原著論文 （英文 2016年~ 東京大学）
◎研究室学生が第一著者の論文 ○研究室サイエンティフィックスタッフ（助教 ポスドク）が第一著書の論文
◎ 50. Feng Z, Yashiro Y, *Tomita K. (* corresponding)
Mechanism of activation of contact-dependent growth inhibition tRNase toxin by the amino acid biogenesis factor CysK in the bacterial competition system.
Nucleic Acids Res., doi: 10.1093/nar/gkae735, 2024 [PubMed] [PDF]
◎49. Liu J, Yashiro Y, Sakaguchi Y, Suzuki T, *Tomita K. (* corresponding)
Substrate specificity of Mycobacterium tuberculosis tRNA terminal nucleotidyltransferase toxin MenT3.
Nucleic Acids Res., doi: 10.1093/nar/gkae177, 2024 [PubMed][PDF]
○48. Yamashita S,*Tomita K. (* corresponding)
Mechanism of U6 snRNA oligouridylation by human TUT1.
Nature Communications, doi: 10.1038/s41467-023-40420-9, 2023 [PubMed]
47.Nagato Y, Yamashita S,Ohashi A, Furukawa H, Takai K, Tomita K, *Tomikawa C. (* corresponding)
Mechanism of tRNA recognition byheterotetrameric glycyl-tRNA synthetase from lactic acid bacteria
J Biochem, doi: 10.1093/jb/mvad043, 2023
◎46. Ju J, Aoyama T, Yashiro Y, Yamashita Y, Kuroyanagi H, *Tomita K. (* corresponding)
Structure of the Caenorhabditis elegans m6A methyltransferase METT10 that regulates SAM homeostasis.
Nucleic Acids Res, doi.org/10.1093/nar/gkad081, 2023 [PubMed] [PDF]
45. *Ohira, T., Minowa, K., Sugiyama, K., Yamashita, S., Sakaguchi, Y., Miyauchi, K., Noguchi, R., Kaneko, A., Orita, I., Fukui, T., *Tomita, K., *Suzuki T. (* corresponding)
Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance.
Nature, doi.org/10.1038/s41586-022-04677-2, 2022 [PubMed] [PDF]
◎44.Wang J, Yashiro Y, Sakaguchi Y, Suzuki T, *Tomita K. (* corresponding)
Mechanistic insights into tRNA cleavage by a contact-dependent growth inhibitor protein and translation factors
Nucleic Acids Res, doi:10.1093/nar/gkac228, 2022 [PubMed] [PDF]
○43. Yashiro Y, Zhang C, Sakaguchi Y, Suzuki T, *Tomita K. (* corresponding)
Molecular basis of glycyl-tRNAGly acetylation by TacT from Salmonella Typhimurium
Cell Reports, doi: 10.1016/j.celrep.2021.110130, 2021 [PubMed][PDF]
○42. Yashiro Y, Sakaguchi Y, Suzuki T, *Tomita K. (* corresponding)
Mechanism of aminoacyl-tRNA acetylation by an aminoacyl-tRNA acetyltransferase AtaT from enterohemorrhagic E. coli
Nature Communications,doi: 10.1038/s41467-020-19281-z, 2020 [PubMed] [PDF]
41. Kurimoto R, Chiba T, Ito Y, Matsushima T, Yano Y, Miyata K, Yashiro Y, Suzuki T, Tomita K, *Asahara H. (* corresponding)
The tRNA pseudouridine synthase TruB1 regulates the maturation of let-7 miRNA
EMBO J., doi: 10.15252/embj.2020104708, 2020 [PubMed]
◎40.Zhang C, Yashiro Y, Sakaguchi Y, Suzuki T, *Tomita K. (* corresponding)
Substrate specificities of Escherichia coli ItaT that acetylates aminoacyl-tRNAs
Nucleic Acids Res., doi: 10.1093/nar/gkaa487, 2020 [PubMed] [PDF]
◎39. Aoyama T, Yamashita S, *Tomita K. (* corresponding)
Mechanistic insights into m6A modification of U6 snRNA by human METTL16
Nucleic Acids Res., doi: 10.1093/nar/gkaa227, Vol 48, No 9, pp5157–5168, 2020 [PubMed] [PDF]
38. Abe T, Nagai R, Shimazaki S, Kondo S, Nishimura S, Sakaguchi Y, Suzuki T, Imataka H, Tomita K, *Takeuchi-Tomita N. (* corresponding)
In vitro yeast reconstituted translation system reveals function of eIF5A for synthesis of long polypeptide
J. Biochem., doi: 10.1093/jb/mvaa022, 2020 [PubMed]
◎37.Liu Y, Martinez A, Yamashita S, *Tomita K. (* corresponding)
Crystal structure of human cytoplasmic tRNAHis-specific 5′-monomethylphosphate capping enzyme
Nucleic Acids Res., doi: 10.1093/nar/gkz1216, Vol 48, No 3, pp1572–1582, 2020 [PubMed] [PDF]
○36. Yamashita S, Nagaike T, *Tomita K. (* corresponding)
Crystal structures of the Lin28-interacting module of human terminal uridylyltransferase that regulates let-7 expression.
Nature Communications, doi: 10.1038/s41467-019-09966-5, 2019 [PubMed] [PDF]
○35. Yashiro Y, Yamashita S, *Tomita K. (* corresponding)
Crystal structure of the enterohemorrhagic Escherichia coli AtaT-AtaR toxin-antitoxin complex.
Structure, doi.10.1016/j.str.2018.11.005, Vol. 27, No3, pp476-484, 2019 [PubMed] [PDF]
34. Taniguchi T, Miyauchi K, Sakaguchi Y, Yamashita S, Soma A, Tomita K, *Suzuki T. (* corresponding)
Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis.
Nature Chemical Biology, doi: 10.1038/s41589-018-0119-z, 2018 [PubMed]
○33. Yamashita S, Takagi Y, Nagaike T, *Tomita K. (* corresponding)
Crystal structures of U6 snRNA-specific terminal uridylyltransferase.
Nature Communications, doi:10.1038/ncomms15788, 2017 [PubMed] [PDF]
32. Kawasaki S, Fujita Y, Nagaike T, Tomita K, *Saito H.(* corresponding)
Synthetic mRNA devices that detect endogenous proteins and distinguish mammalian cells.
Nucleic Acids Res., doi: 10.1093/nar/gkx298, 2017 [PubMed]
○31. Martinez A, Yamashita S, Nagaike T, Sakaguchi Y, Suzuki T, *Tomita K (* corresponding)
Human BCDIN3D Monomethylates Cytoplasmic Histidine Transfer RNA.
Nucleic Acids Res., doi: 10.1093/nar/gkx051, Vol. 45, No 9, pp5423-5436., 2017 [PubMed] [PDF]
30. Mannen T, Yamashita S, Tomita K, Goshima N, *Hirose T. (* corresponding)
The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL.
J Cell Biol. Vol.214, pp45-59, 2016 [PubMed]
○29. Yamashita S, *Tomita K(* corresponding)
Mechanism of 3′-matured tRNA discrimination from 3′-immature tRNA by class-II CCA-adding enzyme.
Structure Vol. 24, No6, pp918-925, 2016 [PubMed] [PDF] [Movie]
2004~2015 （産業技術総合研究所）
○28. Yamashita S, Martinez A, *Tomita K (* corresponding)
Measurement of acceptor-TΨC helix length of tRNA for terminal A76-addition by A-adding enzyme.
Structure Vol. 22, No 5, pp830-842, 2015 [PubMed][PDF]
○27. Takeshita D, Yamashita S & *Tomita K (* corresponding)
Molecular insights into replication initiation by Qβ replicase using ribosomal protein S1.
Nucleic Acids Res. Vol.42, No16, pp10823-10831, 2014 [PubMed]
○26. Yamashita S, Takeshita D, *Tomita K (* corresponding)
Translocation and rotation of tRNA during template-independent RNA polymerizaion by tRNA nucleotidyltransferase.
Structure Vol. 22, No 2, pp315-325, 2014 [PubMed] [PDF]
○25. Takeshita D, Yamashita S & *Tomita K (* corresponding)
Mechanism for template-independent terminal adenylation activity of Qβ replicase.
Structure Vol. 20, No 10, pp1661-1669, 2012 [PubMed] [PDF]
○24. Takeshita D, *Tomita K (* corresponding)
Molecular basis for RNA polymerization by Qβ replicase.
Nature Structural & Molecular Biology Vol.19, No2, pp229-237, 2012 [PubMed] [PDF]
○23. Toh Y, Takeshita D, Nagaike T, Numata T, *Tomita K (*corresponding)
Mechanism for the alternation of the substrate specificities of template-independent RNA polymerases.
Structure Vol.19, No 2, pp232-243, 2011 [PubMed] [PDF]
○22. Takeshita D, *Tomita K (* corresponding)
Assembly of Qβ viral RNA polymerase with host translational elongation factors EF-Tu and -Ts.
Proc Natl Acad Sci U S A. Vol. 107, No 36, pp15733-15738, 2010 [PubMed] [PDF]
○21. Toh Y, Takeshita D, Numata T, Fukai S, Nureki O, *Tomita K (*corresponding)
Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme.
EMBO J. vol. 28, No 21, pp3353-3365, 2009 [PubMed] [PDF]
20. Osawa T, Ito K, Inanaga H, Nureki O, Tomita K, Numata T.
Conserved cysteine residues of GidA are essential for biogenesis of 5 -carboxymethylaminomethyluridine at tRNA anticodon.
Structure Vol. 17, No 5, pp713-724, 2009 [PubMed] [PDF]
○19. Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, *Tomita K (*corresponding)
Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme.
EMBO J. Vol. 27, No 14, pp1944-1952, 2008 [PubMed] [PDF]
○8. Watanabe K, Toh Y, Suto K, Shimizu Y, Oka N, Wada T, *Tomita K (*corresponding)
Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase.
Nature Vol.449, No 7164, pp867-871, 2007 [PubMed] [PDF]
○17. Suto K, Shimizu Y, Watanabe K, Ueda T, Fukai S, Nureki O, *Tomita K (* corresponding)
Crystal structures of leucyl/phenylalanyl-tRNA-protein transferase and its complex with an aminoacyl-tRNA analog.
EMBO J. Vol.25, No 24, pp5942-50, 2006 [PubMed] [PDF]
16. *Tomita K, Ishitani R, Fukai S, Nureki O. (* corresponding)
Complete crystallographic analysis of the dynamics of CCA sequence addition.
Nature Vol. 443, No 7114, 956-960, 2006 [PubMed] [PDF]
15. Tomita K, Fukai S, Ishitani R, Ueda T, Takeuchi N, Vassylyev DG, Nureki O.
Structural basis for template-independent RNA polymerization.
Nature Vol. 430, No 7000, 700-704, 2004 [PubMed] [PDF]
1996年~2004年
●14. Okabe M, Tomita K, Ishitani R, Ishii R, Takeuchi N, Arisaka F, Nureki O, Yokoyama S.
Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure.
EMBO J. Vol. 22, No 21, pp5918-5927, 2003 [PubMed] [PDF]
●13. Li F, Xiong Y, Wang J, Cho HD, Tomita K, Weiner AM, Steitz TA.
Crystal structures of the Bacillus stearothermophilus CCA-adding enzyme and its complexes with ATP or CTP.
Cell Vol. 111, No 6, pp815-824, 2002 [PubMed] [PDF]
12. Tomita K, Weiner AM.
Closely related CC- and A-adding enzymes collaborate to construct and repair the 3′-terminal CCA of tRNA in Synechocystis sp. and Deinococcus radiodurans.
J Biol Chem. Vol. 277, No 50, pp48192-48198, 2002 [PubMed] [PDF]
11.Tomita K, Yokobori S, Oshima T, Ueda T, Watanabe K.
The cephalopod Loligo bleekeri mitochondrial genome: multiplied noncoding regions and transposition of tRNA genes.
J Mol Evol. Vol. 54, No 4, pp486-500, 2002 [PubMed] [PDF]
10. Fey J, Weil JH, Tomita K, Cosset A, Dietrich A, Small I, Marechal-Drouard L.
Role of editing in plant mitochondrial transfer RNAs.
Gene Vol. 286, No 1, pp21-24, 2002 [PubMed] [PDF]
●9. Tomita K, Weiner AM.
Collaboration between CC- and A-adding enzymes to build and repair the 3′-terminal CCA of tRNA in Aquifex aeolicus.
Science Vol. 294, No 5545, pp1334-1336, 2001 [PubMed] [PDF]
8. Cho HD, Tomita K, Suzuki T, Weiner AM.
U2 small nuclear RNA is a substrate for the CCA-adding enzyme (tRNA nucleotidyltransferase).
J Biol Chem. Vol. 277, No 5, pp3447-3455. 2002 [PubMed] [PDF]
●7. Tomita K, Ogawa T, Uozumi T, Watanabe K, Masaki H.
A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops.
Proc Natl Acad Sci U S A., Vol. 97, No 15, pp8278-8283, 2000 [PubMed] [PDF]
6. Fey J, Tomita K, Bergdoll M, Marechal-Drouard L.
Evolutionary and functional aspects of C-to-U editing at position 28 of tRNA(Cys)(GCA) in plant mitochondria.
RNA Vol. 6, No 4, pp470-474, 2000 [PubMed] [PDF]
5. Tomita K, Ueda T, Ishiwa S, Crain PF, McCloskey JA, Watanabe K.
Codon reading patterns in Drosophila melanogaster mitochondria based on their tRNA sequences: a unique wobble rule in animal mitochondria.
Nucleic Acids Res. Vol. 27, No21, pp4291-4297, 1999 [PubMed] [ PDF]
●4. Ogawa T, Tomita K, Ueda T, Watanabe K, Uozumi T, Masaki H.
A cytotoxic ribonuclease targeting specific transfer RNA anticodons.
Science Vol. 283, No 5410, pp2097-2100, 1999 [PubMed] [PDF]
3. Tomita K, Ueda T, Watanabe K.
The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria.
Nucleic Acids Res. Vol. 27, No 7, pp1683-1689, 1999 [PubMed] [PDF]
2. Tomita K, Ueda T, Watanabe K.
7-Methylguanosine at the anticodon wobble position of squid mitochondrial tRNA(Ser)GCU: molecular basis for assignment of AGA/AGG codons as serine in invertebrate mitochondria.
Biochim Biophys Acta. Vol. 1399, No 1, pp78-82, 1998 [PubMed] [PDF]
1. Tomita K, Ueda T, Watanabe K.
RNA editing in the acceptor stem of squid mitochondrial tRNA(Tyr).
Nucleic Acids Res. Vol. 24, No 24, pp4987-4991, 1996 [PubMed] [PDF]
Reviews
5. Yashiro Y, *Tomita K. (*corresponding)
Function and Regulation of Human Terminal Uridylyltransferases.
[Review in Current Advances in the Research of RNA Regulatory Enzymes ]
Front. Genet. doi: 10.3389/fgene.2018.00538, 2018[PubMed] [PDF]
4. *Tomita K & Liu Y. (* corresponding)
Human BCDIN3D is a cytoplasmic tRNAHis -specific 5′-monophosphate methyltransferase.
[Review in Current Advances in the Research of RNA Regulatory Enzymes ]
Front. Genet. doi: 10.3389/fgene.2018.00305, 2018 [PubMed] [PDF]
3. *Tomita K
A possible link between specific transfer RNA methylation and tumorigenic phenotype of breast cancer.
RNA & DISEASE, 4: e1530; doi: 10.14800/rd.1530, 2017 [PDF]
2. *Tomita K
Structures and Functions of Qβ Replicase: Translation factors beyond protein synthesis.
[Review in Special Issue: Functions of the Transfer RNA ]
Int. J. Mol. Sci. 15, 15552-15570; doi:10.3390/ijms150915552; 2014[abstract][PubMed]
1. *Tomita K & Yamashita S (* corresponding)
Molecular mechanisms of template-independent RNA polymerization by tRNA nucleotidyltransferases.
[Review in Molecular Biology of the Transfer RNA Revisited ]
Front. Genet. 5: 36. doi: 10.3389/fgene.2014.00036, 2014 [PubMed]
日本語総説など
18. 富田耕造
[書評] RNAの科学 ー時代を拓く生体分子ー 金井昭夫編
生化学、2024; 96 (5): 日本生化学会
17. 富田耕造
5.1 tRNA遺伝子
ヒトゲノム辞典、2021; 一色出版 ISBN：978-4-910389-12-7 [DM]
16. 八代悠歌、富田耕造
アミノアシル転移RNAを標的とするトキシンの活性制御メカニズム
生化学、2019; 91 (6): 810-814 日本生化学会
15. 富田耕造、山下征輔
古典的ncRNA、tRNAの機能
「ノンコーディングRNAーRNA分子の全体像を俯瞰する」
Dojin Bioscience 25、2016; 3-14. 化学同人
14. 富田耕造、竹下大二郎
Qβ レプリケースによるRNA合成の分子基盤
生化学、2014; 86(3): 391-395 日本生化学会
13. 富田耕造
RNA複製システムにおける生きた分子化石
「生命分子を統合するRNAーその秘められた役割と制御機構」
実験医学増刊号、2013; 31(7): 994-1000.羊土社
12. 富田耕造、竹下大二郎
QβレプリケースによるRNA合成の分子機構
細胞工学、2012; 31(10): 1154-1155. 秀潤社
11. 富田耕造
鋳型非依存的RNA合成酵素の特異性の分子基盤
生化学、2012; 84(5): 355-359. 日本生化学会
10. 富田耕造
「生命科学－つくばの研究者群像」第２章 RNAの世界 (電子版)
2011 つくばサイエンス・アカデミー
9. 富田耕造、沼田征倫
「入門 構造生物学」−放射光X線と中性子で最新の生命現象を読み解く−
– 生命現象の理解に迫る構造生物学研究 –
4.3章 「翻訳」 p111-p119. 2010 共立出版
8. 渡邉和則、董雪松、富田耕造
アミノアシルtRNA蛋白質転移酵素の基質認識、反応触媒の分子機構の解明
生化学、2009; 81(4): 294-298. 日本生化学会
7. 董雪松、 富田耕造
鋳型非依存的RNA合成酵素，CCA付加酵素のRNA合成忠実性維持の分子基盤
実験医学、2008; 26(19): :3058-3061. 羊土社出版
6. 渡邉和則、 富田耕造
tRNAを使うリボソームによらないペプチド結合形成反応
蛋白質核酸酵素、2008; 53(9):1152-1157. 共立出版
5. 富田耕造、濡木理
鋳型を用いないRNA合成の動的分子基盤の解明
蛋白質核酸酵素、2007; 52(7):784-94. 共立出版
4. 富田耕造
タンパク質合成を支えるtRNAの成熟化
生化学、2007; 79(3):222-228. 日本生化学会
3. 富田耕造
RNAの3’末端修復の分子メカニズム
実験医学、2007; 25(1):13-18. 羊土社出版
2. 富田耕造
転移RNA成熟化プロセス:tRNAの末端へのヌクレオチド付加とエディティングの分子機構の類似性
実験医学, 2005; 23(12):1875-1880.羊土社出版
1. 富田耕造、濡木理
鋳型非依存性RNA合成酵素の分子機構、進化
蛋白質核酸酵素, 2003; 48(16):2286-2292.共立出版