Published online 30 January 2019 Nucleic Acids Research, 2019, Vol. 47, No. 5 2143–2159 doi: 10.1093/nar/gkz011 SURVEY AND SUMMARY Matching tRNA modifications in humans to their known and predicted enzymes Downloaded from https://academic.oup.com/nar/article-abstract/47/5/2143/5304329 by Vrije Universiteit Amsterdam user on 12 March 2019 Valerie´ de Crecy-Lagard´ 1,2,*, Pietro Boccaletto3, Carl G. Mangleburg1, Puneet Sharma4,5, Todd M. Lowe 6,*, Sebastian A. Leidel 4,5,7,* and Janusz M. Bujnicki 3,8,* 1Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA, 2Cancer and Genetic Institute, University of Florida, Gainesville, FL 32611, USA, 3Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland, 4Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany, 5Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany, 6Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA, 7Research Group for RNA Biochemistry, Institute of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland and 8Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan,´ Poland Received September 05, 2018; Revised December 28, 2018; Editorial Decision January 03, 2019; Accepted January 10, 2019 ABSTRACT cases in detail and propose candidates whenever possible. Finally, tissue-specific expression analy- tRNA are post-transcriptionally modified by chemi- sis shows that modification genes are highly ex- cal modifications that affect all aspects of tRNA bi- pressed in proliferative tissues like testis and trans- ology. An increasing number of mutations underly- formed cells, but scarcely in differentiated tissues, ing human genetic diseases map to genes encoding with the exception of the cerebellum. Our work pro- for tRNA modification enzymes. However, our knowl- vides a comprehensive up to date compilation of hu- edge on human tRNA-modification genes remains man tRNA modifications and their enzymes that can fragmentary and the most comprehensive RNA mod- be used as a resource for further studies. ification database currently contains information on approximately 20% of human cytosolic tRNAs, pri- marily based on biochemical studies. Recent high- INTRODUCTION throughput methods such as DM-tRNA-seq now al- The acquisition of post-transcriptional chemical modifica- low annotation of a majority of tRNAs for six specific tions is an essential part of the maturation process required base modifications. Furthermore, we identified large to generate functional tRNA molecules (1). Modifications gaps in knowledge when we predicted all cytosolic have different roles in controlling stability, folding and de- and mitochondrial human tRNA modification genes. coding properties of tRNAs and can be determinants or Only 48% of the candidate cytosolic tRNA modifica- anti-determinants for other components of the translation tion enzymes have been experimentally validated in apparatus like e.g. aminoacyl-tRNA synthetases (2,3). In mammals (either directly or in a heterologous sys- addition, tRNA modifications can be recognition elements tem). Approximately 23% of the modification genes of ribonucleases (4), leading to the generation of tRNA fragments that affect multiple cellular processes (5). (cytosolic and mitochondrial combined) remain un- However, very few modifications such as m1G37, 55 or known. We discuss these ‘unidentified enzymes’ t6A37 are present at a specific position of a particular tRNA *To whom correspondence should be addressed. Tel: +1 352 392 9416; Fax: +1 352 392 5922; Email: [email protected] Correspondence may also be addressed to Todd Lowe. Tel: +1 831 459 1511; Email: [email protected] Correspondence may also be addressed to Sebastian Leidel. Tel: +41 31 6314296; Email: [email protected] Correspondence may also be addressed to Janusz Bujnicki. Tel: +48 22 597 0750; Fax: +48 22 597 0715; Email: [email protected] Present address: Carl G. Mangleburg, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. C The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 2144 Nucleic Acids Research, 2019, Vol. 47, No. 5 in (almost) all known organisms. Most of them are specific modifications. The goal of our analysis was to compile a to particular taxons, from species to kingdoms. For exam- comprehensive list of known and predicted tRNA modifica- ple, lysidine (k2C34) is a hallmark of bacteria (6), while ar- tions in Homo sapiens with genes implicated in their biosyn- chaeosine (G+15) is only found in archaea (7). Depending thesis. This analysis allowed for the identification of the re- on the organism, the total number of genes encoding tRNA maining gaps of knowledge in the field of human tRNA modification enzymes varies between as little as eleven in modifications and will help to guide future experiments. some obligate symbionts (8) to around an estimated hun- Furthermore, we have used publicly available datasets in or- dred in humans of which 50 are currently represented in der to determine the expression profiles and proteomic ev- Downloaded from https://academic.oup.com/nar/article-abstract/47/5/2143/5304329 by Vrije Universiteit Amsterdam user on 12 March 2019 MODOMICS (9). idence of known and predicted modification enzymes. Our The near complete sets of tRNA modification genes are work will facilitate access to the current knowledge on hu- currently available for only one organism per domain of life: man tRNA modification enzymes for a wider community Saccharomyces cerevisiae for eukarya, where only one gene of biologists. required for the formation of ncm5U out of cm5U is missing (10), Escherichia coli for bacteria where only the genes for MATERIALS AND METHODS ho5U34 and Acp3U47-formation remain unidentified and Haloferax volcanii for archaea where a handful of genes are The set of human isoacceptor tRNAs (i.e. tRNAs that missing (1). Beyond these three organisms, the annotation are acylated with the same amino acid regardless of the of tRNA modification genes remains scarce, because of sev- anticodon sequence) was extracted from the Genomic eral issues: First, RNA modification enzymes are often part tRNA Database (GtRNAdb): http://gtrnadb.ucsc.edu/ (29) of large multifunctional protein families such as the Ross- and is summarized here: http://gtrnadb.ucsc.edu/genomes/ mann Fold Methyltransferase (RFM) superfamily, which eukaryota/Hsapi19/ can act on other substrates than RNA (11). For example, All modifications present in the sequences of cytoso- some RNA methyltransferases are closely related to protein lic and mitochondrial tRNA of human (H. sapiens), cow methyltransferases or DNA methyltransferases (11). Sec- (Bos taurus), rat (Rattus norvegicus), and mouse (Mus mus- ond, closely related members of orthologous families often culus) were extracted from the MODOMICS database of introduce a similar chemical modification, but in different RNA modification pathways (http://modomics.genesilico. RNAs and at different positions. For example, members of pl/)(9). This provided a first list that was then updated the TrmFO family methylate tRNA or rRNA depending with one modification from the literature5 (m C34 in Leu- on the organism (12). Third, related enzymes can generate CAA-tRNA) and several human modifications detected chemically distinct modifications. For example closely re- with novel tRNAseq methods (30)(m3C20 in Met-CAU- lated Radical-SAM enzymes introduce methyl groups at dif- tRNA and m3C47 in Leu-CAG-tRNA and most Ser- ferent positions of nucleosides like in m2Aorm8A(13). Fi- tRNAs, m1A16 in mito-Arg-TCG-tRNA and m3C32 in nally, the same chemical modification, in particular methyl mito-Thr-UGU-tRNA and mito-Ser-UGA) that were miss- groups, can be introduced by proteins that are dissimilar ing from MODOMICS. The MODOMICS database was (14) or even evolutionarily unrelated having arisen through updated accordingly. non-orthologous gene displacements (15). For example, the High-throughput tRNA-seq modification data was formation of the universal m1G37 is catalyzed by TrmD derived from published study data sets (30–32). The and Trm5, two enzymes of completely different evolution- protein and literature mining tools of NCBI (33)as ary origins in bacteria and in eukarya/archaea (16). The well as the Uniprot resource and Id/Mapping tools combination of these factors has made it difficult to iden- (34) were used to gather data. Gene names were gath- tify enzymes responsible for many tRNA modifications and ered from the HUGO Gene Nomenclature Commit- hence to determine the function of those tRNA modifica- tee (https://www.genenames.org)(35). Protein inter- tions in many species including humans. action data was derived from BioGrid (36) and the Recently, an increasing number of mutations causing ge- predicted mitochondrial localization from MitoCarta netic diseases have been mapped to human genes encod- (https://www.broadinstitute.org/files/shared/metabolism/ ing tRNA