Genomes and Genes
Summary: Enzymes that catalyze the S-adenosyl-L-methionine-dependent methylation of ribonucleotide bases within a transfer RNA molecule. EC 2.1.1.
- Gordon O, Taxis C, Keller P, Benjak A, Stelzer E, Simchen G, et al. Nud1p, the yeast homolog of Centriolin, regulates spindle pole body inheritance in meiosis. EMBO J. 2006;25:3856-68 pubmed..Both functions of Nud1p are connected to the ability of Spc72p to bind to the outer plaque and half-bridge (via Kar1p) of the SPB. ..
- Alian A, Lee T, Griner S, Stroud R, Finer Moore J. Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases. Proc Natl Acad Sci U S A. 2008;105:6876-81 pubmed publisher..Loop residues other than the target U54 make more than half of their hydrogen bonds to the protein via sugar-phosphate moieties, accounting, in part, for the broad consensus sequence for TrmA substrates. ..
- Lindström P, Stuber D, Björk G. Genetic organization and transcription from the gene (trmA) responsible for synthesis of tRNA (uracil-5)-methyltransferase by Escherichia coli. J Bacteriol. 1985;164:1117-23 pubmed..coli K-12 chromosomal map. The level of transcription of trmA in vitro and the expression of protein in minicells equal those of the bla gene of plasmid pBR322. ..
- Muller S, Windhof I, Maximov V, Jurkowski T, Jeltsch A, Förstner K, et al. Target recognition, RNA methylation activity and transcriptional regulation of the Dictyostelium discoideum Dnmt2-homologue (DnmA). Nucleic Acids Res. 2013;41:8615-27 pubmed publisher..As expression levels and binding of DnmA to a target in vivo are apparently not necessarily accompanied by methylation, we propose an additional biological function of DnmA apart from methylation. ..
- Mazauric M, Dirick L, Purushothaman S, Bjork G, Lapeyre B. Trm112p is a 15-kDa zinc finger protein essential for the activity of two tRNA and one protein methyltransferases in yeast. J Biol Chem. 2010;285:18505-15 pubmed publisher..Trm112p is associated with other partners involved in ribosome biogenesis and chromatin remodeling, suggesting that it has additional roles in the cell. ..
- Walbott H, Leulliot N, Grosjean H, Golinelli Pimpaneau B. The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity. Nucleic Acids Res. 2008;36:4929-40 pubmed publisher..We also predict that a large TPsiC loop conformational change has to occur for the flipping of the target uridine into the (Pab)TrmU54 active site during catalysis...
- Tomikawa C, Ochi A, Hori H. The C-terminal region of thermophilic tRNA (m7G46) methyltransferase (TrmB) stabilizes the dimer structure and enhances fidelity of methylation. Proteins. 2008;71:1400-8 pubmed..Moreover, the modified base was identified as m(7)G by two-dimensional thin layer chromatography. Thus, the deletion of the C-terminal region causes nonspecific methylation of N(7) atom of guanine base(s) in tRNA transcripts. ..
- Lee C, Kramer G, Graham D, Appling D. Yeast mitochondrial initiator tRNA is methylated at guanosine 37 by the Trm5-encoded tRNA (guanine-N1-)-methyltransferase. J Biol Chem. 2007;282:27744-53 pubmed..These data suggest that this tRNA modification plays an important role in reading frame maintenance in mitochondrial protein synthesis. ..
- Purushothaman S, Bujnicki J, Grosjean H, Lapeyre B. Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA. Mol Cell Biol. 2005;25:4359-70 pubmed..Indeed, Trm112p is associated with at least four proteins: two tRNA methyltransferases (Trm9p and Trm11p), one putative protein methyltransferase (Mtc6p/Ydr140w), and one protein with a ..
- Gustafsson C, Björk G. The tRNA-(m5U54)-methyltransferase of Escherichia coli is present in two forms in vivo, one of which is present as bound to tRNA and to a 3'-end fragment of 16 S rRNA. J Biol Chem. 1993;268:1326-31 pubmed..However, the complex is not associated with the ribosome and the covalently bound RNA does not affect the tRNA methylating activity of the enzyme. ..
- Gu X, Ivanetich K, Santi D. Recognition of the T-arm of tRNA by tRNA (m5U54)-methyltransferase is not sequence specific. Biochemistry. 1996;35:11652-9 pubmed..Surprisingly, recognition of tRNA by RUMT appears to reside in the three-dimensional structure of the seven-member T-loop rather than in its primary structure. ..
- Anderson J, Phan L, Hinnebusch A. The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2000;97:5173-8 pubmed..Our results provide a demonstration of a two-component tRNA MTase and suggest that binding of AdoMet and tRNA substrates depends on different subunits of the complex. ..
- Kuratani M, Bessho Y, Nishimoto M, Grosjean H, Yokoyama S. Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA. J Mol Biol. 2008;375:1064-75 pubmed publisher..However, an essential Arg16 residue is located at a novel position within motif I. Biochemical assays showed that aTrm56 prefers the L-shaped tRNA to the lambda form as its substrate...
- Ozanick S, Bujnicki J, Sem D, Anderson J. Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding. Nucleic Acids Res. 2007;35:6808-19 pubmed
- Urbonavicius J, Auxilien S, Walbott H, Trachana K, Golinelli Pimpaneau B, Brochier Armanet C, et al. Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer. Mol Microbiol. 2008;67:323-35 pubmed..This functional shift probably occurred in an ancestor of all Thermococcales. This study also provides new evidence in favour of a close relationship between Thermococcales and Nanoarchaea...
- Hagervall T, Edmonds C, McCloskey J, Björk G. Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities. J Biol Chem. 1987;262:8488-95 pubmed..The molecular activity of the methyltransferase activity (nm5s2U34----mnm5s2U34) is 74 min-1, and the steady state concentration of the enzyme is only 78 molecules/genome equivalent in cells growing at a specific growth rate of 1.0/h. ..
- Ny T, Björk G. Cloning and restriction mapping of the trmA gene coding for transfer ribonucleic acid (5-methyluridine)-methyltransferase in Escherichia coli K-12. J Bacteriol. 1980;142:371-9 pubmed..This polypeptide was tentatively identified as the tRNA(m5U)methyltransferase. These results support the earlier suggestion that the trmA gene is the structural gene for the tRNA(m5U)methyltransferase. ..
- Guan M, Yan Q, Li X, Bykhovskaya Y, Gallo Teran J, Hajek P, et al. Mutation in TRMU related to transfer RNA modification modulates the phenotypic expression of the deafness-associated mitochondrial 12S ribosomal RNA mutations. Am J Hum Genet. 2006;79:291-302 pubmed..These findings indicate that the mutated TRMU, acting as a modifier factor, modulates the phenotypic manifestation of the deafness-associated 12S rRNA mutations. ..
- Madsen C, Mengel Jørgensen J, Kirpekar F, Douthwaite S. Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res. 2003;31:4738-46 pubmed..coli m(5)U RNA methyltransferases are identified, and a more appropriate designation for YbjF would be RumB (RNA uridine methyltransferases B), in line with the recent nomenclature change for YgcA (now RumA). ..
- Schara U, von Kleist Retzow J, Lainka E, Gerner P, Pyle A, Smith P, et al. Acute liver failure with subsequent cirrhosis as the primary manifestation of TRMU mutations. J Inherit Metab Dis. 2011;34:197-201 pubmed publisher..We suggest that TRMU deficiency should be considered in infants with acute liver disease. ..
- Pintard L, Lecointe F, Bujnicki J, Bonnerot C, Grosjean H, Lapeyre B. Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop. EMBO J. 2002;21:1811-20 pubmed..We propose that each eukaryotic enzyme is located in a different cell compartment, in which it would methylate a different RNA that can adopt a very similar secondary structure. ..
- Nishimasu H, Ishitani R, Yamashita K, Iwashita C, Hirata A, Hori H, et al. Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase. Proc Natl Acad Sci U S A. 2009;106:8180-5 pubmed publisher..Our TrmFO-tRNA docking model, in combination with mutational analyses, suggests a catalytic mechanism, in which the methylene of MTHF is directly transferred onto U54, and then the exocyclic methylene of U54 is reduced by FADH(2)...
- Sasarman F, Antonicka H, Horvath R, Shoubridge E. The 2-thiouridylase function of the human MTU1 (TRMU) enzyme is dispensable for mitochondrial translation. Hum Mol Genet. 2011;20:4634-43 pubmed publisher..This study demonstrates that MTU1 is not required for mitochondrial translation at normal steady-state levels of tRNAs, and that it may possess an as yet uncharacterized function in another sulfur-trafficking pathway...
- Christian T, Lahoud G, Liu C, Hoffmann K, Perona J, Hou Y. Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5. RNA. 2010;16:2484-92 pubmed publisher..Key roles for the conserved R145 side chain in stabilizing a proposed oxyanion at G37-O(6), and for E185 as a general base to accept the proton from G37-N(1), are suggested based on the mutational analysis. ..
- Guelorget A, Roovers M, Gu rineau V, Barbey C, Li X, Golinelli Pimpaneau B. Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase. Nucleic Acids Res. 2010;38:6206-18 pubmed publisher..When A59 is absent in tRNA(Asp), only A57 is modified. Identification of the methylated positions in tRNAAsp by mass spectrometry confirms that (Pab)TrmI methylates the first adenine of an AA sequence...
- Hayrapetyan A, Grosjean H, Helm M. Effect of a quaternary pentamine on RNA stabilization and enzymatic methylation. Biol Chem. 2009;390:851-61 pubmed publisher..heat denaturation, electrophoretic behavior, and ability of tRNA to be methylated in vitro by purified tRNA methyltransferases under various salt conditions...
- Ochi A, Makabe K, Kuwajima K, Hori H. Flexible recognition of the tRNA G18 methylation target site by TrmH methyltransferase through first binding and induced fit processes. J Biol Chem. 2010;285:9018-29 pubmed publisher..The result clearly showed that the binding of TrmH to tRNA is composed of at least three steps, the first bi-molecular binding and the subsequent two uni-molecular induced-fit processes...
- Brzezicha B, Schmidt M, Makalowska I, Jarmolowski A, Pienkowska J, Szweykowska Kulinska Z. Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the pre-tRNA Leu (CAA). Nucleic Acids Res. 2006;34:6034-43 pubmed..To our knowledge, this is the first report showing intron-dependent methylation of humanpre-tRNA Leu (CAA) and identification of human gene encoding tRNA methylase responsible for this reaction. ..
- Persson B, J ger G, Gustafsson C. The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2'-O-methyltransferase activity. Nucleic Acids Res. 1997;25:4093-7 pubmed..We suggest that the spoU gene be renamed trmH (tRNA methylation)...
- Takeda H, Toyooka T, Ikeuchi Y, Yokobori S, Okadome K, Takano F, et al. The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus. Genes Cells. 2006;11:1353-65 pubmed..Recently, it was reported that E. coli TrmD methylates yeast tRNA(Phe) harboring a sequence A36G37. Thus, recognition of the purine36G37 sequence is probably common to eubacteria TrmD proteins. ..
- Gu X, Santi D. Covalent adducts between tRNA (m5U54)-methyltransferase and RNA substrates. Biochemistry. 1992;31:10295-302 pubmed..It is speculated that covalent binary RUMT-RNA adducts may serve as depots of enzyme-tRNA complexes primed for methylation, or in unknown roles with RNAs other than tRNA. ..
- Gu W, Hurto R, Hopper A, Grayhack E, Phizicky E. Depletion of Saccharomyces cerevisiae tRNA(His) guanylyltransferase Thg1p leads to uncharged tRNAHis with additional m(5)C. Mol Cell Biol. 2005;25:8191-201 pubmed..We developed a new method to map m(5)C residues in RNA and localized the additional m(5)C to positions 48 and 50. This is the first documented example of the accumulation of additional modifications in a eukaryotic tRNA species. ..
- Gruneberg U, Campbell K, Simpson C, Grindlay J, Schiebel E. Nud1p links astral microtubule organization and the control of exit from mitosis. EMBO J. 2000;19:6475-88 pubmed..Thus, in nud1-2 cells the failure of Tem1p to interact with Cdc15p at the SPB probably prevents mitotic exit. ..
- Urbonavicius J, Durand J, Bj rk G. Three modifications in the D and T arms of tRNA influence translation in Escherichia coli and expression of virulence genes in Shigella flexneri. J Bacteriol. 2002;184:5348-57 pubmed..Moreover, lack of Psi55 in tRNA of human pathogen Shigella flexneri leads to a reduced expression of several virulence-associated genes...
- Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H, et al. Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure. 2004;12:593-602 pubmed publisher..Based on Gua18 modeling onto the active site, we propose that once Gua18 binds, the phosphate group activates Arg41, which then deprotonates the 2'-OH group for methylation...
- Kalhor H, Clarke S. Novel methyltransferase for modified uridine residues at the wobble position of tRNA. Mol Cell Biol. 2003;23:9283-92 pubmed..These results suggest a role for this potentially reversible methyl esterification reaction when cells are under stress. ..
- Kealey J, Santi D. Identification of the catalytic nucleophile of tRNA (m5U54)methyltransferase. Biochemistry. 1991;30:9724-8 pubmed..The tritium was shown to be associated with Cys 324 of the methyltransferase, which unequivocally identifies this residue as the catalytic nucleophile. ..
- Becker M, Muller S, Nellen W, Jurkowski T, Jeltsch A, Ehrenhofer Murray A. Pmt1, a Dnmt2 homolog in Schizosaccharomyces pombe, mediates tRNA methylation in response to nutrient signaling. Nucleic Acids Res. 2012;40:11648-58 pubmed publisher..Taken together, this work reveals a novel connection between nutrient signaling and tRNA methylation that thus may link tRNA methylation to processes downstream of nutrient signaling like ribosome biogenesis and translation initiation. ..
- Yao L, James T, Kealey J, Santi D, Schmitz U. The dynamic NMR structure of the T psi C-loop: implications for the specificity of tRNA methylation. J Biomol NMR. 1997;9:229-44 pubmed..For the methylation, RUMT would simply have to break the tertiary interactions between the D- and T-loops, leading to a melting of the T-arm structure and making U54 available for methylation. ..
- Adams I, Kilmartin J. Localization of core spindle pole body (SPB) components during SPB duplication in Saccharomyces cerevisiae. J Cell Biol. 1999;145:809-23 pubmed..We present a model for SPB duplication where binding of SPB components to either end of the bridge structure ensures two separate SPBs. ..
- Songe Møller L, van den Born E, Leihne V, Vågbø C, Kristoffersen T, Krokan H, et al. Mammalian ALKBH8 possesses tRNA methyltransferase activity required for the biogenesis of multiple wobble uridine modifications implicated in translational decoding. Mol Cell Biol. 2010;30:1814-27 pubmed publisher..However, the selenocysteine-specific tRNA (tRNASec) is aberrantly modified in the Alkbh8-/- mice, and for the selenoprotein Gpx1, we indeed observed reduced recoding of the UGA stop codon to selenocysteine. ..
- Bujnicki J, Feder M, Ayres C, Redman K. Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases. Nucleic Acids Res. 2004;32:2453-63 pubmed
- Barraud P, Golinelli Pimpaneau B, Atmanene C, Sanglier S, Van Dorsselaer A, Droogmans L, et al. Crystal structure of Thermus thermophilus tRNA m1A58 methyltransferase and biophysical characterization of its interaction with tRNA. J Mol Biol. 2008;377:535-50 pubmed publisher..From our results, we propose that the conserved residues that form the catalytic cavity (D170, Y78, and Y194) are essential for fashioning an optimized shape of the catalytic pocket. ..
- De Crecy Lagard V, Marck C, Brochier Armanet C, Grosjean H. Comparative RNomics and modomics in Mollicutes: prediction of gene function and evolutionary implications. IUBMB Life. 2007;59:634-58 pubmed
- Agarwalla S, Kealey J, Santi D, Stroud R. Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli. J Biol Chem. 2002;277:8835-40 pubmed..We propose to name this gene rumA and accordingly name the protein product as RumA for RNA uridine methyltransferase. ..
- Yan Q, Li X, Faye G, Guan M. Mutations in MTO2 related to tRNA modification impair mitochondrial gene expression and protein synthesis in the presence of a paromomycin resistance mutation in mitochondrial 15 S rRNA. J Biol Chem. 2005;280:29151-7 pubmed..These functional conservations imply that human MTO2 may act as a modifier gene, modulating the phenotypic expression of the deafness-associated A1491G or C1409T mutation in mitochondrial 12 S rRNA. ..
- Chen B, Sun D, Yang L, Zhang C, Yang A, Zhu Y, et al. Mitochondrial ND5 T12338C, tRNA(Cys) T5802C, and tRNA(Thr) G15927A variants may have a modifying role in the phenotypic manifestation of deafness-associated 12S rRNA A1555G mutation in three Han Chinese pedigrees. Am J Med Genet A. 2008;146A:1248-58 pubmed publisher..Therefore, these mtDNA mutations may have a potential modifier role in increasing the penetrance and expressivity of the deafness-associated 12S rRNA A1555G mutation in those Chinese pedigrees. ..
- Goto Ito S, Ito T, Ishii R, Muto Y, Bessho Y, Yokoyama S. Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5. Proteins. 2008;72:1274-89 pubmed publisher..The positive charges on the surface of D2-D3 may be involved in tRNA binding. Therefore, these findings suggest that the interaction between D1 and D3 is not persistent, and that the D2-D3 region plays the major role in tRNA methylation...
- Matsumoto K, Toyooka T, Tomikawa C, Ochi A, Takano Y, Takayanagi N, et al. RNA recognition mechanism of eukaryote tRNA (m7G46) methyltransferase (Trm8-Trm82 complex). FEBS Lett. 2007;581:1599-604 pubmed..The tertiary base pairs were important but not essential for the methyl-transfer to yeast tRNA(Phe) transcript, suggesting that these base pairs support the induced fit of the G46 base into the catalytic pocket. ..
- Studte P, Zink S, Jablonowski D, Bär C, von der Haar T, Tuite M, et al. tRNA and protein methylase complexes mediate zymocin toxicity in yeast. Mol Microbiol. 2008;69:1266-77 pubmed publisher..Sup35, we observe that SUP45 overexpression and sup45 mutants suppress zymocin. Intriguingly, this suppression correlates with upregulated levels of tRNA species targeted by zymocin's tRNase activity. ..
- Motorin Y, Helm M. RNA nucleotide methylation. Wiley Interdiscip Rev RNA. 2011;2:611-31 pubmed publisher..WIREs RNA 2011 2 611-631 DOI: 10.1002/wrna.79 For further resources related to this article, please visit the WIREs website. ..