Two-subunit enzymes involved in eukaryotic post-transcriptional tRNA modification

References

• Hopper AK. Transfer RNA post-transcriptional processing, turnover, and subcellular dynamics in the yeast Saccharomyces cerevisiae. Genetics 2013; 194:43-67; PMID:23633143; http://dx.doi.org/10.1534/genetics.112.147470
   PubMed Web of Science ®Google Scholar
• El Yacoubi B, Bailly M, de Crecy-Lagard V. Biosynthesis and function of posttranscriptional modifications of transfer RNAs. Ann Rev Genet 2012; 46:69-95; PMID:22905870; http://dx.doi.org/10.1146/annurev-genet-110711-155641
   PubMedGoogle Scholar
• Purushothaman SK, Bujnicki JM, 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; PMID:15899842; http://dx.doi.org/10.1128/MCB.25.11.4359-4370.2005
   PubMed Web of Science ®Google Scholar
• Heurgue-Hamard V, Graille M, Scrima N, Ulryck N, Champ S, van Tilbeurgh H, Buckingham RH. The zinc finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. J Biol Chem 2006; 281:36140-8; PMID:17008308; http://dx.doi.org/10.1074/jbc.M608571200
   PubMedGoogle Scholar
• Mazauric MH, Dirick L, Purushothaman SK, Bjork GR, 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; PMID:20400505; http://dx.doi.org/10.1074/jbc.M110.113100
   PubMed Web of Science ®Google Scholar
• Chen C, Huang B, Anderson JT, Bystrom AS. Unexpected accumulation of ncm(5)U and ncm(5)S(2) (U) in a trm9 mutant suggests an additional step in the synthesis of mcm(5)U and mcm(5)S(2)U. PloS one 2011; 6:e20783; PMID:21687733; http://dx.doi.org/10.1371/journal.pone.0020783
   PubMed Web of Science ®Google Scholar
• Figaro S, Wacheul L, Schillewaert S, Graille M, Huvelle E, Mongeard R, Zorbas C, Lafontaine DL, Heurgue-Hamard V. Trm112 is required for Bud23-mediated methylation of the 18S rRNA at position G1575. Mol Cell Biol 2012; 32:2254-67; PMID:22493060; http://dx.doi.org/10.1128/MCB.06623-11
   PubMed Web of Science ®Google Scholar
• Sardana R, Johnson AW. The methyltransferase adaptor protein Trm112 is involved in biogenesis of both ribosomal subunits. Mol Biol Cell 2012; 23:4313-22; PMID:22956767; http://dx.doi.org/10.1091/mbc.E12-05-0370
   PubMedGoogle Scholar
• Pintard L, Lecointe F, Bujnicki JM, 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; PMID:11927565; http://dx.doi.org/10.1093/emboj/21.7.1811
   PubMed Web of Science ®Google Scholar
• Guy MP, Podyma BM, Preston MA, Shaheen HH, Krivos KL, Limbach PA, Hopper AK, Phizicky EM. Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop. RNA 2012; 18:1921-33; PMID:22912484; http://dx.doi.org/10.1261/rna.035287.112
   PubMed Web of Science ®Google Scholar
• Guy MP, Phizicky EM. Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes. RNA 2015; 21:61-74; PMID:25404562; http://dx.doi.org/10.1261/rna.047639.114
   PubMedGoogle Scholar
• Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, et al. The minimal gene complement of Mycoplasma genitalium. Science 1995; 270:397-403; PMID:7569993; http://dx.doi.org/10.1126/science.270.5235.397
   PubMed Web of Science ®Google Scholar
• Machnicka MA, Milanowska K, Osman Oglou O, Purta E, Kurkowska M, Olchowik A, Januszewski W, Kalinowski S, Dunin-Horkawicz S, Rother KM, et al. MODOMICS: a database of RNA modification pathways–2013 update. Nucleic Acids Res 2013; 41:D262-7; PMID:23118484; http://dx.doi.org/10.1093/nar/gks1007
   PubMed Web of Science ®Google Scholar
• Agris PF, Vendeix FA, Graham WD. tRNA's wobble decoding of the genome: 40 years of modification. J Mol Biol 2007; 366:1-13; PMID:17187822; http://dx.doi.org/10.1016/j.jmb.2006.11.046
   PubMed Web of Science ®Google Scholar
• Helm M, Giege R, Florentz C. A Watson-Crick base-pair-disrupting methyl group (m1A9) is sufficient for cloverleaf folding of human mitochondrial tRNALys. Biochemistry 1999; 38:13338-46; PMID:10529209; http://dx.doi.org/10.1021/bi991061g
   PubMed Web of Science ®Google Scholar
• Kadaba S, Krueger A, Trice T, Krecic AM, Hinnebusch AG, Anderson J. Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae. Genes Dev 2004; 18:1227-40; PMID:15145828; http://dx.doi.org/10.1101/gad.1183804
   PubMed Web of Science ®Google Scholar
• Alexandrov A, Chernyakov I, Gu W, Hiley SL, Hughes TR, Grayhack EJ, Phizicky EM. Rapid tRNA decay can result from lack of nonessential modifications. Mol Cell 2006; 21:87-96; PMID:16387656; http://dx.doi.org/10.1016/j.molcel.2005.10.036
   PubMed Web of Science ®Google Scholar
• Grosjean H. Nucleic acids are not boring long polymers of only four types of nucleotides: a guided tour. In: Grosjean H, ed. DNA and RNA Modification Enzymes: Structure Mechanism, Function and Evolution. Austin, TX: Landes Bioscience, 2009:1-12.
   Google Scholar
• Phizicky EM, Hopper AK. tRNA biology charges to the front. Genes Dev 2010; 24:1832-60; PMID:20810645; http://dx.doi.org/10.1101/gad.1956510
   PubMed Web of Science ®Google Scholar
• Torres AG, Batlle E, Ribas de Pouplana L. Role of tRNA modifications in human diseases. Trends in Mol Med 2014; 20:306-14; http://dx.doi.org/10.1016/j.molmed.2014.01.008
   PubMed Web of Science ®Google Scholar
• Sprinzl M, Grueter F, Spelzhaus A, Gauss DH. Compilation of tRNA sequences. Nucleic Acids Res 1980; 8:r1-r22; PMID:6986608; http://dx.doi.org/10.1093/nar/8.1.1
   PubMedGoogle Scholar
• Kammen HO, Marvel CC, Hardy L, Penhoet EE. Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase I. J Biol Chem 1988; 263:2255-63; PMID:3276686
   PubMed Web of Science ®Google Scholar
• Lecointe F, Simos G, Sauer A, Hurt EC, Motorin Y, Grosjean H. Characterization of yeast protein Deg1 as pseudouridine synthase (Pus3) catalyzing the formation of psi 38 and psi 39 in tRNA anticodon loop. J Biol Chem 1998; 273:1316-23; PMID:9430663; http://dx.doi.org/10.1074/jbc.273.3.1316
   PubMed Web of Science ®Google Scholar
• Blaby IK, Majumder M, Chatterjee K, Jana S, Grosjean H, de Crecy-Lagard V, Gupta R. Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii. RNA 2011; 17:1367-80; PMID:21628430; http://dx.doi.org/10.1261/rna.2712811
   PubMedGoogle Scholar
• Kaya Y, Ofengand J. A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. RNA 2003; 9:711-21; PMID:12756329; http://dx.doi.org/10.1261/rna.5230603
   PubMedGoogle Scholar
• Behm-Ansmant I, Urban A, Ma X, Yu YT, Motorin Y, Branlant C. The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Psi-synthase also acting on tRNAs. RNA 2003; 9:1371-82; PMID:14561887; http://dx.doi.org/10.1261/rna.5520403
   PubMed Web of Science ®Google Scholar
• Muller S, Urban A, Hecker A, Leclerc F, Branlant C, Motorin Y. Deficiency of the tRNATyr:Psi 35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ACA sRNA-guided machinery. Nucleic Acids Res 2009; 37:1308-22; PMID:19139072; http://dx.doi.org/10.1093/nar/gkn1037
   PubMed Web of Science ®Google Scholar
• El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crecy-Lagard V. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. Nucleic Acids Res 2009; 37:2894-909; PMID:19287007; http://dx.doi.org/10.1093/nar/gkp152
   PubMedGoogle Scholar
• El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG, de Crecy-Lagard V. A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J 2011; 30:882-93; PMID:21285948; http://dx.doi.org/10.1038/emboj.2010.363
   PubMed Web of Science ®Google Scholar
• Srinivasan M, Mehta P, Yu Y, Prugar E, Koonin EV, Karzai AW, Sternglanz R. The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A. EMBO J 2011; 30:873-81; PMID:21183954; http://dx.doi.org/10.1038/emboj.2010.343
   PubMed Web of Science ®Google Scholar
• Deutsch C, El Yacoubi B, de Crecy-Lagard V, Iwata-Reuyl D. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem 2012; 287:13666-73; PMID:22378793; http://dx.doi.org/10.1074/jbc.M112.344028
   PubMed Web of Science ®Google Scholar
• Perrochia L, Crozat E, Hecker A, Zhang W, Bareille J, Collinet B, van Tilbeurgh H, Forterre P, Basta T. In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya. Nucleic Acids Res 2013; 41:1953-64; PMID:23258706; http://dx.doi.org/10.1093/nar/gks1287
   PubMed Web of Science ®Google Scholar
• Bystrom AS, Hjalmarsson KJ, Wikstrom PM, Bjork GR. The nucleotide sequence of an Escherichia coli operon containing genes for the tRNA(m1G)methyltransferase, the ribosomal proteins S16 and L19 and a 21-K polypeptide. EMBO J 1983; 2:899-905; PMID:6357787
   PubMed Web of Science ®Google Scholar
• Bjork GR, Jacobsson K, Nilsson K, Johansson MJ, Bystrom AS, Persson OP. A primordial tRNA modification required for the evolution of life? EMBO J 2001; 20:231-9; PMID:11226173; http://dx.doi.org/10.1093/emboj/20.1.231
   PubMed Web of Science ®Google Scholar
• Gupta A, Kumar PH, Dineshkumar TK, Varshney U, Subramanya HS. Crystal structure of Rv2118c: an AdoMet-dependent methyltransferase from Mycobacterium tuberculosis H37Rv. J Mol Biol 2001; 312:381-91; PMID:11554794; http://dx.doi.org/10.1006/jmbi.2001.4935
   PubMedGoogle Scholar
• Losey HC, Ruthenburg AJ, Verdine GL. Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA. Nat Struct Mol Biol 2006; 13:153-9; PMID:16415880; http://dx.doi.org/10.1038/nsmb1047
   PubMed Web of Science ®Google Scholar
• Barraud P, Golinelli-Pimpaneau B, Atmanene C, Sanglier S, Van Dorsselaer A, Droogmans L, Dardel F, Tisne C. Crystal structure of Thermus thermophilus tRNA m1A58 methyltransferase and biophysical characterization of its interaction with tRNA. J Mol Biol 2008; 377:535-50; PMID:18262540; http://dx.doi.org/10.1016/j.jmb.2008.01.041
   PubMed Web of Science ®Google Scholar
• Elias Y, Huang RH. Biochemical and structural studies of A-to-I editing by tRNA:A34 deaminases at the wobble position of transfer RNA. Biochemistry 2005; 44:12057-65; PMID:16142903; http://dx.doi.org/10.1021/bi050499f
   PubMedGoogle Scholar
• Spears JL, Rubio MA, Gaston KW, Wywial E, Strikoudis A, Bujnicki JM, Papavasiliou FN, Alfonzo JD. A single zinc ion is sufficient for an active Trypanosoma brucei tRNA editing deaminase. J Biol Chem 2011; 286:20366-74; PMID:21507956; http://dx.doi.org/10.1074/jbc.M111.243568
   PubMedGoogle Scholar
• Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 2009; 37:D93-7; PMID:18984615; http://dx.doi.org/10.1093/nar/gkn787
   PubMed Web of Science ®Google Scholar
• Aldinger CA, Leisinger AK, Gaston KW, Limbach PA, Igloi GL. The absence of A-to-I editing in the anticodon of plant cytoplasmic tRNA (Arg) ACG demands a relaxation of the wobble decoding rules. RNA Biol 2012; 9:1239-46; PMID:22922796; http://dx.doi.org/10.4161/rna.21839
   PubMed Web of Science ®Google Scholar
• Crick FH. Codon–anticodon pairing: the wobble hypothesis. J Mol Biol 1966; 19:548-55; PMID:5969078; http://dx.doi.org/10.1016/S0022-2836(66)80022-0
   PubMed Web of Science ®Google Scholar
• Murphy FVt, Ramakrishnan V. Structure of a purine-purine wobble base pair in the decoding center of the ribosome. Nat Struct Mol Biol 2004; 11:1251-2; PMID:15558050; http://dx.doi.org/10.1038/nsmb866
   PubMed Web of Science ®Google Scholar
• Gerber AP, Keller W. An adenosine deaminase that generates inosine at the wobble position of tRNAs. Science 1999; 286:1146-9; PMID:10550050; http://dx.doi.org/10.1126/science.286.5442.1146
   PubMed Web of Science ®Google Scholar
• Wolf J, Gerber AP, Keller W. tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli. EMBO J 2002; 21:3841-51; PMID:12110595; http://dx.doi.org/10.1093/emboj/cdf362
   PubMed Web of Science ®Google Scholar
• Kim DU, Hayles J, Kim D, Wood V, Park HO, Won M, Yoo HS, Duhig T, Nam M, Palmer G, et al. Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nat Biotech 2010; 28:617-23; http://dx.doi.org/10.1038/nbt.1628
   PubMed Web of Science ®Google Scholar
• Torres AG, Piñeyro D, Filonava L, Stracker TH, Batlle E, Ribas de Pouplana L. A-to-I editing on tRNAs: Biochemical, biological and evolutionary implications. FEBS Lett 2014; 588:4279-86; PMID:25263703; http://dx.doi.org/10.1016/j.febslet.2014.09.025
   PubMedGoogle Scholar
• Tsutsumi S, Sugiura R, Ma Y, Tokuoka H, Ohta K, Ohte R, Noma A, Suzuki T, Kuno T. Wobble inosine tRNA modification is essential to cell cycle progression in G(1)/S and G(2)/M transitions in fission yeast. J Biol Chem 2007; 282:33459-65; PMID:17875641; http://dx.doi.org/10.1074/jbc.M706869200
   PubMedGoogle Scholar
• Kuratani M, Ishii R, Bessho Y, Fukunaga R, Sengoku T, Shirouzu M, Sekine S, Yokoyama S. Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus. J Biol Chem 2005; 280:16002-8; PMID:15677468; http://dx.doi.org/10.1074/jbc.M414541200
   PubMedGoogle Scholar
• Ragone FL, Spears JL, Wohlgamuth-Benedum JM, Kreel N, Papavasiliou FN, Alfonzo JD. The C-terminal end of the Trypanosoma brucei editing deaminase plays a critical role in tRNA binding. RNA 2011; 17:1296-306; PMID:21602302; http://dx.doi.org/10.1261/rna.2748211
   PubMedGoogle Scholar
• Auxilien S, Crain PF, Trewyn RW, Grosjean H. Mechanism, specificity and general properties of the yeast enzyme catalysing the formation of inosine 34 in the anticodon of transfer RNA. J Mol Biol 1996; 262:437-58; PMID:8893855; http://dx.doi.org/10.1006/jmbi.1996.0527
   PubMed Web of Science ®Google Scholar
• Rubio MA, Pastar I, Gaston KW, Ragone FL, Janzen CJ, Cross GA, Papavasiliou FN, Alfonzo JD. An adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U deamination of DNA. Proc Natl Acad Sci U S A 2007; 104:7821-6; PMID:17483465; http://dx.doi.org/10.1073/pnas.0702394104
   PubMed Web of Science ®Google Scholar
• Basavappa R, Sigler PB. The 3 A crystal structure of yeast initiator tRNA: functional implications in initiator/elongator discrimination. EMBO J 1991; 10:3105-11; PMID:1915284
   PubMed Web of Science ®Google Scholar
• LaCava J, Houseley J, Saveanu C, Petfalski E, Thompson E, Jacquier A, Tollervey D. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 2005; 121:713-24; PMID:15935758; http://dx.doi.org/10.1016/j.cell.2005.04.029
   PubMed Web of Science ®Google Scholar
• Vanacova S, Wolf J, Martin G, Blank D, Dettwiler S, Friedlein A, Langen H, Keith G, Keller W. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 2005; 3:e189; PMID:15828860; http://dx.doi.org/10.1371/journal.pbio.0030189
   PubMed Web of Science ®Google Scholar
• Kadaba S, Wang X, Anderson JT. Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA. RNA 2006; 12:508-21; PMID:16431988; http://dx.doi.org/10.1261/rna.2305406
   PubMed Web of Science ®Google Scholar
• Schneider C, Anderson JT, Tollervey D. The exosome subunit Rrp44 plays a direct role in RNA substrate recognition. Mol Cell 2007; 27:324-31; PMID:17643380; http://dx.doi.org/10.1016/j.molcel.2007.06.006
   PubMed Web of Science ®Google Scholar
• Anderson J, Phan L, Cuesta R, Carlson BA, Pak M, Asano K, Bjork GR, Tamame M, Hinnebusch AG. The essential Gcd10p-Gcd14p nuclear complex is required for 1- methyladenosine modification and maturation of initiator methionyl-tRNA. Genes Dev 1998; 12:3650-62; PMID:9851972; http://dx.doi.org/10.1101/gad.12.23.3650
   PubMed Web of Science ®Google Scholar
• Zuin A, Gabrielli N, Calvo IA, Garcia-Santamarina S, Hoe KL, Kim DU, Park HO, Hayles J, Ayte J, Hidalgo E. Mitochondrial dysfunction increases oxidative stress and decreases chronological life span in fission yeast. PloS One 2008; 3:e2842; PMID:18665268; http://dx.doi.org/10.1371/journal.pone.0002842
   PubMed Web of Science ®Google Scholar
• Harashima S, Hinnebusch AG. Multiple GCD genes required for repression of GCN4, a transcriptional activator of amino acid biosynthetic genes in Saccharomyces cerevisiae. Mol Cell Biol 1986; 6:3990-8; PMID:3540603
   PubMed Web of Science ®Google Scholar
• Garcia-Barrio MT, Naranda T, Vazquez de Aldana CR, Cuesta R, Hinnebusch AG, Hershey JW, Tamame M. GCD10, a translational repressor of GCN4, is the RNA-binding subunit of eukaryotic translation initiation factor-3. Genes Dev 1995; 9:1781-96; PMID:7542616; http://dx.doi.org/10.1101/gad.9.14.1781
   PubMedGoogle Scholar
• Cuesta R, Hinnebusch AG, Tamame M. Identification of GCD14 and GCD15, novel genes required for translational repression of GCN4 mRNA in Saccharomyces cerevisiae. Genetics 1998; 148:1007-20; PMID:9539420
   PubMed Web of Science ®Google Scholar
• Calvo O, Cuesta R, Anderson J, Gutierrez N, Garcia-Barrio MT, Hinnebusch AG, Tamame M. GCD14p, a repressor of GCN4 translation, cooperates with Gcd10p and Lhp1p in the maturation of initiator methionyl-tRNA in Saccharomyces cerevisiae. Mol Cell Biol 1999; 19:4167-81; PMID:10330157
   PubMed Web of Science ®Google Scholar
• Anderson J, Phan L, Hinnebusch AG. 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; PMID:10779558; http://dx.doi.org/10.1073/pnas.090102597
   PubMedGoogle Scholar
• Ozanick SG, Bujnicki JM, Sem DS, Anderson JT. 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; PMID:17932071; http://dx.doi.org/10.1093/nar/gkm574
   PubMed Web of Science ®Google Scholar
• Bujnicki JM. In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea. FEBS Lett 2001; 507:123-7; PMID:11684083; http://dx.doi.org/10.1016/S0014-5793(01)02962-3
   PubMed Web of Science ®Google Scholar
• Ozanick S, Krecic A, Andersland J, Anderson JT. The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans. RNA 2005; 11:1281-90; PMID:16043508; http://dx.doi.org/10.1261/rna.5040605
   PubMed Web of Science ®Google Scholar
• Droogmans L, Roovers M, Bujnicki JM, Tricot C, Hartsch T, Stalon V, Grosjean H. Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Nucleic Acids Res 2003; 31:2148-56; PMID:12682365; http://dx.doi.org/10.1093/nar/gkg314
   PubMed Web of Science ®Google Scholar
• Roovers M, Wouters J, Bujnicki JM, Tricot C, Stalon V, Grosjean H, Droogmans L. A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res 2004; 32:465-76; PMID:14739239; http://dx.doi.org/10.1093/nar/gkh191
   PubMed Web of Science ®Google Scholar
• Varshney U, Ramesh V, Madabushi A, Gaur R, Subramanya HS, RajBhandary UL. Mycobacterium tuberculosis Rv2118c codes for a single-component homotetrameric m1A58 tRNA methyltransferase. Nucleic Acids Res 2004; 32:1018-27; PMID:14960715; http://dx.doi.org/10.1093/nar/gkh207
   PubMedGoogle Scholar
• Tomikawa C, Ohira T, Inoue Y, Kawamura T, Yamagishi A, Suzuki T, Hori H. Distinct tRNA modifications in the thermo-acidophilic archaeon, Thermoplasma acidophilum. FEBS Lett 2013; 587:3575-80; PMID:24076028; http://dx.doi.org/10.1016/j.febslet.2013.09.021
   PubMedGoogle Scholar
• Kim SH, Suddath FL, Quigley GJ, McPherson A, Sussman JL, Wang AH, Seeman NC, Rich A. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 1974; 185:435-40; PMID:4601792; http://dx.doi.org/10.1126/science.185.4149.435
   PubMed Web of Science ®Google Scholar
• Gautheret D, Damberger SH, Gutell RR. Identification of base-triples in RNA using comparative sequence analysis. J Mol Biol 1995; 248:27-43; PMID:7537339; http://dx.doi.org/10.1006/jmbi.1995.0200
   PubMed Web of Science ®Google Scholar
• Alexandrov A, Grayhack EJ, Phizicky EM. tRNA m7G methyltransferase Trm8p/Trm82p: evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p. RNA 2005; 11:821-30; PMID:15811913; http://dx.doi.org/10.1261/rna.2030705
   PubMed Web of Science ®Google Scholar
• Chernyakov I, Whipple JM, Kotelawala L, Grayhack EJ, Phizicky EM. Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1. Genes Dev 2008; 22:1369-80; PMID:18443146; http://dx.doi.org/10.1101/gad.1654308
   PubMed Web of Science ®Google Scholar
• Dewe JM, Whipple JM, Chernyakov I, Jaramillo LN, Phizicky EM. The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications. RNA 2012; 18:1886-96; PMID:22895820; http://dx.doi.org/10.1261/rna.033654.112
   PubMed Web of Science ®Google Scholar
• Tomikawa C, Yokogawa T, Kanai T, Hori H. N7-Methylguanine at position 46 (m7G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network. Nucleic Acids Res 2010; 38:942-57; PMID:19934251; http://dx.doi.org/10.1093/nar/gkp1059
   PubMed Web of Science ®Google Scholar
• Alexandrov A, Martzen MR, Phizicky EM. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 2002; 8:1253-66; PMID:12403464; http://dx.doi.org/10.1017/S1355838202024019
   PubMed Web of Science ®Google Scholar
• Martzen MR, McCraith SM, Spinelli SL, Torres FM, Fields S, Grayhack EJ, Phizicky EM. A biochemical genomics approach for identifying genes by the activity of their products. Science 1999; 286:1153-5; PMID:10550052; http://dx.doi.org/10.1126/science.286.5442.1153
   PubMedGoogle Scholar
• Okamoto M, Fujiwara M, Hori M, Okada K, Yazama F, Konishi H, Xiao Y, Qi G, Shimamoto F, Ota T, et al. tRNA Modifying Enzymes, NSUN2 and METTL1, Determine Sensitivity to 5-Fluorouracil in HeLa Cells. PLoS Genet 2014; 10:e1004639; PMID:25233213; http://dx.doi.org/10.1371/journal.pgen.1004639
   PubMed Web of Science ®Google Scholar
• Cartlidge RA, Knebel A, Peggie M, Alexandrov A, Phizicky EM, Cohen P. The tRNA methylase METTL1 is phosphorylated and inactivated by PKB and RSK in vitro and in cells. EMBO J 2005; 24:1696-705; PMID:15861136; http://dx.doi.org/10.1038/sj.emboj.7600648
   PubMedGoogle Scholar
• Michaud J, Kudoh J, Berry A, Bonne-Tamir B, Lalioti MD, Rossier C, Shibuya K, Kawasaki K, Asakawa S, Minoshima S, et al. Isolation and characterization of a human chromosome 21q22.3 gene (WDR4) and its mouse homologue that code for a WD-repeat protein. Genomics 2000; 68:71-9; PMID:10950928; http://dx.doi.org/10.1006/geno.2000.6258
   PubMedGoogle Scholar
• De Bie LG, Roovers M, Oudjama Y, Wattiez R, Tricot C, Stalon V, Droogmans L, Bujnicki JM. The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase. J Bact 2003; 185:3238-43; PMID:12730187; http://dx.doi.org/10.1128/JB.185.10.3238-3243.2003
   PubMed Web of Science ®Google Scholar
• Zegers I, Gigot D, van Vliet F, Tricot C, Aymerich S, Bujnicki JM, Kosinski J, Droogmans L. Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase. Nucleic Acids Res 2006; 34:1925-34; PMID:16600901; http://dx.doi.org/10.1093/nar/gkl116
   PubMed Web of Science ®Google Scholar
• Leulliot N, Chaillet M, Durand D, Ulryck N, Blondeau K, van Tilbeurgh H. Structure of the yeast tRNA m7G methylation complex. Structure 2008; 16:52-61; PMID:18184583; http://dx.doi.org/10.1016/j.str.2007.10.025
   PubMed Web of Science ®Google Scholar
• Purta E, van Vliet F, Tricot C, De Bie LG, Feder M, Skowronek K, Droogmans L, Bujnicki JM. Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis. Proteins 2005; 59:482-8; PMID:15789416; http://dx.doi.org/10.1002/prot.20454
   PubMed Web of Science ®Google Scholar
• Matsumoto K, Toyooka T, Tomikawa C, Ochi A, Takano Y, Takayanagi N, Endo Y, Hori H. RNA recognition mechanism of eukaryote tRNA (m7G46) methyltransferase (Trm8-Trm82 complex). FEBS Lett 2007; 581:1599-604; PMID:17382321; http://dx.doi.org/10.1016/j.febslet.2007.03.023
   PubMed Web of Science ®Google Scholar
• Purta E, van Vliet F, Tkaczuk KL, Dunin-Horkawicz S, Mori H, Droogmans L, Bujnicki JM. The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase. BMC Mol Biol 2006; 7:23; PMID:16848900; http://dx.doi.org/10.1186/1471-2199-7-23
   PubMedGoogle Scholar
• Somme J, Van Laer B, Roovers M, Steyaert J, Versees W, Droogmans L. Characterization of two homologous 2'-O-methyltransferases showing different specificities for their tRNA substrates. RNA 2014; 20:1257-71; PMID:24951554; http://dx.doi.org/10.1261/rna.044503.114
   PubMed Web of Science ®Google Scholar
• Benitez-Paez A, Villarroya M, Douthwaite S, Gabaldon T, Armengod ME. YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. RNA 2010; 16:2131-43; PMID:20855540; http://dx.doi.org/10.1261/rna.2245910
   PubMed Web of Science ®Google Scholar
• Caldas T, Binet E, Bouloc P, Costa A, Desgres J, Richarme G. The FtsJ/RrmJ heat shock protein of Escherichia coli is a 23 S ribosomal RNA methyltransferase. J Biol Chem 2000; 275:16414-9; PMID:10748051; http://dx.doi.org/10.1074/jbc.M001854200
   PubMed Web of Science ®Google Scholar
• Bugl H, Fauman EB, Staker BL, Zheng F, Kushner SR, Saper MA, Bardwell JC, Jakob U. RNA methylation under heat shock control. Mol Cell 2000; 6:349-60; PMID:10983982; http://dx.doi.org/10.1016/S1097-2765(00)00035-6
   PubMed Web of Science ®Google Scholar
• Feder M, Pas J, Wyrwicz LS, Bujnicki JM. Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases. Gene 2003; 302:129-38; PMID:12527203; http://dx.doi.org/10.1016/S0378-1119(02)01097-1
   PubMed Web of Science ®Google Scholar
• Freude K, Hoffmann K, Jensen LR, Delatycki MB, des Portes V, Moser B, Hamel B, van Bokhoven H, Moraine C, Fryns JP, et al. Mutations in the FTSJ1 gene coding for a novel S-adenosylmethionine-binding protein cause nonsyndromic X-linked mental retardation. Am J Hum Genet 2004; 75:305-9; PMID:15162322; http://dx.doi.org/10.1086/422507
   PubMed Web of Science ®Google Scholar
• Ramser J, Winnepenninckx B, Lenski C, Errijgers V, Platzer M, Schwartz CE, Meindl A, Kooy RF. A splice site mutation in the methyltransferase gene FTSJ1 in Xp11.23 is associated with non-syndromic mental retardation in a large Belgian family (MRX9). J Med Genet 2004; 41:679-83; PMID:15342698; http://dx.doi.org/10.1136/jmg.2004.019000
   PubMed Web of Science ®Google Scholar
• Froyen G, Bauters M, Boyle J, Van Esch H, Govaerts K, van Bokhoven H, Ropers HH, Moraine C, Chelly J, Fryns JP, et al. Loss of SLC38A5 and FTSJ1 at Xp11.23 in three brothers with non-syndromic mental retardation due to a microdeletion in an unstable genomic region. Human Genet 2007; 121:539-47; http://dx.doi.org/10.1007/s00439-007-0343-1
   PubMed Web of Science ®Google Scholar
• Takano K, Nakagawa E, Inoue K, Kamada F, Kure S, Goto Y. A loss-of-function mutation in the FTSJ1 gene causes nonsyndromic X-linked mental retardation in a Japanese family. Am J Med Genet 2008; 147B:479-84; PMID:18081026; http://dx.doi.org/10.1002/ajmg.b.30638
   PubMedGoogle Scholar
• Liu RJ, Zhou M, Fang ZP, Wang M, Zhou XL, Wang ED. The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL. Nucleic Acids Res 2013; 41:7828-42; PMID:23804755; http://dx.doi.org/10.1093/nar/gkt568
   PubMedGoogle Scholar
• Clouet d'Orval B, Bortolin ML, Gaspin C, Bachellerie JP. Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. Nucleic Acids Res 2001; 29:4518-29; PMID:11713301; http://dx.doi.org/10.1093/nar/29.22.4518
   PubMed Web of Science ®Google Scholar
• Joardar A, Malliahgari SR, Skariah G, Gupta R. 2′-O-methylation of the wobble residue of elongator pre-tRNA(Met) in Haloferax volcanii is guided by a box C/D RNA containing unique features. RNA Biol 2011; 8:782-91; PMID:21654217; http://dx.doi.org/10.4161/rna.8.5.16015
   PubMed Web of Science ®Google Scholar
• Pintard L, Bujnicki JM, Lapeyre B, Bonnerot C. MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase. EMBO J 2002; 21:1139-47; PMID:11867542; http://dx.doi.org/10.1093/emboj/21.5.1139
   PubMed Web of Science ®Google Scholar
• Lapeyre B, Purushothaman SK. Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs at a late processing stage. Mol Cell 2004; 16:663-9; PMID:15546625; http://dx.doi.org/10.1016/j.molcel.2004.10.022
   PubMed Web of Science ®Google Scholar
• Shi Y, Stefan CJ, Rue SM, Teis D, Emr SD. Two novel WD40 domain-containing proteins, Ere1 and Ere2, function in the retromer-mediated endosomal recycling pathway. Mol Biol Cell 2011; 22:4093-107; PMID:21880895; http://dx.doi.org/10.1091/mbc.E11-05-0440
   PubMed Web of Science ®Google Scholar
• Nyswaner KM, Checkley MA, Yi M, Stephens RM, Garfinkel DJ. Chromatin-associated genes protect the yeast genome from Ty1 insertional mutagenesis. Genetics 2008; 178:197-214; PMID:18202368; http://dx.doi.org/10.1534/genetics.107.082602
   PubMed Web of Science ®Google Scholar
• Begley U, Dyavaiah M, Patil A, Rooney JP, DiRenzo D, Young CM, Conklin DS, Zitomer RS, Begley TJ. Trm9-catalyzed tRNA modifications link translation to the DNA damage response. Mol Cell 2007; 28:860-70; PMID:18082610; http://dx.doi.org/10.1016/j.molcel.2007.09.021
   PubMed Web of Science ®Google Scholar
• Fu D, Brophy JA, Chan CT, Atmore KA, Begley U, Paules RS, Dedon PC, Begley TJ, Samson LD. Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. Mol Cell Biol 2010; 30:2449-59; PMID:20308323; http://dx.doi.org/10.1128/MCB.01604-09
   PubMed Web of Science ®Google Scholar
• Kalhor HR, Clarke S. Novel methyltransferase for modified uridine residues at the wobble position of tRNA. Mol Cell Biol 2003; 23:9283-92; PMID:14645538; http://dx.doi.org/10.1128/MCB.23.24.9283-9292.2003
   PubMed Web of Science ®Google Scholar
• Lu J, Huang B, Esberg A, Johansson MJ, Bystrom AS. The Kluyveromyces lactis gamma-toxin targets tRNA anticodons. RNA 2005; 11:1648-54; PMID:16244131; http://dx.doi.org/10.1261/rna.2172105
   PubMed Web of Science ®Google Scholar
• Jablonowski D, Zink S, Mehlgarten C, Daum G, Schaffrath R. tRNAGlu wobble uridine methylation by Trm9 identifies Elongator's key role for zymocin-induced cell death in yeast. Mol Microbiol 2006; 59:677-88; PMID:16390459; http://dx.doi.org/10.1111/j.1365-2958.2005.04972.x
   PubMed Web of Science ®Google Scholar
• Studte P, Zink S, Jablonowski D, Bar C, von der Haar T, Tuite MF, Schaffrath R. tRNA and protein methylase complexes mediate zymocin toxicity in yeast. Mol Microbiol 2008; 69:1266-77; PMID:18657261; http://dx.doi.org/10.1111/j.1365-2958.2008.06358.x
   PubMed Web of Science ®Google Scholar
• Songe-Moller L, van den Born E, Leihne V, Vagbo CB, Kristoffersen T, Krokan HE, Kirpekar F, Falnes PO, Klungland A. 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; PMID:20123966; http://dx.doi.org/10.1128/MCB.01602-09
   PubMed Web of Science ®Google Scholar
• Okada K, Muneyoshi Y, Endo Y, Hori H. Production of yeast (m2G10) methyltransferase (Trm11 and Trm112 complex) in a wheat germ cell-free translation system. Nucleic Acids Symp Ser 2009:303-4; PMID:19749381; http://dx.doi.org/10.1093/nass/nrp152
   PubMedGoogle Scholar
• Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. Global analysis of protein expression in yeast. Nature 2003; 425:737-41; PMID:14562106; http://dx.doi.org/10.1038/nature02046
   PubMed Web of Science ®Google Scholar
• Liger D, Mora L, Lazar N, Figaro S, Henri J, Scrima N, Buckingham RH, van Tilbeurgh H, Heurgue-Hamard V, Graille M. Mechanism of activation of methyltransferases involved in translation by the Trm112 'hub' protein. Nucleic Acids Res 2011; 39:6249-59; PMID:21478168; http://dx.doi.org/10.1093/nar/gkr176
   PubMedGoogle Scholar
• Heurgue-Hamard V, Champ S, Mora L, Merkulova-Rainon T, Kisselev LL, Buckingham RH. The glutamine residue of the conserved GGQ motif in Saccharomyces cerevisiae release factor eRF1 is methylated by the product of the YDR140w gene. J Biol Chem 2005; 280:2439-45; PMID:15509572; http://dx.doi.org/10.1074/jbc.M407252200
   PubMedGoogle Scholar
• Polevoda B, Span L, Sherman F. The yeast translation release factors Mrf1p and Sup45p (eRF1) are methylated, respectively, by the methyltransferases Mtq1p and Mtq2p. J Biol Chem 2006; 281:2562-71; PMID:16321977; http://dx.doi.org/10.1074/jbc.M507651200
   PubMedGoogle Scholar
• Nakahigashi K, Kubo N, Narita S, Shimaoka T, Goto S, Oshima T, Mori H, Maeda M, Wada C, Inokuchi H. HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination. Proc Natl Acad Sci U S A 2002; 99:1473-8; PMID:11805295; http://dx.doi.org/10.1073/pnas.032488499
   PubMedGoogle Scholar
• Heurgue-Hamard V, Champ S, Engstrom A, Ehrenberg M, Buckingham RH. The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors. EMBO J 2002; 21:769-78; PMID:11847124; http://dx.doi.org/10.1093/emboj/21.4.769
   PubMedGoogle Scholar
• Das K, Acton T, Chiang Y, Shih L, Arnold E, Montelione GT. Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site. Proc Natl Acad Sci U S A 2004; 101:4041-6; PMID:14999102; http://dx.doi.org/10.1073/pnas.0400189101
   PubMedGoogle Scholar
• Gustafsson C, Persson BC. Identification of the rrmA gene encoding the 23S rRNA m1G745 methyltransferase in Escherichia coli and characterization of an m1G745-deficient mutant. J Bact 1998; 180:359-65; PMID:9440525
   PubMed Web of Science ®Google Scholar
• Liu M, Douthwaite S. Resistance to the macrolide antibiotic tylosin is conferred by single methylations at 23S rRNA nucleotides G748 and A2058 acting in synergy. Proc Natl Acad Sci U S A 2002; 99:14658-63; PMID:12417742; http://dx.doi.org/10.1073/pnas.232580599
   PubMed Web of Science ®Google Scholar
• White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW. Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits. Mol Cell Biol 2008; 28:3151-61; PMID:18332120; http://dx.doi.org/10.1128/MCB.01674-07
   PubMed Web of Science ®Google Scholar