On the role of ribosylthymine in prokaryotic tRNA function

Beyond the Anticodon: tRNA Core Modifications and Their Impact on Structure, Translation and Stress Adaptation

Transfer RNAs (tRNAs) are heavily decorated with post-transcriptional chemical modifications. Approximately 100 different modifications have been identified in tRNAs, and each tRNA typically contains 5-15 modifications that are incorporated at specific sites along the tRNA sequence. These modifications may be classified into two groups according to their position in the three-dimensional tRNA structure, i.e., modifications in the tRNA core and modifications in the anticodon-loop (ACL) region. Since many modified nucleotides in the tRNA core are involved in the formation of tertiary interactions implicated in tRNA folding, these modifications are key to tRNA stability and resistance to RNA decay pathways. In comparison to the extensively studied ACL modifications, tRNA core modifications have generally received less attention, although they have been shown to play important roles beyond tRNA stability. Here, we review and place in perspective selected data on tRNA core modifications. We present their impact on tRNA structure and stability and report how these changes manifest themselves at the functional level in translation, fitness and stress adaptation.

Crystal structure of the RNA-recognition motif of Drosophila melanogaster tRNA (uracil-5-)-methyltransferase homolog A

Human tRNA (uracil-5-)-methyltransferase 2 homolog A (TRMT2A) is the dedicated enzyme for the methylation of uridine 54 in transfer RNA (tRNA). Human TRMT2A has also been described as a modifier of polyglutamine (polyQ)-derived neuronal toxicity. The corresponding human polyQ pathologies include Huntington's disease and constitute a family of devastating neurodegenerative diseases. A polyQ tract in the corresponding disease-linked protein causes neuronal death and symptoms such as impaired motor function, as well as cognitive impairment. In polyQ disease models, silencing of TRMT2A reduced polyQ-associated cell death and polyQ protein aggregation, suggesting this protein as a valid drug target against this class of disorders. In this paper, the 1.6 Å resolution crystal structure of the RNA-recognition motif (RRM) from Drosophila melanogaster, which is a homolog of human TRMT2A, is described and analysed.

Conserved 5-methyluridine tRNA modification modulates ribosome translocation

While the centrality of post-transcriptional modifications to RNA biology has long been acknowledged, the function of the vast majority of modified sites remains to be discovered. Illustrative of this, there is not yet a discrete biological role assigned for one the most highly conserved modifications, 5-methyluridine at position 54 in tRNAs (m 5 U54). Here, we uncover contributions of m 5 U54 to both tRNA maturation and protein synthesis. Our mass spectrometry analyses demonstrate that cells lacking the enzyme that installs m 5 U in the T-loop (TrmA in E. coli , Trm2 in S. cerevisiae ) exhibit altered tRNA modifications patterns. Furthermore, m 5 U54 deficient tRNAs are desensitized to small molecules that prevent translocation in vitro. This finding is consistent with our observations that, relative to wild-type cells, trm2 Δ cell growth and transcriptome-wide gene expression are less perturbed by translocation inhibitors. Together our data suggest a model in which m 5 U54 acts as an important modulator of tRNA maturation and translocation of the ribosome during protein synthesis.

Human TRMT2A methylates tRNA and contributes to translation fidelity

5-Methyluridine (m5U) is one of the most abundant RNA modifications found in cytosolic tRNA. tRNA methyltransferase 2 homolog A (hTRMT2A) is the dedicated mammalian enzyme for m5U formation at tRNA position 54. However, its RNA binding specificity and functional role in the cell are not well understood. Here we dissected structural and sequence requirements for binding and methylation of its RNA targets. Specificity of tRNA modification by hTRMT2A is achieved by a combination of modest binding preference and presence of a uridine in position 54 of tRNAs. Mutational analysis together with cross-linking experiments identified a large hTRMT2A-tRNA binding surface. Furthermore, complementing hTRMT2A interactome studies revealed that hTRMT2A interacts with proteins involved in RNA biogenesis. Finally, we addressed the question of the importance of hTRMT2A function by showing that its knockdown reduces translation fidelity. These findings extend the role of hTRMT2A beyond tRNA modification towards a role in translation.

Small-molecule modulators of TRMT2A decrease PolyQ aggregation and PolyQ-induced cell death

Polyglutamine (polyQ) diseases are characterized by an expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats encoding for an uninterrupted prolonged polyQ tract. We previously identified TRMT2A as a strong modifier of polyQ-induced toxicity in an unbiased large-scale screen in Drosophila melanogaster. This work aimed at identifying and validating pharmacological TRMT2A inhibitors as treatment opportunities for polyQ diseases in humans. Computer-aided drug discovery was implemented to identify human TRMT2A inhibitors. Additionally, the crystal structure of one protein domain, the RNA recognition motif (RRM), was determined, and Biacore experiments with the RRM were performed. The identified molecules were validated for their potency to reduce polyQ aggregation and polyQ-induced cell death in human HEK293T cells and patient derived fibroblasts. Our work provides a first step towards pharmacological inhibition of this enzyme and indicates TRMT2A as a viable drug target for polyQ diseases.

TRMT2A is a novel cell cycle regulator that suppresses cell proliferation

During the maturation of transfer RNA (tRNA), a variety of chemical modifications can be introduced at specific nucleotide positions post-transcriptionally. 5-Methyluridine (m⁵U) is one of the most common and conserved modifications from eubacteria to eukaryotes. Although TrmA protein in Escherichia coli and Trm2p protein in Saccharomyces cerevisiae, which are responsible for the 5-methylation of uracil at position 54 (m⁵U54) on tRNA, are well characterized, the biological function of the U54 methylation responsible enzyme in mammalian species remains largely unexplored. Here, we show that the mammalian tRNA methyltransferase 2 homolog A (TRMT2A) protein harbors an RNA recognition motif in the N-terminus and the conserved uracil-C5-methyltransferase domain of the TrmA family in the C-terminus. TRMT2A predominantly localizes to the nucleus in HeLa cells. TRMT2A-overexpressing cells display decreased cell proliferation and altered DNA content, while TRMT2A-deficient cells exhibit increased growth. Thus, our results reveal the inhibitory role of TRMT2A on cell proliferation and cell cycle control, providing evidence that TRMT2A is a candidate cell cycle regulator in mammals.

Transfer RNA Modification

Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica contains 31 different modified nucleosides, which are all, except for one (Queuosine[Q]), synthesized on an oligonucleotide precursor, which through specific enzymes later matures into tRNA. The corresponding structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The syntheses of some of them (e.g.,several methylated derivatives) are catalyzed by one enzyme, which is position and base specific, but synthesis of some have a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N6-threonyladenosine [t6A],and Q). Several of the modified nucleosides are essential for viability (e.g.,lysidin, t6A, 1-methylguanosine), whereas deficiency in others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those, which are present in the body of the tRNA, have a primarily stabilizing effect on the tRNA. Thus, the ubiquitouspresence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.

Transfer RNA Modification: Presence, Synthesis, and Function

Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica serovar Typhimurium contains 33 different modified nucleosides, which are all, except one (Queuosine [Q]), synthesized on an oligonucleotide precursor, which by specific enzymes later matures into tRNA. The structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The synthesis of the tRNA-modifying enzymes is not regulated similarly, and it is not coordinated to that of their substrate, the tRNA. The synthesis of some of them (e.g., several methylated derivatives) is catalyzed by one enzyme, which is position and base specific, whereas synthesis of some has a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N  6-cyclicthreonyladenosine [ct6A], and Q). Several of the modified nucleosides are essential for viability (e.g., lysidin, ct6A, 1-methylguanosine), whereas the deficiency of others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those that are present in the body of the tRNA primarily have a stabilizing effect on the tRNA. Thus, the ubiquitous presence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.

The crystal structure of a novel SAM-dependent methyltransferase PH1915 from Pyrococcus horikoshii

The S-adenosyl-L-methionine (SAM)-dependent methyltransferases represent a diverse and biologically important class of enzymes. These enzymes utilize the ubiquitous methyl donor SAM as a cofactor to methylate proteins, small molecules, lipids, and nucleic acids. Here we present the crystal structure of PH1915 from Pyrococcus horikoshii OT3, a predicted SAM-dependent methyltransferase. This protein belongs to the Cluster of Orthologous Group 1092, and the presented crystal structure is the first representative structure of this protein family. Based on sequence and 3D structure analysis, we have made valuable functional insights that will facilitate further studies for characterizing this group of proteins. Specifically, we propose that PH1915 and its orthologs are rRNA- or tRNA-specific methyltransferases.

Recognition of the T-arm of tRNA by tRNA (m5U54)-methyltransferase is not sequence specific

tRNA (m5U54)-methyltransferase (RUMT) catalyzes the methylation of U54 of tRNAs. In contrast to enzymes which recognize a particular tRNA, RUMT recognizes features common to all tRNAs. We have shown that these features reside in the T-arm of tRNA and constructed a minimal consensus sequence for RUMT recognition and catalysis (Gu et al., 1991b). Here, we have mutated each conserved T-loop residue and conserved T-stem base pair to bases or base pairs which are not observed in Escherichia coli tRNA. The substrate specificity of RUMT for 30 in vitro synthesized T-arm mutants of tRNAPhe and 37 mutants of the 17-mer analog of the T-arm derived from tRNA1Val was investigated. A 2-5 base pair stem was essential for recognition of the T-arm by RUMT, but the base composition of the stem was unimportant. The 7-base size of the T-loop maintained by the stem was essential for RUMT recognition. For tRNA, most base substitutions in the 7-base loop did not eliminate RUMT activity, except for any mutation of the methyl acceptor U54 and the C56G mutation. The effect of base and base pair mutations on Kcat or the rate of methylation by RUMT was more striking than the effect on the Kd for binding to RUMT. In comparison with mutations in the T-loop of intact tRNA, base mutation in the T-loop of the 17-mer T-arm had a more deleterious effect on binding and methylation. Surprisingly, recognition of tRNA by RUMT appears to reside in the three-dimensional structure of the seven-member T-loop rather than in its primary structure.

In vitro analysis of translational rate and accuracy with an unmodified tRNA

Escherichia coli tRNA(Phe) transcript lacking all the modified nucleosides was investigated in an in vitro translation system. To estimate the affinity of tRNA toward EF-Tu, Kd and K-1 were measured by the nuclease protection assay, and it was shown that the absence of modifications decreases ternary complex stability less than 2-fold. The activity of unmodified Phe-tRNA(Phe) on E. coli ribosomes was compared to modified Phe-tRNA(Phe) using the framework of the kinetic proofreading mechanism (Thompson & Dix, 1982) with both cognate and noncognate codons. Values of the individual rate constants in the elongation process showed that the modifications increased the accuracy of translation by (1) decreasing the rate of dipeptide synthesis and (2) increasing the rate of rejection with noncognate codons.

The gene for a tRNA modifying enzyme, m5U54-methyltransferase, is essential for viability in Escherichia coli

One of the most abundant modified nucleosides in tRNA is 5-methyluridine (m5U or rT, ribothymidine). The enzyme tRNA(m5U54)methyltransferase [S-adenosyl-L-methionine:tRNA (uracil-5-)-methyltransferase, EC 2.1.1.35] (the trmA gene product) catalyzes S-adenosylmethionine-dependent methylation of the uracil in position 54 (T psi C loop) in all Escherichia coli tRNAs to form m5U. Hitherto no modified nucleoside in tRNA has been shown to be essential for growth, although their importance in fine tuning the function of tRNA is well established. In this paper, we show that the structural gene trmA is essential for viability, although the known catalytic activity of the tRNA(m5U54)methyltransferase is not.

High-level expression of Escherichia coli tRNA (m5U54)-methyltransferase

A cloning and high-expression system for tRNA (m5U54)-methyltransferase (RUMT) is described. Polymerase chain reaction (PCR) was used to replicate the coding sequence and create flanking restriction sites for cloning. The PCR product was then inserted into expression vectors containing the tac and PL promoters. With the PL promoter, induced cells produced about 1.5% of their soluble protein as catalytically active RUMT. With the tac promoter, up to 8% of the total cell protein was active enzyme, and RUMT was purified to near homogeneity in three steps.

Purification of transfer RNA (m5U54)-methyltransferase from Escherichia coli. Association with RNA

tRNA (m5U54)-methyltransferase (EC 2.1.1.35) catalyzes the transfer of methyl groups from S-adenosyl-L-methionine to transfer ribonucleic acid (tRNA) and thereby forming 5-methyluridine (m5U, ribosylthymine) in position 54 of tRNA. This enzyme, which is involved in the biosynthesis of all tRNA chains in Escherichia coli, was purified 5800-fold. A hybrid plasmid carrying trmA, the structural gene for tRNA (m5U54)-methyltransferase was used to amplify genetically the production of this enzyme 40-fold. The purest fraction contained three polypeptides of 42 kDa, 41 kDa and 32 kDa and a heterogeneous 48-57-kDa RNA-protein complex. All the polypeptides seem to be related to the 42/41-kDa polypeptides previously identified as the tRNA (m5U54)-methyltransferase. RNA comprises about 50% (by mass) of the complex. The RNA seems not to be essential for the methylation activity, but may increase the activity of the enzyme. The amino acid composition is presented and the N-terminal sequence of the 42-kDa polypeptide was found to be: Met-Thr-Pro-Glu-His-Leu-Pro-Thr-Glu-Gln-Tyr-Glu-Ala-Gln-Leu-Ala-Glu-Lys- . The tRNA (m5U54)-methyltransferase has a pI of 4.7 and a pH optimum of 8.0. The enzyme does not require added cations but is stimulated by Mg2+. The apparent Km for tRNA and S-adenosyl-L-methionine are 80 nM and 17 microM, respectively.

Alteration of tRNA modification in eukaryotes: causes and consequences

To evaluate the role of the modified nucleosides in tRNA function, especially their involvement in regulatory mechanisms of development, differentiation, or neoplastic transformation we use the following organisms: eubacteria, the slime mold D. discoideum, the topminnow Xiphophorus, and mice. Ribosylthymine, a common modified nucleoside at position 54 in tRNAs of prokaryotes and the major class of eukaryotic elongator tRNAs, is involved in the binding to the ribosomal A-site and is important for the proper functioning of tRNA during translation. Alterations in the extent of this modification occur early in the development of D. discoideum. The fully methylated species are found on polysomes, actively synthesizing protein. The partially methylated tRNAs accumulate in the nuclei, and might be involved in regulatory mechanisms at the transcriptional level. The Q base, a modified deazaguanine derivative, is present at position 34, the first position of the anticodon of tRNAAsn, tRNATyr, and tRNAHis. Alterations in the extent of this modification occur in corresponding tRNAs during the first minutes after the onset of development in D. discoideum and before final differentiation into spores, indicating that Q is important for developmental processes. Changes in the modification of G34 to Q34 in specific tRNAs of the melanophoric system of the topminnow Xiphophorus further support the view that Q is necessary in differentiation. In plasmacytomas and in Ehrlich ascites tumor cells of mice, the amount of unmodified G34 in corresponding tRNAs is correlated to the growth rate, density, or age of the tumor cells.

Regulation of tRNA methyltransferase activities by spermidine and putrescine. Inhibition of polyamine synthesis and tRNA methylation by alpha-methylornithine or 1,3-diaminopropan-2-ol in Dictyostelium

Inhibitors of polyamine synthesis (alpha-methylornithine and 1,3-diaminopropan-2-ol) were used to study the relationship between polyamine synthesis and specific methylations of tRNA in Dictyostelium discoideum during vegetative growth. Polyamine concentrations were found to be 10 mM for putrescine, 1.6 mM for spermidine and 7 mM for 1,3-diaminopropane throughout the growth stage. On treatment of growing amoebae with alpha-methylornithine or with 1,3-diaminopropan-2-ol (each at 5 mM), the syntheses of putrescine, spermidine and 1,3-diaminopropane were arrested within 4h. After polyamine synthesis had ceased, the incorporation of methyl groups into tRNA was considerably decreased under conditions that had no effect on the incorporation of uridine into tRNA, or on net syntheses of protein and of DNA. The following nucleosides in tRNA were concerned: 1 methyladenosine, 5-methylcytidine, 7-methylguanosine, 2-methylguanosine, N2N2-dimethylguanosine and 5-methyluridine (ribosylthymine). The corresponding tRNA methyltransferases, determined in Mg2+-free enzyme extracts, proved to be inactive unless polyamines were added. Putrescine and/or spermidine at concentrations of 10 mM or 1-2 mM respectively stimulate the transmethylation reaction in vitro to a maximal rate and to an optimal extent at exactly the same concentrations as found in vegetative cells. In contrast, 1,3-diaminopropane, which is formed from spermidine, does not affect the methylation of tRNA in vitro at physiological concentrations. Putrescine and/or spermidine stabilize the tRNA methyltransferases in crude extracts in the presence but not in the absence of the substrate tRNA. The results support the view that S-adenosylmethionine-dependent transmethylation reactions can be regulated by alterations of polyamine concentrations in vivo.