{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T11:55:13Z","timestamp":1790423713467,"version":"4.1.0"},"reference-count":188,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2017,3,8]],"date-time":"2017-03-08T00:00:00Z","timestamp":1488931200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["HD000412-28"],"award-info":[{"award-number":["HD000412-28"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Transfer RNAs (tRNAs) contain sequence diversity beyond their anticodons and the large variety of nucleotide modifications found in all kingdoms of life. Some modifications stabilize structure and fit in the ribosome whereas those to the anticodon loop modulate messenger RNA (mRNA) decoding activity more directly. The identities of tRNAs with some universal anticodon loop modifications vary among distant and parallel species, likely to accommodate fine tuning for their translation systems. This plasticity in positions 34 (wobble) and 37 is reflected in codon use bias. Here, we review convergent evidence that suggest that expansion of the eukaryotic tRNAome was supported by its dedicated RNA polymerase III transcription system and coupling to the precursor\u2010tRNA chaperone, La protein. We also review aspects of eukaryotic tRNAome evolution involving G34\/A34 anticodon\u2010sparing, relation to A34 modification to inosine, biased codon use and regulatory information in the redundancy (synonymous) component of the genetic code. We then review interdependent anticodon loop modifications involving position 37 in eukaryotes. This includes the  eukaryote\u2010specific  tRNA  modification,  3\u2010methylcytidine\u201032  (m3C32)  and  the  responsible  gene,  TRM140  and  homologs  which  were  duplicated  and  subspecialized  for  isoacceptor\u2010specific substrates and dependence on i6A37 or t6A37. The genetics of tRNA function is relevant to health directly and as disease modifiers.<\/jats:p>","DOI":"10.3390\/biom7010026","type":"journal-article","created":{"date-parts":[[2017,3,8]],"date-time":"2017-03-08T07:42:58Z","timestamp":1488958978000},"page":"26","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["Factors\u00a0That\u00a0Shape\u00a0Eukaryotic\u00a0tRNAomes:\u00a0 Processing,\u00a0Modification\u00a0and\u00a0Anticodon\u2013Codon\u00a0Use"],"prefix":"10.3390","volume":"7","author":[{"given":"Richard","family":"Maraia","sequence":"first","affiliation":[{"name":"Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA"},{"name":"Commissioned Corps, U.S. Public Health Service, Rockville, MD, 20016, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5266-2688","authenticated-orcid":false,"given":"Aneeshkumar","family":"Arimbasseri","sequence":"additional","affiliation":[{"name":"Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2017,3,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1146\/annurev-genom-090413-025405","article-title":"The pivotal regulatory landscape of RNA modifications","volume":"15","author":"Li","year":"2014","journal-title":"Annu. Rev. Genomics Hum. Genet."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/j.chembiol.2013.10.015","article-title":"Posttranscriptional RNA Modifications: Playing Metabolic Games in a Cell\u2019s Chemical Legoland","volume":"21","author":"Helm","year":"2014","journal-title":"Chem. Biol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.febslet.2009.11.052","article-title":"Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes","volume":"584","author":"Grosjean","year":"2010","journal-title":"FEBS Lett."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.cell.2012.01.050","article-title":"A role for tRNA modifications in genome structure and codon usage","volume":"149","author":"Novoa","year":"2012","journal-title":"Cell"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1017\/S1355838202022021","article-title":"tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features","volume":"8","author":"Marck","year":"2002","journal-title":"RNA"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e1501860","DOI":"10.1126\/sciadv.1501860","article-title":"Saturation of recognition elements blocks evolution of new tRNA identities","volume":"2","author":"Bello","year":"2016","journal-title":"Sci Adv."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"788","DOI":"10.1038\/nsmb978","article-title":"Idiosyncratic tuning of tRNAs to achieve uniform ribosome binding","volume":"12","author":"Olejniczak","year":"2005","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.molcel.2008.04.026","article-title":"Different aa-tRNAs are selected uniformly on the ribosome","volume":"31","author":"Ledoux","year":"2008","journal-title":"Mol. Cell"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1261\/rna.896108","article-title":"Analysis of genomic tRNA sets from Bacteria, Archaea, and Eukarya points to anticodon-codon hydrogen bonds as a major determinant of tRNA compositional variations","volume":"14","author":"Targanski","year":"2008","journal-title":"RNA"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1261\/rna.036038.112","article-title":"tRNA residues evolved to promote translational accuracy","volume":"19","author":"Shepotinovskaya","year":"2013","journal-title":"RNA"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Bloom-Ackermann, Z., Navon, S., Gingold, H., Towers, R., Pilpel, Y., and Dahan, O. (2014). A comprehensive tRNA deletion library unravels the genetic architecture of the tRNA pool. PLoS Genet., 10.","DOI":"10.1371\/journal.pgen.1004084"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e01339","DOI":"10.7554\/eLife.01339","article-title":"tRNA genes rapidly change in evolution to meet novel translational demands","volume":"2","author":"Yona","year":"2013","journal-title":"eLife"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Sagi, D., Rak, R., Gingold, H., Adir, I., Maayan, G., Dahan, O., Broday, L., Pilpel, Y., and Rechavi, O. (2016). Tissue- and Time-Specific Expression of Otherwise Identical tRNA Genes. PLoS Genet., 12.","DOI":"10.1371\/journal.pgen.1006264"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1126\/science.1249749","article-title":"RNA function. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration","volume":"345","author":"Ishimura","year":"2014","journal-title":"Science"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1016\/j.cell.2013.05.049","article-title":"Rate-limiting steps in yeast protein translation","volume":"153","author":"Shah","year":"2013","journal-title":"Cell"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1038\/nrg2899","article-title":"Synonymous but not the same: The causes and consequences of codon bias","volume":"12","author":"Plotkin","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2419","DOI":"10.1073\/pnas.1211077110","article-title":"Environmental perturbations lift the degeneracy of the genetic code to regulate protein levels in bacteria","volume":"110","author":"Subramaniam","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1261\/rna.044115.113","article-title":"Different types of secondary information in the genetic code","volume":"20","author":"Maraia","year":"2014","journal-title":"RNA"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.molcel.2015.05.035","article-title":"Codon Bias as a Means to Fine-Tune Gene Expression","volume":"59","author":"Quax","year":"2011","journal-title":"Mol. Cell"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"D184","DOI":"10.1093\/nar\/gkv1309","article-title":"GtRNAdb 2.0: An expanded database of transfer RNA genes identified in complete and draft genomes","volume":"44","author":"Chan","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Glanzmann, B., Moller, M., le Roex, N., Tromp, G., Hoal, E.G., and van Helden, P.D. (2016). The complete genome sequence of the African buffalo (Syncerus caffer). BMC Genom., 17.","DOI":"10.1186\/s12864-016-3364-0"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"4728","DOI":"10.1093\/nar\/gkr066","article-title":"Comparative whole genome sequencing reveals phenotypic tRNA gene duplication in spontaneous Schizosaccharomyces pombe La mutants","volume":"39","author":"Iben","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1358","DOI":"10.1261\/rna.032151.111","article-title":"Yeast tRNAomics: tRNA gene copy number variation and codon use provide bioinformatics evidence of a new wobble pair in a eukaryote","volume":"18","author":"Iben","year":"2012","journal-title":"RNA"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1016\/j.gene.2013.11.049","article-title":"tRNA gene copy number variation in humans","volume":"536","author":"Iben","year":"2014","journal-title":"Gene"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1853","DOI":"10.4161\/rna.27361","article-title":"Diversity of human tRNA genes from the 1000-genomes project","volume":"10","author":"Parisien","year":"2013","journal-title":"RNA Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nature03481","article-title":"The genome of the social amoeba Dictyostelium discoideum","volume":"435","author":"Eichinger","year":"2005","journal-title":"Nature"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"6137","DOI":"10.1093\/nar\/gkl725","article-title":"Diversity of tRNA genes in eukaryotes","volume":"34","author":"Goodenbour","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"S\u00f6ll, D., and RajBhandary, U.L. (1995). tRNA: Structure, Biosynthesis, and Function, ASM Press.","DOI":"10.1128\/9781555818333"},{"key":"ref_29","unstructured":"Sebald, M. (2012). Genetics and Molecular Biology of Anaerobic Bacteria, Springer."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/nrmicro2507","article-title":"Evolution of multisubunit RNA polymerases in the three domains of life","volume":"9","author":"Werner","year":"2011","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/nrm3152","article-title":"Multisubunit RNA polymerases IV and V: Purveyors of non-coding RNA for plant gene silencing","volume":"12","author":"Haag","year":"2011","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1093\/molbev\/msp316","article-title":"The increase in the number of subunits in eukaryotic RNA polymerase III relative to RNA polymerase II is due to the permanent recruitment of general transcription factors","volume":"27","author":"Carter","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Drouin, G., and Carter, R. (2010). Evolution of Eukaryotic RNA Polymerases. eLS.","DOI":"10.1002\/9780470015902.a0022872"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"4576","DOI":"10.1128\/MCB.00127-08","article-title":"Visual analysis of the yeast 5S rRNA gene transcriptome: Regulation and role of La protein","volume":"28","author":"French","year":"2008","journal-title":"Mol. Cell Biol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1101\/gad.1049103","article-title":"tRNA transfers to the limelight","volume":"17","author":"Hopper","year":"2003","journal-title":"Genes Dev."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1832","DOI":"10.1101\/gad.1956510","article-title":"tRNA biology charges to the front","volume":"24","author":"Phizicky","year":"2010","journal-title":"Genes Dev."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1016\/j.bbagrm.2012.10.006","article-title":"Transcription termination by the eukaryotic RNA polymerase III","volume":"1829","author":"Arimbasseri","year":"2013","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"e27639","DOI":"10.4161\/trns.27369","article-title":"Comparative overview of RNA polymerase II and III transcription cycles, with focus on RNA polymerase III termination and reinitiation","volume":"5","author":"Arimbasseri","year":"2014","journal-title":"Transcription"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1128\/jb.122.3.855-865.1975","article-title":"Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast","volume":"122","author":"Waldron","year":"1975","journal-title":"J. Bacteriol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"3857","DOI":"10.1101\/gad.12.24.3857","article-title":"The RNA cleavage activity of RNA polymerase III is mediated by an essential TFIIS-like subunit and is important for transcription termination","volume":"12","author":"Chedin","year":"1998","journal-title":"Genes Dev."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1128\/MCB.01733-12","article-title":"Distinguishing core and holoenzyme mechanisms of transcription termination by RNA polymerase III","volume":"33","author":"Arimbasseri","year":"2013","journal-title":"Mol. Cell. Biol"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/j.cell.2011.07.034","article-title":"Linking RNA polymerase backtracking to genome instability in E. coli.","volume":"146","author":"Dutta","year":"2011","journal-title":"Cell"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"115","DOI":"10.4161\/trns.1.3.13735","article-title":"Genome stability control by checkpoint regulation of tRNA gene transcription","volume":"1","author":"Clelland","year":"2010","journal-title":"Transcription"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1038\/nsmb.1857","article-title":"Replication stress checkpoint signaling controls tRNA gene transcription","volume":"17","author":"Nguyen","year":"2010","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1261\/rna.1478709","article-title":"A comprehensive analysis of the La-motif protein superfamily","volume":"15","author":"Deragon","year":"2009","journal-title":"RNA"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1038\/nature16143","article-title":"Molecular structures of unbound and transcribing RNA polymerase III","volume":"528","author":"Hoffmann","year":"2015","journal-title":"Nature"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/nature16317","article-title":"Structural biology: A transcriptional specialist resolved","volume":"528","author":"Maraia","year":"2015","journal-title":"Nature"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1016\/0092-8674(83)90540-8","article-title":"Purified RNA polymerase III accurately and efficiently terminates transcription of 5S RNA genes","volume":"34","author":"Cozzarelli","year":"1983","journal-title":"Cell"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1016\/j.molcel.2015.04.002","article-title":"Mechanism of Transcription Termination by RNA Polymerase III Utilizes a Non-template Strand Sequence-Specific Signal Element","volume":"58","author":"Arimbasseri","year":"2015","journal-title":"Mol. Cell"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1080\/15476286.2015.1116677","article-title":"A high density of cis-information terminates RNA Polymerase III on a 2-rail track","volume":"13","author":"Arimbasseri","year":"2016","journal-title":"RNA Biol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/0092-8674(81)90522-5","article-title":"Nucleotide sequences in Xenopus 5S DNA required for transcription termination","volume":"24","author":"Bogenhagen","year":"1981","journal-title":"Cell"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.gene.2014.11.034","article-title":"A methods review on use of nonsense suppression to study 3\u2032 end formation and other aspects of tRNA biogenesis","volume":"556","author":"Rijal","year":"2015","journal-title":"Gene"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"18350","DOI":"10.1073\/pnas.0506415102","article-title":"Human La is Found at RNA Polymerase III-Transcribed Genes In Vivo","volume":"102","author":"Fairley","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2371","DOI":"10.1101\/gad.11.18.2371","article-title":"Identification of an autonomously initiating RNA polymerase III holoenzyme containing a novel factor that is selectively inactivated during protein synthesis inhibition","volume":"11","author":"Wang","year":"1997","journal-title":"Genes Dev."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1128\/MCB.25.2.621-636.2005","article-title":"Mutations in the RNA Polymerase III Subunit Rpc11p That Decrease RNA 3\u2032 Cleavage Activity Increase 3\u2032-Terminal Oligo(U) Length and La-Dependent tRNA Processing","volume":"25","author":"Huang","year":"2005","journal-title":"Mol. Cell Biol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/0092-8674(84)90083-7","article-title":"Purified lupus antigen La recognizes an oligouridylate stretch common to the 3\u2032 termini of RNA polymerase III transcripts","volume":"36","author":"Stefano","year":"1984","journal-title":"Cell"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/nsmb.1573","article-title":"Precursor-product discrimination by La protein during tRNA metabolism","volume":"16","author":"Bayfield","year":"2009","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"3650","DOI":"10.1101\/gad.12.23.3650","article-title":"The essential Gcd10p-Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA","volume":"12","author":"Anderson","year":"1998","journal-title":"Genes Dev."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1261\/rna.2307206","article-title":"The La protein functions redundantly with tRNA modification enzymes to ensure tRNA structural stability","volume":"12","author":"Copela","year":"2006","journal-title":"RNA"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1002\/wrna.64","article-title":"3\u2032 processing of eukaryotic precursor tRNAs","volume":"2","author":"Maraia","year":"2011","journal-title":"WIRES RNA"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"4934","DOI":"10.1021\/bi100408z","article-title":"tRNA stabilization by modified nucleotides","volume":"49","author":"Motorin","year":"2010","journal-title":"Biochemistry"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/j.bbagrm.2010.01.011","article-title":"Conserved and divergent features of the structure and function of La and La-related proteins (LARPs)","volume":"1799","author":"Bayfield","year":"2010","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1038\/nsmb1110","article-title":"Separate RNA-binding surfaces on the multifunctional La protein mediate distinguishable activities in tRNA maturation","volume":"13","author":"Huang","year":"2006","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"6562","DOI":"10.1093\/emboj\/cdg625","article-title":"A La protein requirement for efficient pre-tRNA folding","volume":"22","author":"Chakshusmathi","year":"2003","journal-title":"EMBO J."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.1073\/pnas.1017085108","article-title":"An intrinsically disordered C terminus allows the La protein to assist the biogenesis of diverse noncoding RNA precursors","volume":"108","author":"Kucera","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"5472","DOI":"10.1074\/jbc.M111.276071","article-title":"RNA chaperone activity of the human La protein is mediated by a variant RNA recognition motif","volume":"287","author":"Naeeni","year":"2012","journal-title":"J. Biol. Chem."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1146\/annurev.biochem.71.090501.150003","article-title":"The La protein","volume":"71","author":"Wolin","year":"2002","journal-title":"Annu. Rev. Biochem."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1101\/sqb.2006.71.051","article-title":"Molecular chaperones and quality control in noncoding RNA biogenesis","volume":"71","author":"Wolin","year":"2006","journal-title":"Cold Spring Harb. Symp. Quant. Biol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/S0092-8674(00)80220-2","article-title":"The yeast La protein is required for the 3\u2032 endonucleolytic cleavage that matures tRNA precursors","volume":"89","author":"Yoo","year":"1997","journal-title":"Cell"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"7442","DOI":"10.1093\/emboj\/17.24.7442","article-title":"A role for the yeast La protein in U6 snRNP assembly: evidence that the La protein is a molecular chaperone for RNA polymerase III transcripts","volume":"17","author":"Pannone","year":"1998","journal-title":"EMBO J."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1093\/emboj\/19.7.1650","article-title":"U snRNP assembly in yeast involves the La protein","volume":"19","author":"Xue","year":"2000","journal-title":"EMBO J."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1214","DOI":"10.1261\/rna.1050408","article-title":"Competition between the Rex1 exonuclease and the La protein affects both Trf4p-mediated RNA quality control and pre-tRNA maturation","volume":"14","author":"Copela","year":"2008","journal-title":"RNA"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"10698","DOI":"10.1093\/nar\/gku761","article-title":"Integrity of SRP RNA is ensured by La and the nuclear RNA quality control machinery","volume":"42","author":"Leung","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.molcel.2016.05.026","article-title":"The Lupus Autoantigen La Prevents Mis-channeling of tRNA Fragments into the Human MicroRNA Pathway","volume":"63","author":"Hasler","year":"2016","journal-title":"Mol. Cell"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1083\/jcb.106.3.545","article-title":"A 5S rRNA\/L5 complex is a precursor to ribosome assembly in mammalian cells","volume":"106","author":"Steitz","year":"1998","journal-title":"J. Cell Biol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1261\/rna.7263905","article-title":"RNA chaperone activity of protein components of human Ro RNPs","volume":"11","author":"Belisova","year":"2005","journal-title":"RNA"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"2052","DOI":"10.1128\/MCB.00131-15","article-title":"Quality Control Pathways for Nucleus-Encoded Eukaryotic tRNA Biosynthesis and Subcellular Trafficking","volume":"35","author":"Hopper","year":"2015","journal-title":"Mol. Cell. Biol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1017\/S1355838202027851","article-title":"Dual function of the tRNA(m5U54)methyltransferase in tRNA maturation","volume":"8","author":"Johansson","year":"2002","journal-title":"RNA"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1101\/gad.1183804","article-title":"Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae","volume":"18","author":"Kadaba","year":"2004","journal-title":"Genes Dev."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1261\/rna.2305406","article-title":"Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA","volume":"12","author":"Kadaba","year":"2006","journal-title":"RNA"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"2505","DOI":"10.1128\/MCB.20.7.2505-2516.2000","article-title":"Defects in tRNA Processing and Nuclear Export Induce GCN4 Translation Independently of Phosphorylation of the \u03b1 Subunit of Eukaryotic Translation Initiation Factor 2","volume":"20","author":"Qiu","year":"2000","journal-title":"Mol. Cell. Biol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"2082","DOI":"10.1126\/science.282.5396.2082","article-title":"Proofreading and aminoacylation of tRNAs before export from the nucleus","volume":"282","author":"Lund","year":"1998","journal-title":"Science"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1146\/annurev.genet.40.110405.090412","article-title":"Protein homeostasis and the phenotypic manifestation of genetic diversity: Principles and mechanisms","volume":"44","author":"Jarosz","year":"2010","journal-title":"Annu. Rev. Genet."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1038\/24550","article-title":"Hsp90 as a capacitor for morphological evolution","volume":"396","author":"Rutherford","year":"1998","journal-title":"Nature"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1016\/j.tibs.2016.03.003","article-title":"RNA Polymerase III Advances: Structural and tRNA Functional Views","volume":"41","author":"Arimbasseri","year":"2016","journal-title":"Trends Biochem. Sci."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"1816","DOI":"10.1093\/nar\/gkl085","article-title":"The RNA polymerase III-dependent family of genes in hemiascomycetes: Comparative RNomics, decoding strategies, transcription and evolutionary implications","volume":"34","author":"Marck","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"4279","DOI":"10.1016\/j.febslet.2014.09.025","article-title":"A-to-I editing on tRNAs: biochemical, biological and evolutionary implications","volume":"588","author":"Torres","year":"2014","journal-title":"FEBS Lett."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"2705","DOI":"10.1093\/nar\/12.6.2705","article-title":"Enzymatic conversion of adenosine to inosine in the wobble position of yeast tRNAAsp: the dependence on the anticodon sequence","volume":"12","author":"Haumont","year":"1984","journal-title":"Nucleic Acids Res."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1006\/jmbi.1996.0527","article-title":"Mechanism, specificity and general properties of the yeast enzyme catalysing the formation of inosine 34 in the anticodon of transfer RNA","volume":"262","author":"Auxilien","year":"1996","journal-title":"J. Mol. Biol."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"10502","DOI":"10.1073\/pnas.1105645108","article-title":"Retrograde nuclear import of tRNA precursors is required for modified base biogenesis in yeast","volume":"108","author":"Ohira","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1002\/j.1460-2075.1987.tb04778.x","article-title":"Enzymatic conversion of guanosine 3\u2032 adjacent to the anticodon of yeast tRNAPhe to N1-methylguanosine and the wye nucleoside: Dependence on the anticodon sequence","volume":"6","author":"Droogmans","year":"1987","journal-title":"EMBO J."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jmb.2006.11.046","article-title":"tRNA\u2019s wobble decoding of the genome: 40 years of modification","volume":"366","author":"Agris","year":"2007","journal-title":"J. Mol. Biol."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1016\/j.molcel.2007.09.021","article-title":"Trm9-Catalyzed tRNA Modifications Link Translation to the DNA Damage Response","volume":"28","author":"Begley","year":"2007","journal-title":"Mol. Cell"},{"key":"ref_94","doi-asserted-by":"crossref","unstructured":"Arimbasseri, A.G., Blewett, N.H., Iben, J.R., Lamichhane, T.N., Cherkasova, V., Hafner, M., and Maraia, R.J. (2015). RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification. PLoS Genet., 11.","DOI":"10.1371\/journal.pgen.1005671"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"9698","DOI":"10.1073\/pnas.90.20.9698","article-title":"Neural BC1 RNA as an evolutionary marker: Guinea pig remains a rodent","volume":"90","author":"Martignetti","year":"1993","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1017\/S1355838201002485","article-title":"Neuronal BC1 RNA structure: evolutionary conversion of a tRNAAla domain into an extended stem-loop structure","volume":"7","author":"Rozhdestvensky","year":"2001","journal-title":"RNA"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"28300","DOI":"10.1038\/srep28300","article-title":"BC1 RNA motifs required for dendritic transport in vivo","volume":"6","author":"Robeck","year":"2016","journal-title":"Sci Rep."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.biochi.2015.04.013","article-title":"The importance of codon-anticodon interactions in translation elongation","volume":"114","year":"2015","journal-title":"Biochimie"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"5145","DOI":"10.1093\/nar\/gkv277","article-title":"Inosine modifications in human tRNAs are incorporated at the precursor tRNA level","volume":"43","author":"Torres","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.1126\/science.286.5442.1146","article-title":"An adenosine deaminase that generates inosine at the wobble position of tRNAs","volume":"286","author":"Gerber","year":"1999","journal-title":"Science"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.4161\/15476286.2014.992273","article-title":"Distribution and frequencies of post-transcriptional modifications in tRNAs","volume":"11","author":"Machnicka","year":"2014","journal-title":"RNA Biol."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1261\/rna.054064.115","article-title":"Lack of tRNA-i6A modification causes mitochondrial-like metabolic deficiency in S. pombe by limiting activity of cytosolic tRNATyr, not mito-tRNA","volume":"22","author":"Lamichhane","year":"2016","journal-title":"RNA"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1038\/nsmb.2466","article-title":"Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding","volume":"20","author":"Pechmann","year":"2013","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1016\/j.cell.2012.09.019","article-title":"Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells","volume":"151","author":"Marguerat","year":"2012","journal-title":"Cell"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"1718","DOI":"10.1126\/science.1083811","article-title":"Selective charging of tRNA isoacceptors explains patterns of codon usage","volume":"300","author":"Elf","year":"2003","journal-title":"Science"},{"key":"ref_106","doi-asserted-by":"crossref","unstructured":"Elf, J., and Ehrenberg, M. (2005). What makes ribosome-mediated transcriptional attenuation sensitive to amino acid limitation?. PLoS Comput. Biol., 1.","DOI":"10.1371\/journal.pcbi.0010002"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"13302","DOI":"10.1038\/ncomms13302","article-title":"tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence","volume":"7","author":"Chionh","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_108","doi-asserted-by":"crossref","unstructured":"S\u00f6ll, D., and RajBhandary, U.L. (1995). tRNA: Structure, biosynthesis, and function, ASM Press.","DOI":"10.1128\/9781555818333"},{"key":"ref_109","doi-asserted-by":"crossref","unstructured":"S\u00f6ll, D., and RajBhandary, U.L. (1995). tRNA: Structure, biosynthesis, and function, ASM Press.","DOI":"10.1128\/9781555818333"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1093\/nar\/gkh185","article-title":"Decoding the genome: A modified view","volume":"32","author":"Agris","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"3301","DOI":"10.1128\/MCB.01542-07","article-title":"Eukaryotic wobble uridine modifications promote a functionally redundant decoding system","volume":"28","author":"Johansson","year":"2008","journal-title":"Mol. Cell Biol."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"9283","DOI":"10.1128\/MCB.23.24.9283-9292.2003","article-title":"Novel methyltransferase for modified uridine residues at the wobble position of tRNA","volume":"23","author":"Kalhor","year":"2003","journal-title":"Mol. Cell Biol."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1016\/0005-2787(78)90171-5","article-title":"Pairing properties of the methylester of 5-carboxymethyl uridine in the wobble position of yeast tRNA3Arg","volume":"518","author":"Weissenbach","year":"1978","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1038\/nchembio0308-162","article-title":"It\u2019s a mod mod tRNA world","volume":"4","author":"Maraia","year":"2008","journal-title":"Nat. Chem. Biol."},{"key":"ref_115","doi-asserted-by":"crossref","unstructured":"Chan, C.T.Y., Dyavaiah, M., DeMott, M.S., Taghizadeh, K., Dedon, P.C., and Begley, T.J. (2010). A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet., 6.","DOI":"10.1371\/journal.pgen.1001247"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1038\/ncomms1938","article-title":"Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins","volume":"3","author":"Chan","year":"2012","journal-title":"Nat. Commun."},{"key":"ref_117","doi-asserted-by":"crossref","unstructured":"Fern\u00e1ndez-V\u00e1zquez, J., Vargas-P\u00e9rez, I., Sans\u00f3, M., Buhne, K., Carmona, M., Paulo, E., Hermand, D., Rodr\u00edguez-Gabriel, M., Ayt\u00e9, J., and Leidel, S. (2013). Modification of tRNALys UUU by elongator is essential for efficient translation of stress mRNAs. PLoS Genet., 9.","DOI":"10.1371\/journal.pgen.1003647"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1080\/15476286.2015.1031947","article-title":"Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses","volume":"12","author":"Endres","year":"2015","journal-title":"RNA Biol."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1021\/tx400438d","article-title":"A System of RNA Modifications and Biased Codon Use Controls Cellular Stress Response at the Level of Translation","volume":"27","author":"Dedon","year":"2014","journal-title":"Chem Res Toxicol."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"4287","DOI":"10.1016\/j.febslet.2014.09.038","article-title":"tRNA modifications regulate translation during cellular stress","volume":"588","author":"Gu","year":"2014","journal-title":"FEBS Lett."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1126\/science.6753149","article-title":"Translational efficiency of transfer RNA\u2019s: Uses of an extended anticodon","volume":"218","author":"Yarus","year":"1982","journal-title":"Science"},{"key":"ref_122","doi-asserted-by":"crossref","unstructured":"Bjork, G.R., and Hagervall, T.G. (2014). Transfer RNA Modification: Presence, Synthesis, and Function. EcoSal Plus, 6.","DOI":"10.1128\/ecosalplus.esp-0007-2013"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/nchembio.1137","article-title":"A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification","volume":"9","author":"Miyauchi","year":"2013","journal-title":"Nat. Chem. Biol."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"1529","DOI":"10.4161\/15476286.2014.992277","article-title":"Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t6A), a universal modification of tRNA","volume":"11","author":"Thiaville","year":"2014","journal-title":"RNA Biol."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"29","DOI":"10.15698\/mic2016.01.473","article-title":"Global translational impacts of the loss of the tRNA modification t6A in yeast","volume":"3","author":"Thiaville","year":"2016","journal-title":"Microb. Cell"},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1111\/mmi.13209","article-title":"Essentiality of threonylcarbamoyladenosine (t6A), a universal tRNA modification, in bacteria","volume":"98","author":"Thiaville","year":"2015","journal-title":"Mol. Microbiol."},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"1846","DOI":"10.1261\/rna.2628611","article-title":"Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases","volume":"17","author":"Lamichhane","year":"2011","journal-title":"RNA"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"D159","DOI":"10.1093\/nar\/gkn772","article-title":"tRNAdb 2009: Compilation of tRNA sequences and tRNA genes","volume":"37","author":"Juhling","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"D262","DOI":"10.1093\/nar\/gks1007","article-title":"MODOMICS: A database of RNA modification pathways--2013 update","volume":"41","author":"Machnicka","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"4900","DOI":"10.1128\/MCB.01041-13","article-title":"Human cells have a limited set of tRNA anticodon loop substrates of the tRNA isopentenyltransferase TRIT1 tumor suppressor","volume":"33","author":"Lamichhane","year":"2013","journal-title":"Mol. Cell Biol."},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"7346","DOI":"10.1093\/nar\/gku390","article-title":"A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs","volume":"42","author":"Suzuki","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"2918","DOI":"10.1128\/MCB.00278-13","article-title":"Lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast","volume":"33","author":"Lamichhane","year":"2013","journal-title":"Mol. Cell Biol."},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1261\/rna.056259.116","article-title":"Evolving specificity of tRNA 3-methyl-cytidine-32 (m3C32) modification: A subset of tRNAsSer requires N6-isopentenylation of A37","volume":"22","author":"Arimbasseri","year":"2016","journal-title":"RNA"},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1261\/rna.047639.114","article-title":"Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes","volume":"21","author":"Guy","year":"2015","journal-title":"RNA"},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1002\/humu.22897","article-title":"Defects in tRNA Anticodon Loop 2\u2032-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations in FTSJ1","volume":"36","author":"Guy","year":"2015","journal-title":"Hum. Mutat."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1261\/rna.053165.115","article-title":"The i6A37 tRNA modification is essential for proper decoding of UUX-Leucine codons during rpoS and iraP translation","volume":"22","author":"Aubee","year":"2016","journal-title":"RNA"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1128\/JB.01013-13","article-title":"The MiaA tRNA Modification Enzyme Is Necessary for Robust RpoS Expression in Escherichia coli","volume":"196","author":"Thompson","year":"2014","journal-title":"J. Bacteriol."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1080\/15476286.2015.1008360","article-title":"Two-subunit enzymes involved in eukaryotic post-transcriptional tRNA modification","volume":"11","author":"Guy","year":"2014","journal-title":"RNA Biol."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"2142","DOI":"10.1038\/sj.emboj.7601105","article-title":"Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA","volume":"25","author":"Noma","year":"2006","journal-title":"EMBO J."},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"3380","DOI":"10.1093\/nar\/23.17.3380","article-title":"C to U editing and modifications during the maturation of the mitochondrial tRNAAsp in marsupials","volume":"23","author":"Morl","year":"1995","journal-title":"Nucleic Acids Res."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"942","DOI":"10.1093\/nar\/gkp1059","article-title":"N7-Methylguanine at position 46 (m7G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network","volume":"38","author":"Tomikawa","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"2304","DOI":"10.1093\/nar\/gkq1180","article-title":"Pseudouridine at position 55 in tRNA controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium Thermus thermophilus","volume":"39","author":"Ishida","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1074\/jbc.M510136200","article-title":"C to U Editing Stimulates A to I Editing in the Anticodon Loop of a Cytoplasmic Threonyl tRNA in Trypanosoma brucei","volume":"281","author":"Rubio","year":"2006","journal-title":"J. Biol. Chem."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"10952","DOI":"10.1093\/nar\/gkv980","article-title":"Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine","volume":"43","author":"Hartmann","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_145","doi-asserted-by":"crossref","unstructured":"Kernohan, K.D., Dyment, D.A., Pupavac, M., Cramer, Z., McBride, A., Bernard, G., Straub, I., Tetreault, M., Hartley, T., and Huang, L. (2017). Matchmaking facilitates the diagnosis of an autosomal-recessive mitochondrial disease caused by biallelic mutation of the tRNA isopentenyltransferase (TRIT1) gene. Hum Mutat.","DOI":"10.1002\/humu.23196"},{"key":"ref_146","doi-asserted-by":"crossref","unstructured":"Yarham, J.W., Lamichhane, T.N., Pyle, A., Mattijssen, S., Baruffini, E., Bruni, F., Donnini, C., Vassilev, A., He, L., and Blakely, E.L. (2014). Defective i6A37 Modification of Mitochondrial and Cytosolic tRNAs Results from Pathogenic Mutations in TRIT1 and Its Substrate tRNA. PLoS Genet., 10.","DOI":"10.1371\/journal.pgen.1004424"},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1261\/rna.2652611","article-title":"A domain of the actin binding protein Abp140 is the yeast methyltransferase responsible for 3-methylcytidine modification in the tRNA anti-codon loop","volume":"17","author":"Haider","year":"2011","journal-title":"RNA"},{"key":"ref_148","doi-asserted-by":"crossref","unstructured":"Han, L., Marcus, E., D\u2019Silva, S., and Phizicky, E.M. (2016). S. cerevisiae Trm140 has two recognition modes for 3-methylcytidine modification of the anticodon loop of tRNA substrates. RNA, 406\u2013419.","DOI":"10.1261\/rna.059667.116"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1080\/15476286.2015.1008358","article-title":"Diversity in mechanism and function of tRNA methyltransferases","volume":"12","author":"Swinehart","year":"2015","journal-title":"RNA Biol."},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1089\/dna.2011.1437","article-title":"Transfer RNA methytransferases and their corresponding modifications in budding yeast and humans: Activities, predications, and potential roles in human health","volume":"31","author":"Towns","year":"2012","journal-title":"DNA Cell Biol."},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1261\/rna.2653411","article-title":"Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae","volume":"17","author":"Noma","year":"2011","journal-title":"RNA"},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1007\/s00239-005-0311-0","article-title":"Evolution of +1 Programmed Frameshifting Signals and Frameshift-Regulating tRNAs in the Order Saccharomycetales","volume":"63","author":"Farabaugh","year":"2006","journal-title":"J. Mol. Evol."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1017\/S1355838299982201","article-title":"Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: Identification of the gene and substrate specificity of the enzyme","volume":"5","author":"Motorin","year":"1999","journal-title":"RNA"},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"2020","DOI":"10.15252\/embj.201489282","article-title":"Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders","volume":"33","author":"Blanco","year":"2014","journal-title":"EMBO J."},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"1532","DOI":"10.1261\/rna.051524.115","article-title":"NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs","volume":"21","author":"Haag","year":"2015","journal-title":"RNA"},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"1811","DOI":"10.1093\/emboj\/21.7.1811","article-title":"Trm7p catalyses the formation of two 2\u2032-O-methylriboses in yeast tRNA anticodon loop","volume":"21","author":"Pintard","year":"2002","journal-title":"EMBO J."},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1016\/j.molmed.2014.01.008","article-title":"Role of tRNA modifications in human diseases","volume":"20","author":"Torres","year":"2014","journal-title":"Trends Mol. Med."},{"key":"ref_159","doi-asserted-by":"crossref","unstructured":"Lai, C.W., Chen, H.L., Lin, K.Y., Liu, F.C., Chong, K.Y., Cheng, W.T., and Chen, C.M. (2014). FTSJ2, a heat shock-inducible mitochondrial protein, suppresses cell invasion and migration. PLoS One, 9.","DOI":"10.1371\/journal.pone.0090818"},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"31386","DOI":"10.1074\/jbc.M113.515692","article-title":"Mitochondrial ribosomal RNA (rRNA) methyltransferase family members are positioned to modify nascent rRNA in foci near the mitochondrial DNA nucleoid","volume":"288","author":"Lee","year":"2013","journal-title":"J. Biol. Chem."},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"27415","DOI":"10.1074\/jbc.M113.501569","article-title":"Partitioning of the nuclear and mitochondrial tRNA 3\u2032-end processing activities between two different proteins in Schizosaccharomyces pombe","volume":"288","author":"Zhang","year":"2013","journal-title":"J. Biol. Chem."},{"key":"ref_162","doi-asserted-by":"crossref","unstructured":"Dittmar, K.A., Goodenbour, J.M., and Pan, T. (2006). Tissue-Specific Differences in Human Transfer RNA Expression. PLoS Genet., 2.","DOI":"10.1371\/journal.pgen.0020221"},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"e14295","DOI":"10.7554\/eLife.14295","article-title":"Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation","volume":"5","author":"Ishimura","year":"2016","journal-title":"eLife"},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1261\/rna.5070303","article-title":"Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9","volume":"9","author":"Jackman","year":"2003","journal-title":"RNA"},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"11583","DOI":"10.1093\/nar\/gks910","article-title":"A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase\u2014extensive moonlighting in mitochondrial tRNA biogenesis","volume":"40","author":"Vilardo","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.ajhg.2016.06.013","article-title":"Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies","volume":"99","author":"Metodiev","year":"2016","journal-title":"Am. J. Human Genet."},{"key":"ref_167","doi-asserted-by":"crossref","unstructured":"Igoillo-Esteve, M., Genin, A., Lambert, N., Desir, J., Pirson, I., Abdulkarim, B., Simonis, M., Drielsma, A., Marselli, L., and Marchetti, P. (2013). tRNA methyltransferase homolog gene TRMT10A mutation in young onset diabetes and primary microcephaly in humans. PLoS Genet., 9.","DOI":"10.1371\/journal.pgen.1003888"},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1136\/jmedgenet-2014-102282","article-title":"TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly","volume":"51","author":"Gillis","year":"2014","journal-title":"J. Med. Genet."},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"912","DOI":"10.12688\/f1000research.7106.1","article-title":"Case Report: Compound heterozygous nonsense mutations in TRMT10A are associated with microcephaly, delayed development, and periventricular white matter hyperintensities","volume":"4","author":"Narayanan","year":"2015","journal-title":"F1000Research"},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"e21","DOI":"10.1111\/dme.13024","article-title":"tRNA methyltransferase homologue gene TRMT10A mutation in young adult-onset diabetes with intellectual disability, microcephaly and epilepsy","volume":"33","author":"Yew","year":"2016","journal-title":"Diabet. Med."},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"3167","DOI":"10.1002\/ajmg.a.37341","article-title":"Homozygous deletion of TRMT10A as part of a contiguous gene deletion in a syndrome of failure to thrive, delayed puberty, intellectual disability and diabetes mellitus","volume":"167A","author":"Zung","year":"2015","journal-title":"Am. J. Med. Genet. Part A"},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1126\/science.1120976","article-title":"Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2","volume":"311","author":"Goll","year":"2006","journal-title":"Science"},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1146\/annurev.biochem.74.010904.153721","article-title":"Eukaryotic cytosine methyltransferases","volume":"74","author":"Goll","year":"2005","journal-title":"Annu. Rev. Biochem."},{"key":"ref_174","doi-asserted-by":"crossref","unstructured":"Kaiser, S., Jurkowski, T.P., Kellner, S., Schneider, D., Jeltsch, A., and Helm, M. (2016). The RNA methyltransferase Dnmt2 methylates DNA in the structural context of a tRNA. RNA Biol., 1\u201311.","DOI":"10.1080\/15476286.2016.1236170"},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"1590","DOI":"10.1101\/gad.586710","article-title":"RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage","volume":"24","author":"Schaefer","year":"2010","journal-title":"Genes Dev."},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1016\/j.celrep.2013.07.046","article-title":"The RNA methyltransferase Dnmt2 is required for efficient Dicer-2-dependent siRNA pathway activity in Drosophila","volume":"4","author":"Durdevic","year":"2013","journal-title":"Cell Rep."},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.biochi.2015.02.022","article-title":"Somatic cancer mutations in the DNMT2 tRNA methyltransferase alter its catalytic properties","volume":"112","author":"Elhardt","year":"2015","journal-title":"Biochimie"},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1146\/annurev-genet-110410-132531","article-title":"Human mitochondrial tRNAs: Biogenesis, function, structural aspects, and diseases","volume":"45","author":"Suzuki","year":"2011","journal-title":"Annu. Rev. Genet."},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1002\/wrna.27","article-title":"Mitochondrial tRNA mutations and disease","volume":"1","author":"Yarham","year":"2010","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"158","DOI":"10.3389\/fgene.2014.00158","article-title":"Transfer RNA and human disease","volume":"5","author":"Abbott","year":"2014","journal-title":"Front. Genet."},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1038\/nrg3861","article-title":"Emerging roles of tRNA in adaptive translation, signalling dynamics and disease","volume":"16","author":"Kirchner","year":"2015","journal-title":"Nat. Rev. Genet."},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1002\/emmm.201100626","article-title":"Aminoacyl-tRNA synthetases in medicine and disease","volume":"5","author":"Yao","year":"2013","journal-title":"EMBO Mol. Med."},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1038\/nrmicro2472","article-title":"Cellular mechanisms that control mistranslation","volume":"8","author":"Reynolds","year":"2010","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"14338","DOI":"10.1073\/pnas.0504070102","article-title":"Why highly expressed proteins evolve slowly","volume":"102","author":"Drummond","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1016\/j.molmed.2015.04.005","article-title":"Type 2 diabetes as a protein misfolding disease","volume":"21","author":"Mukherjee","year":"2015","journal-title":"Trends Mol. Med."},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1507\/endocrj.EJ11-0099","article-title":"Functional loss of Cdkal1, a novel tRNA modification enzyme, causes the development of type 2 diabetes","volume":"58","author":"Wei","year":"2010","journal-title":"Endocr. J."},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"3598","DOI":"10.1172\/JCI58056","article-title":"Deficit of tRNALys modification by Cdkal1 causes the development of type 2 diabetes in mice","volume":"121","author":"Wei","year":"2011","journal-title":"J. Clin. Invest."},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"12588","DOI":"10.1073\/pnas.0404957101","article-title":"Tissue-specific codon usage and the expression of human genes","volume":"101","author":"Plotkin","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Biomolecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-273X\/7\/1\/26\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T18:30:00Z","timestamp":1760207400000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-273X\/7\/1\/26"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3,8]]},"references-count":188,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,3]]}},"alternative-id":["biom7010026"],"URL":"https:\/\/doi.org\/10.3390\/biom7010026","relation":{},"ISSN":["2218-273X"],"issn-type":[{"value":"2218-273X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,3,8]]}}}