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Charging the Code — Trna Modification Complexes Available online at www.sciencedirect.com ScienceDirect Charging the code — tRNA modification complexes 1,2,4 1,3,4 Roscisław Krutyhołowa , Karol Zakrzewski and 1 Sebastian Glatt All types of cellular RNAs are post-transcriptionally modified, of RNA bases in and around the anticodon impacts on constituting the so called ‘epitranscriptome’. In particular, their intrinsic geometry and canonical Watson–Crick base tRNAs and their anticodon stem loops represent major pair interactions between codons and anticodons [5–7]. modification hotspots. The attachment of small chemical These alterations strongly influence the dynamics of groups at the heart of the ribosomal decoding machinery can tRNA selection at the ribosomal A-site [8] and subse- directly affect translational rates, reading frame maintenance, quently affect the local elongation speed, co-translational co-translational folding dynamics and overall proteome folding dynamics [9], proteome stability and cell survival stability. The variety of tRNA modification patterns is driven by [10]. tRNA modifications were initially thought to be the activity of specialized tRNA modifiers and large routinely and uniformly added to their respective tRNA modification complexes. Notably, the absence or dysfunction molecules. To date, it is becoming increasingly clear that of these cellular machines is correlated with several human most of them are dynamically regulated in response to pathophysiologies. In this review, we aim to highlight the most environmental cues [11,12] and an intense cross talk recent scientific progress and summarize currently available between various modifications and their pathways structural information of the most prominent eukaryotic tRNA emerges [13]. Here, we aim to provide a comprehensive modifiers. summary of the respective modification enzymes that produce this plethora of posttranscriptional modifications Addresses patterns. We summarize available structural and func- 1 Max Planck Research Group at the Malopolska Centre of tional knowledge concerning the most abundant families Biotechnology, Jagiellonian University, Krakow, Poland 2 of tRNA modification enzymes. Our focus lies on the Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Poland main modification cascades and known macromolecular 3 Postgraduate School of Molecular Medicine, Warsaw, Poland assemblies that target the ASL in eukaryotes (Figure 1). These partially highly complex molecular machines are Corresponding author: Glatt, Sebastian ([email protected]) 4 not only important guardians of the proteome and regu- These authors contributed equally. latory factors of translational elongation, but are also clinically very important. The pathophysiological conse- Current Opinion in Structural Biology 2019, 55:138–146 quences and clinical implications of disease-causing This review comes from a themed issue on Macromolecular assemblies mutations in tRNA modifiers are very well covered by recent expert reviews [14–17]. Edited by Ilya A Vakser and Andrzej Joachimiak For a complete overview see the Issue and the Editorial (t)RNA methyltransferases Available online 16th May 2019 Methylations affect multiple properties of tRNA mole- https://doi.org/10.1016/j.sbi.2019.03.014 cules, including folding dynamics, thermostability, mat- ã 0959-440X/ 2019 The Authors. Published by Elsevier Ltd. This is an uration as well as protection from cleavage or priming for open access article under the CC BY-NC-ND license (http://creative- the synthesis of subsequent modifications [18,19]. commons.org/licenses/by-nc-nd/4.0/). Eukaryotic tRNA methyltransferases (TRMs) typically utilize S-adenosyl methionine (SAM) as a methyl group donor which results in formation of a S-adenosyl-L- Introduction homocysteine and a methylated product [20]. In the The ‘Modomics’ database for RNA modification [1] cur- following section, we aim to highlight structurally char- rently lists 200 unique chemical modifications of RNA, acterized TRMs and describe their selectivity for certain with around half of them being detected in tRNAs of all tRNA species and specific base positions within the known species [2–4]. Despite their strong sequence vari- respective ASLs (Figure 2). ation, all cellular tRNAs need to fold into almost identical three-dimensional structures to fit the relatively narrow In detail, Trm1, which conducts a double methylation of tRNA binding sites of the ribosome during translation the exocyclic nitrogen of G26, which promotes a proper elongation. The possibility of incorporating chemical folding of multiple tRNA species by enforcing a water- 2 groups, which contribute additional biophysical proper- mediated interaction of m2 G26 with a nearby cytosine Ser Thr ties to the individual RNA bases, vastly expands the range [21,22]. In yeast, Trm140 binds tRNA and tRNA 3 6 of suitable sequences that can fold into the characteristic and catalyzes m C32 in a i A37-dependent manner [23]. L-shaped tRNA structure. In addition, the modification In human, Trm140 functionally corresponds to the Current Opinion in Structural Biology 2019, 55:138–146 www.sciencedirect.com Structure and function of tRNA modification enzymes Krutyhołowa, Zakrzewski and Glatt 139 Figure 1 Methylation 3’ Pseudouridilation 2 m 2G26 - Trm1 Um 44 Ψ27 - Pus1, Pus2 3 Ψ m C32 - Trm140 28 - Pus1 Ψ30 - Pus1 U/Cm - Trm7 (Ftsj2) 32 2 2 26 m G; m 2G Ψ31 - Pus6 Xm34 - Trm7 (Ftsj2) 5 Ψ32 - Pus8, Pus9 m C34 - Trm4, Nsun2,3 Ψ 5 27 5’ Ψ34 - Pus1 mcm U34 - Trm9 Ψ 5 Ψ 28 5 35 - Pus1, Pus7 mchm U34 - Abh8 40 m C Ψ 1 36 - Pus1 m I37 - Trm5 1 Ψ Ψ Ψ38 - Pus3 1 39 m m C37 - Trm5 Ψ39 - Pus3 5 m C38 - Dnmt2 Ψ 30 5 1 Ψ m C Thiolation 38 m Ψ39 - Nep1 5 2 m C40 - Dnmt2 s U34 - Mtu1, Ncs2/6 1 1 2 Um - Trm44 37 I m G; m I s U37 - Cdkal1 44 Ψ 31 Modifications at 34 yW s2U Wybutosine 3 m C 32 6 6 yW - Tyw1,2,3,4 Q34 - Tgt Ψ t A i A 37 4 36 ac C - Nat10 Ψ U/Cm 6 6 34 t /i modifications 5 τm U 34 - ? 33 6 35 Ψ t A37 - Sua5 5 f C34 - Abh1 6 i A37 - Trit1 5 nm U34 - Gtpbp3? Ψ 5 34 I Xm m C Adenine deamination 5 2 5-carboxymethyluridine Q nm U s U I34 - Adat2, Adat3 5 5 5 4 5 (m/n)cm U34 - Elp123456 f C τm UacC mchm U I37 - Adar2,(Adarb1) Current Opinion in Structural Biology tRNA modifications occurring within the tRNA anticodon region. Overview of the tRNA anticodon loop in cartoon representation. Individual modifications are grouped, highlighted, and labeled. Respectively from the left methylation (indigo), modification of position 34 (violet), 5-carboxymethyluridin (light green), pseudouridylation (rose), thiolation (yellow), 6 6 wybutosine (yW; blue) N6-isopentenyladenosine (i A) and N6-threonylcarbamoyladenosine (t A) (red), adenine deamination (teal). Modifications Glu occurring within anticodon region are plotted and highlighted on a model tRNA (PDB ID 2CV2). 5 Methyltransferase-like (Mettl) 2, 6 and 8 proteins [24,25]. for Nsun6, which catalyzes the m C72 modification [35 ]. Although Mettl2/6/8 are currently not structurally charac- Trm5 is another multifunctional enzyme, capable of con- 1 terized, structures of the Mettl3/Mettl14 complex that ducting m modification at G37 or I37. Interestingly, Trm5 6 provides N -adenosine methylation [26–28] and the also plays a role in some archaeal species during wybutosine Phe methyltransferase domain of Mettl16 [29] provide new (yW37) synthesis. Trm5 was co-crystalized with tRNA insights into the METTL protein family. The known and a SAM cleavage product [36 ]. Available structure structure of human Ftsj2, a homolog of yeast Trm7, elucidates both the Trm5-tRNA interaction and the moon- 0 reveals a typical class I TRM fold [18]. In yeast, 2 -O lightingactivityofTrm5inarchaea[36 ].Anothermember ribose methylation provided by Trm7 is guided by its of the class Dnmt2, historically considered a DNA-specific 5 interactions with Trm732 and Trm734, which drive the methyltransferase [37], provides a m C tRNA modification 5 reactions at positions 32 and 34, respectively [30]. Trm4 at C38 and C40 [38]. m C38 was demonstrated to prevent the 5 5 catalyzes modifications at positions m C48 and m C49; generation of tRNA-derived fragments [39], which appear 5 however, it is also capable of generating m C34 and due to the tRNA cleavage under stress conditions and may 5 m C40 [31]. Archaeal Trm4 was co-crystalized in the act as regulatory RNAs [40]. Although available structures presence of a naturally occurring inhibitor sinefungin do not provide an explicit explanation for tRNA recogni- [32]. In human, Trm4 has two functional counterparts, tion, the enzymatic activity of a fungal Dnmt2 was recently 5 Nsun2 and Nsun3 catalyzing m modifications in the found to be stimulated by the presence of queuosine [41 ]. nucleus and mitochondria, respectively. In addition to its tRNA modification activity, Nsun2 was reported to Pseudouridine synthases methylate miRNAs [33]. Methylation of the wobble Pseudouridylation is one of the most widely spread mod- cytosine provided by Nsun3 is required for initiation of ification in all types of RNAs, including tRNAs, snRNAs, 5 Met 5-formylcytidine (f C34) synthesis on tRNA [34]. The rRNA, ncRNAs, and mRNAs, and occurs in each domain first known structure of Nsun family member was solved of life [42]. This altered form of a uridine base arises www.sciencedirect.com Current Opinion in Structural Biology 2019, 55:138–146 140 Macromolecular assemblies Figure 2 Mettl3 • Mettl14 Trm1 (Trmt1) Dnmt2 (M.HsaIIP) CTM RRM RRM CTD Mettl3 Mettl14 Mettl2,6,8 2 m 2G26 Trm5 (Trmt5) Ftsj2 (Trm7) 5 m C40 5 3 m C38 m C32 RRM 5 Nm32 m C37 5 5 5 m C34 mcm U34 mchm U34 Trm4 (Ncl1, Nsun2) Trm9 • Trm112 Abh8 RRM Trm9-like AlkB-like domain RRM Trm9 Trm112 Current Opinion in Structural Biology Structural overview of methyltransferases acting on the ASL of tRNA. tRNA methyltransferases share a structurally similar TRM domain (dark blue) and an RNA recognition motif (RRM, orange).
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