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’-O-methylation 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 anti-bacterial 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.
Highlights
The existence of the SpoU-TrmD (SPOUT) RNA methyltransferase superfamily was first predicted by bioinformatics studies [1,2,3]
In 1993, Koonin and Rudd predicted the spoU gene product to be an RNA methyltransferase based on the similarity of its deduced amino acid sequence to that of Streptomyces azureus Tsr [1], which catalyzes methylation of the ribose of adenosine (A) at position 1067 in 23S rRNA to form 2’-O-methyladenosine (Am1067) [4]
The structures of modified nucleosides covered in this review together with their positions in tRNA and the responsible enzymes are summarized in Figures 1 and 2, respectively: the structures of modified nucleosides are presented according to the MODOMICS database [5]
Summary
The existence of the SpoU-TrmD (SPOUT) RNA methyltransferase superfamily was first predicted by bioinformatics studies [1,2,3]. Tsr and yeast Pet, which catalyzes methylation of the ribose of guanosine (G) at position 2270 in mitochondrial 21S rRNA to form 2’-O-methylguanosine (Gm2270) [6] They reported that the three RNA 2’-O-methyltransferases have three conserved motifs, termed motifs 1, 2 and 3. The common feature of SPOUT RNA methyltransferases is the formation of a deep trefoil (topological) knot in the catalytic domain (Figure 4). Together, these bioinformatics and crystal structure studies established the basic concept of the SPOUT RNA methyltransferase superfamily. Members of SPOUT RNA methyltransferase superfamily are classified as class IV enzymes, whose catalytic domain forms a deep trefoil (topological) knot. RNA methyltransferase superfamily and their modified nucleosides in tRNA are focused owing to space limitation
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