matsuda, Hiroyuki Hori, Ryota Yamagami
   RNA (New York, N.Y.) 30(6) 710-727 2024年5月16日

10. Escherichia coli tRNA (Gm18) methyltransferase (TrmH) requires the correct localization of its methylation site (G18) in the D-loop for efficient methylation.
    Yoh Kohno, Asako Ito, Aya Okamoto, Ryota Yamagami, Akira Hirata, Hiroyuki Hori
    Journal of biochemistry 175(1) 43-56 2023年12月20日

11. RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life.
    McCauley O Meyer, Ryota Yamagami, Saehyun Choi, Christine D Keating, Philip C Bevilacqua
    Science advances 9(38) eadh5152-15 2023年9月22日

12. RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life.
    McCauley O Meyer, Ryota Yamagami, Saehyun Choi, Christine D Keating, Philip C Bevilacqua
    bioRxiv : the preprint server for biology 2023年2月27日  

13. Structure-seq of tRNAs and other short RNAs in droplets and in vivo.
    McCauley O Meyer, Saehyun Choi, Christine D Keating, Philip C Bevilacqua, Ryota Yamagami
    Methods in enzymology 691 81-126 2023年

14. Functional analysis of tRNA modification enzymes using mutational profiling.
    Ryota Yamagami, Hiroyuki Hori
    Methods in enzymology 692 69-101 2023年

15. Application of mutational profiling: New functional analyses reveal the tRNA recognition mechanism of tRNA m1A22 methyltransferase.
    Ryota Yamagami, Hiroyuki Hori
    Journal of Biological Chemistry 299(1) 102759-102759 2022年12月1日

16. A selective and sensitive detection system for 4-thiouridine modification in RNA
    Yuzuru Sugio, Ryota Yamagami, Naoki Shigi, Hiroyuki Hori
    RNA 2022年11月21日

17. Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress.
    Ryota Yamagami, Jacob P. Sieg, Sarah M. Assmann, Philip C. Bevilacqua
    Proceedings of the National Academy of Sciences of the United States of America 119(25) e2201237119 2022年6月21日  査読

18. Required Elements in tRNA for Methylation by the Eukaryotic tRNA (Guanine-N2-) Methyltransferase (Trm11-Trm112 Complex)
    Yu Nishida, Shiho Ohmori, Risa Kakizono, Kunpei Kawai, Miyu Namba, Kazuki Okada, Ryota Yamagami, Akira Hirata, Hiroyuki Hori
    International Journal of Molecular Sciences 23(7) 4046-4046 2022年4月6日

19. Functional Roles of Chelated Magnesium Ions in RNA Folding and Function
    Ryota Yamagami, Jacob P. Sieg, Philip C. Bevilacqua
    Biochemistry 60(31) 2374-2386 2021年8月10日

20. Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots.
    Mohammad Kayedkhordeh*, Ryota Yamagami*, Philip C. Bevilacqua, David H. Mathews
    Methods in Molecular Biology (Clifton, N.J.) 2167 113-143 2021年

21. Single-nucleotide control of tRNA folding cooperativity under near-cellular conditions.
    Kathleen A. Leamy*, Ryota Yamagami*, Neela H. Yennawar, Philip C. Bevilacqua
    Proceedings of the National Academy of Sciences of the United States of America 116(46) 23075-23082 2019年11月12日  査

22. Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis by RNA and DNA Enzymes.
    Ryota Yamagami, Ruochuan Huang, Philip C. Bevilacqua
    Biochemistry 58(38) 3971-3979 2019年9月24日

23. Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.
    Ryota Yamagami, Mohammad Kayedkhordeh, David H. Mathews, Philip C. Bevilacqua
    Nucleic Acids Research 47(1) 29-42 2019年1月10日

24. Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA.
    Hori H, Kawamura T, Awai T, Ochi A, Yamagami R, Tomikawa C, Hirata A
    Microorganisms 6(4) 2018年10月

25. Consumption of N5, N10-methylenetetrahydrofolate in Thermus thermophilus under nutrient-poor condition
    Yamagami, R., Miyake, R., Fukumoto, A., Nakashima, M., Hori, H.
    Journal of Biochemistry 164(2) 141-152 2018年8月

26. Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis
    Yamagami, R., Bingaman, J.L., Frankel, E.A., Bevilacqua, P.C.
    Nature Communications 9(1) 2149 2018年6月

27. Long and branched polyamines are required for maintenance of the ribosome, tRNA(His) and tRNA(Tyr) in Thermus thermophilus cells at high temperatures
    Misa Nakashima, Ryota Yamagami, Chie Tomikawa, Yuki Ochi, Toshiyuki Moriya, Haruichi Asahara, Dominique Fourmy, Satoko Yoshizawa, Tairo Oshima, Hiroyuki Hori
    Genes to Cells 22(7) 628-645 2017年7月  査読有り

28. Folate-/FAD-dependent tRNA methyltransferase from Thermus thermophilus regulates other modifications in tRNA at low temperatures
    Ryota Yamagami, Chie Tomikawa, Naoki Shigi, Ai Kazayama, Shin-ichi Asai, Hiroyuki Takuma, Akira Hirata, Dominique Fourmy, Haruichi Asahara, Kimitsuna Watanabe …
    Genes to Cells 21(7) 740-754 2016年7月

29. Regulation of protein synthesis via the network between modified nucleosides in tRNA and tRNA modification enzymes in Thermus thermophilus, a thermophilic eubacterium.
    Hiroyuki Hori, Ryota Yamagami, Chie Tomikawa
    Modified Nucleic Acids in Biology and Medicine. 73-89 2016年

30. In vitro dihydrouridine formation by tRNA dihydrouridine synthase from Thermus thermophilus, an extreme-thermophilic eubacterium
    Hiroaki Kusuba, Takeshi Yoshida, Eri Iwasaki, Takako Awai, Ai Kazayama, Akira Hirata, Chie Tomikawa, Ryota Yamagami, Hiroyuki Hori
    Journal of Biochemistry 158(6) 513-521 2015年12月

31. Improved solid-phase DNA probe method for tRNA purification: large-scale preparation and alteration of DNA fixation
    Ai Kazayama, Ryota Yamagami, Takashi Yokogawa, Hiroyuki Hori
    Journal of Biochemistry 157(5) 411-418 2015年5月

32. The Catalytic Domain of Topological Knot tRNA Methyltransferase (TrmH) Discriminates between Substrate tRNA and Nonsubstrate tRNA via an Induced-fit Process
    Anna Ochi, Koki Makabe, Ryota Yamagami, Akira Hirata, Reiko Sakaguchi, Ya-Ming Hou, Kazunori Watanabe, Osamu Nureki, Kunihiro Kuwajima, Hiroyuki Hori
    Journal of Biological Chemistry 288(35) 25562-25574 2013年8月

33. The tRNA Recognition Mechanism of Folate/FAD-dependent tRNA Methyltransferase (TrmFO)
    Ryota Yamagami, Koki Yamashita, Hiroshi Nishimasu, Chie Tomikawa, Anna Ochi, Chikako Iwashita, Akira Hirata, Ryuichiro Ishitani, Osamu Nureki, Hiroyuki Hori
    Journal of Biological Chemistry 287(51) 42480-42494 2012年12月

34. X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity
    Akira Hirata, Kosuke Fujishima, Ryota Yamagami, Takuya Kawamura, Jillian F. Banfield, Akio Kanai, Hiroyuki Hori
    Nucleic Acids Research 40(20) 10554-10566 2012年11月