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For: Ochi A, Makabe K, Yamagami R, Hirata A, Sakaguchi R, Hou YM, Watanabe K, Nureki O, Kuwajima K, Hori H. The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and nonsubstrate tRNA via an induced-fit process. J Biol Chem 2013;288:25562-25574. [PMID: 23867454 DOI: 10.1074/jbc.m113.485128] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
Number Cited by Other Article(s)
1
Pierpont CL, Baroch JJ, Church MJ, Miller SR. Idiosyncratic genome evolution of the thermophilic cyanobacterium Synechococcus at the limits of phototrophy. THE ISME JOURNAL 2024;18:wrae184. [PMID: 39319368 PMCID: PMC11456837 DOI: 10.1093/ismejo/wrae184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 08/19/2024] [Accepted: 09/23/2024] [Indexed: 09/26/2024]
2
Kohno Y, Ito A, Okamoto A, Yamagami R, Hirata A, Hori H. Escherichia coli tRNA (Gm18) methyltransferase (TrmH) requires the correct localization of its methylation site (G18) in the D-loop for efficient methylation. J Biochem 2023;175:43-56. [PMID: 37844264 PMCID: PMC11640301 DOI: 10.1093/jb/mvad076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/08/2023] [Accepted: 09/27/2023] [Indexed: 10/18/2023]  Open
3
Dahlstrom TJ, Capraro DT, Jennings PA, Finke JM. Knotting Optimization and Folding Pathways of a Go-Model with a Deep Knot. J Phys Chem B 2022;126:10221-10236. [PMID: 36424347 DOI: 10.1021/acs.jpcb.2c05588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
4
Strassler SE, Bowles IE, Dey D, Jackman JE, Conn GL. Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases. J Biol Chem 2022;298:102393. [PMID: 35988649 PMCID: PMC9508554 DOI: 10.1016/j.jbc.2022.102393] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 10/25/2022]  Open
5
Kleiber N, Lemus-Diaz N, Stiller C, Heinrichs M, Mai MMQ, Hackert P, Richter-Dennerlein R, Höbartner C, Bohnsack KE, Bohnsack MT. The RNA methyltransferase METTL8 installs m3C32 in mitochondrial tRNAsThr/Ser(UCN) to optimise tRNA structure and mitochondrial translation. Nat Commun 2022;13:209. [PMID: 35017528 PMCID: PMC8752778 DOI: 10.1038/s41467-021-27905-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/14/2021] [Indexed: 12/30/2022]  Open
6
Motorin Y, Helm M. RNA nucleotide methylation: 2021 update. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022;13:e1691. [PMID: 34913259 DOI: 10.1002/wrna.1691] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 12/14/2022]
7
Danchin A, Sekowska A, You C. One-carbon metabolism, folate, zinc and translation. Microb Biotechnol 2020;13:899-925. [PMID: 32153134 PMCID: PMC7264889 DOI: 10.1111/1751-7915.13550] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022]  Open
8
Hirata A, Okada K, Yoshii K, Shiraishi H, Saijo S, Yonezawa K, Shimizu N, Hori H. Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition. Nucleic Acids Res 2020;47:10942-10955. [PMID: 31586407 PMCID: PMC6847430 DOI: 10.1093/nar/gkz856] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/20/2019] [Accepted: 10/02/2019] [Indexed: 12/18/2022]  Open
9
Barraud P, Tisné C. To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs. IUBMB Life 2019;71:1126-1140. [PMID: 30932315 PMCID: PMC6850298 DOI: 10.1002/iub.2041] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/10/2019] [Indexed: 12/12/2022]
10
Hori H. Regulatory Factors for tRNA Modifications in Extreme- Thermophilic Bacterium Thermus thermophilus. Front Genet 2019;10:204. [PMID: 30906314 PMCID: PMC6418473 DOI: 10.3389/fgene.2019.00204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/26/2019] [Indexed: 01/02/2023]  Open
11
RNA Modifications Modulate Activation of Innate Toll-Like Receptors. Genes (Basel) 2019;10:genes10020092. [PMID: 30699960 PMCID: PMC6410116 DOI: 10.3390/genes10020092] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 12/13/2022]  Open
12
Krishnamohan A, Jackman JE. A Family Divided: Distinct Structural and Mechanistic Features of the SpoU-TrmD (SPOUT) Methyltransferase Superfamily. Biochemistry 2018;58:336-345. [PMID: 30457841 DOI: 10.1021/acs.biochem.8b01047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
13
Hori H, Kawamura T, Awai T, Ochi A, Yamagami R, Tomikawa C, Hirata A. Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA. Microorganisms 2018;6:E110. [PMID: 30347855 PMCID: PMC6313347 DOI: 10.3390/microorganisms6040110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022]  Open
14
McKenney KM, Rubio MAT, Alfonzo JD. Binding synergy as an essential step for tRNA editing and modification enzyme codependence in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2018;24:56-66. [PMID: 29042505 PMCID: PMC5733570 DOI: 10.1261/rna.062893.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/02/2017] [Indexed: 05/10/2023]
15
Tomikawa C, Takai K, Hori H. Kinetic characterization of substrate-binding sites of thermostable tRNA methyltransferase (TrmB). J Biochem 2017;163:133-142. [DOI: 10.1093/jb/mvx068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/01/2017] [Indexed: 11/13/2022]  Open
16
Transfer RNA methyltransferases with a SpoU-TrmD  (SPOUT) fold and their modified nucleosides in  tRNA. Biomolecules 2017;7:biom7010023. [PMID: 28264529 PMCID: PMC5372735 DOI: 10.3390/biom7010023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 02/23/2017] [Indexed: 11/22/2022]  Open
17
Jackson SE, Suma A, Micheletti C. How to fold intricately: using theory and experiments to unravel the properties of knotted proteins. Curr Opin Struct Biol 2016;42:6-14. [PMID: 27794211 DOI: 10.1016/j.sbi.2016.10.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/06/2016] [Accepted: 10/03/2016] [Indexed: 11/15/2022]
18
Christian T, Sakaguchi R, Perlinska AP, Lahoud G, Ito T, Taylor EA, Yokoyama S, Sulkowska JI, Hou YM. Methyl transfer by substrate signaling from a knotted protein fold. Nat Struct Mol Biol 2016;23:941-948. [PMID: 27571175 PMCID: PMC5429141 DOI: 10.1038/nsmb.3282] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/27/2016] [Indexed: 12/13/2022]
19
Rana AK, Ankri S. Reviving the RNA World: An Insight into the Appearance of RNA Methyltransferases. Front Genet 2016;7:99. [PMID: 27375676 PMCID: PMC4893491 DOI: 10.3389/fgene.2016.00099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/23/2016] [Indexed: 12/13/2022]  Open
20
Zhou M, Long T, Fang ZP, Zhou XL, Liu RJ, Wang ED. Identification of determinants for tRNA substrate recognition by Escherichia coli C/U34 2'-O-methyltransferase. RNA Biol 2016;12:900-11. [PMID: 26106808 PMCID: PMC4615657 DOI: 10.1080/15476286.2015.1050576] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
21
Yamagami R, Tomikawa C, Shigi N, Kazayama A, Asai SI, Takuma H, Hirata A, Fourmy D, Asahara H, Watanabe K, Yoshizawa S, Hori H. Folate-/FAD-dependent tRNA methyltransferase from Thermus thermophilus regulates other modifications in tRNA at low temperatures. Genes Cells 2016;21:740-54. [PMID: 27238446 DOI: 10.1111/gtc.12376] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/19/2016] [Indexed: 11/29/2022]
22
Swinehart WE, Jackman JE. Diversity in mechanism and function of tRNA methyltransferases. RNA Biol 2016;12:398-411. [PMID: 25626150 DOI: 10.1080/15476286.2015.1008358] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]  Open
23
Hori H, Terui Y, Nakamoto C, Iwashita C, Ochi A, Watanabe K, Oshima T. Effects of polyamines from Thermus thermophilus, an extreme-thermophilic eubacterium, on tRNA methylation by tRNA (Gm18) methyltransferase (TrmH). J Biochem 2015;159:509-17. [PMID: 26721905 DOI: 10.1093/jb/mvv130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/05/2015] [Indexed: 12/13/2022]  Open
24
Liu RJ, Long T, Zhou M, Zhou XL, Wang ED. tRNA recognition by a bacterial tRNA Xm32 modification enzyme from the SPOUT methyltransferase superfamily. Nucleic Acids Res 2015. [PMID: 26202969 PMCID: PMC4551947 DOI: 10.1093/nar/gkv745] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
25
Takuma H, Ushio N, Minoji M, Kazayama A, Shigi N, Hirata A, Tomikawa C, Ochi A, Hori H. Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI). J Biol Chem 2015;290:5912-25. [PMID: 25593312 DOI: 10.1074/jbc.m114.606038] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
26
A divalent metal ion-dependent N(1)-methyl transfer to G37-tRNA. ACTA ACUST UNITED AC 2014;21:1351-1360. [PMID: 25219964 DOI: 10.1016/j.chembiol.2014.07.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/20/2014] [Accepted: 07/22/2014] [Indexed: 01/09/2023]
27
Somme J, Van Laer B, Roovers M, Steyaert J, Versées W, Droogmans L. Characterization of two homologous 2'-O-methyltransferases showing different specificities for their tRNA substrates. RNA (NEW YORK, N.Y.) 2014;20:1257-71. [PMID: 24951554 PMCID: PMC4105751 DOI: 10.1261/rna.044503.114] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 05/08/2014] [Indexed: 05/18/2023]
28
Subramanian M, Srinivasan T, Sudarsanam D. Examining the Gm18 and m(1)G Modification Positions in tRNA Sequences. Genomics Inform 2014;12:71-5. [PMID: 25031570 PMCID: PMC4099351 DOI: 10.5808/gi.2014.12.2.71] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/20/2014] [Accepted: 03/26/2014] [Indexed: 12/30/2022]  Open
29
Hori H. Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet 2014;5:144. [PMID: 24904644 PMCID: PMC4033218 DOI: 10.3389/fgene.2014.00144] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/04/2014] [Indexed: 12/26/2022]  Open
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