Transfer RNA methyltransferases with a SpoU-TrmD (SPOUT) fold and their modified nucleosides in tRNA

Abstract

The existence of SpoU-TrmD (SPOUT) RNA methyltransferase superfamily was first predicted by bioinformatics. SpoU is the previous name of TrmH, which catalyzes the 2'-Omethylation of ribose of G18 in tRNA; TrmD catalyzes the formation of N1-methylguanosine at position 37 in tRNA. Although SpoU (TrmH) and TrmD were originally considered to be unrelated, the bioinformatics study suggested that they might share a common evolution origin and form a single superfamily. The common feature of SPOUT RNA methyltransferases is the formation of a deep trefoil knot in the catalytic domain. In the past decade, the SPOUT RNA methyltransferase superfamily has grown; furthermore, knowledge concerning the functions of their modified nucleosides in tRNA has also increased. Some enzymes are potential targets in the design of antibacterial drugs. In humans, defects in some genes may be related to carcinogenesis. In this review, recent findings on the tRNA methyltransferases with a SPOUT fold and their methylated nucleosides in tRNA, including classification of tRNA methyltransferases with a SPOUT fold; knot structures, domain arrangements, subunit structures and reaction mechanisms; tRNA recognition mechanisms, and functions of modified nucleosides synthesized by this superfamily, are summarized. Lastly, the future perspective for studies on tRNA modification enzymes are considered.

Keywords: knot; RNA modification; SpoU‐TrmD; methyltransferase; tRNA.

Figure 1

Structures and abbreviated names of the modified nucleosides described in this review. The modifications are colored in red.

Figure 2

Modification positions in tRNA and the responsible SpoU-TrmD (SPOUT) tRNA methyltransferases. The secondary structure of tRNA is represented in cloverleaf structure. The conserved nucleotides in tRNA are depicted as follows: adenosine, A; guanosine, G; cytidine, C; uridine, U; purine, R; pseudouridine, Ψ. The modified positions are numbered and the associated enzymes are indicated in red. The structures of modified nucleosides and abbreviations of their names are shown in Figure 1.

Figure 3

The conserved motifs in the TrmH (SpoU) and TrmD families. The amino acid sequence alignment is based on the reference [3], and has been modified in accordance with biochemical data. Color (blue and red) letters indicate the conserved amino acid residues, reported by Anantharaman et al. [3]. Red letters indicate the amino acid residues that are essential for the methyl-transfer reaction by Thermus thermophilus TrmH. Numbers indicate the positions of amino acid residues in T. thermophilus TrmH. T. thermophilus: Thermus thermophilus; E. coli: Eshcerichia coli; S. aureus: Streptomyces aureus.

Figure 4

(A) Topological knot structures in TrmH (SpoU) and TrmD. The representations of topologies are in accordance with the references [10,15,19]. Circles, triangles and S-adenosyl-l-methionine (AdoMet) indicate α-helices, β-strands and AdoMet binding site, respectively. (B) Cartoon models of T. thermophilus TrmH (Protein Data Bank ID: 1v2x) and Escherichia coli TrmD (Protein Data Bank ID: 1p9p) subunits. To show the knot structures, the C-terminal regions of catalytic domains are colored in cyan. The C-terminal domain of E. coli TrmD is indicated in blue. The bound AdoMet and S-adenosyl-l-homocysteine (AdoHcy) are shown by stick models.

Figure 5

Domain structures of tRNA methyltransferases with a SPOUT fold. This figure is based on that by Tkaczuk et al. [29] and has been modified by data from recent crystal structure studies. The catalytic domain with a SPOUT fold is represented as “SPOUT”. “α” and “β” represent α-helices and β-strands, respectively. The HDPD-like domain indicates the His-Asp phosphodiesterase-like domain. S. cerevisiae: Saccharomyces cerevisiae; H. influenzae: Haemophilus influenzae; P. horikoshii: Pyrococcus horikoshii; P. abyssi: Pyrococcus abyssi; T. acidophilum: Thermoplasma acidophilum; S. acidocaldarius: Sulfolobus acidocaldarius.

Figure 6

Schematic drawing of the hypothetical catalytic mechanism of T. thermophilus TrmH.

Figure 7

Structure of tRNA-TrmD-sinefungin ternary complex. The Protein Data Bank ID is 4yvi. TrmD and tRNA are shown by cartoon models. G36 (magenta) and G37 (red) bases in tRNA are highlighted by stick models. Two subunits of TrmD are colored in green and cyan.

Figure 8

Model of the immune response and Gm18 methylation in tRNA. Transfer RNA from H. influenzae, a respiratory infectious bacterium, induces dimer formation by Toll like receptor-7 (TLR7), the immune response is then stimulated via binding of the proteins, MyD88, IRAK1 and IRAK4. In contrast, human and E. coli tRNAs do not stimulate TLR7 because they contain the Gm18 modification. The E. coli trmH gene disruptant strain does not show any obvious phenotype under laboratory culture conditions [7]. Both Gm18 modification and TrmH are required for survival of E. coli in animal gut.