Transfer RNA Methyltransferases from  Thermoplasma acidophilum, a Thermoacidophilic Archaeon

Kawamura, Takahiro; Anraku, Ryou; Hasegawa, Takahiro; Tomikawa, Chie; Hori, Hiroyuki

doi:10.3390/ijms16010091

Cited by 15 publications

(12 citation statements)

References 65 publications

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“…A similar phenomenon was observed in the case of Thermoplasma acidophilum Trm56 (Figure 5) [43]. A bioinformatics study has predicted that this protein has a His-Asp phosphodiesterase (HDPD)-like domain at its C-terminal region [29].…”

Section: Knot Structures Domain Arrangements Subunit Structures supporting

confidence: 66%

“…A bioinformatics study has predicted that this protein has a His-Asp phosphodiesterase (HDPD)-like domain at its C-terminal region [29]. The purified protein showed Trm56 (tRNA (Cm56) methyltransferase) activity [43], strongly suggesting that the catalytic domain of T. acidophilum Trm56 forms a SPOUT fold even though the protein has a polypeptide region of 130 amino acids at the C-terminus.…”

Section: Knot Structures Domain Arrangements Subunit Structures mentioning

confidence: 99%

“…The product of T. acidophilum Ta0931 gene is a unique member in the Trm56 family, because it has an additional HDPD-like domain at its C-terminal region (Figure 5) [43] (see Section 3). …”

Section: Transfer Rna Recognition Mechanismmentioning

confidence: 99%

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

Hori

2017

Biomolecules

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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.

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Section: Knot Structures Domain Arrangements Subunit Structures supporting

confidence: 66%

Section: Knot Structures Domain Arrangements Subunit Structures mentioning

confidence: 99%

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

Hori

2017

Biomolecules

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“…It is noteworthy that archaeal species somehow escaped this thorough analysis, and only a few tRNA species are included in available databases. Archaeal enzymes are mostly characterized by sequence homology followed by functional tests to confirm the initial hypothesis on their predicted activity, as archaeal tRNA methyltransferase (aTrm56) [14,15]. …”

Section: Introductionmentioning

confidence: 99%

Next‐Generation Sequencing‐Based RiboMethSeq Protocol for Analysis of tRNA 2′‐O‐Methylation

et al. 2017

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Analysis of RNA modifications by traditional physico-chemical approaches is labor intensive, requires substantial amounts of input material and only allows site-by-site measurements. The recent development of qualitative and quantitative approaches based on next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA species. The Illumina sequencing-based RiboMethSeq protocol was initially developed and successfully applied for mapping of ribosomal RNA (rRNA) 2′-O-methylations. This method also gives excellent results in the quantitative analysis of rRNA modifications in different species and under varying growth conditions. However, until now, RiboMethSeq was only employed for rRNA, and the whole sequencing and analysis pipeline was only adapted to this long and rather conserved RNA species. A deep understanding of RNA modification functions requires large and global analysis datasets for other important RNA species, namely for transfer RNAs (tRNAs), which are well known to contain a great variety of functionally-important modified residues. Here, we evaluated the application of the RiboMethSeq protocol for the analysis of tRNA 2′-O-methylation in Escherichia coli and in Saccharomyces cerevisiae. After a careful optimization of the bioinformatic pipeline, RiboMethSeq proved to be suitable for relative quantification of methylation rates for known modified positions in different tRNA species.

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“…In a recent study, we found that tRNA Met i from T. acidophilum contains G + modification similar to that of tRNA Met m ( 32 ). Furthermore, we found that tRNA Leu UAG from T. acidophilum has two G + modifications at positions 13 and 15 ( 33 ) (see Figure 4A ).…”

Section: Introductionmentioning

confidence: 85%

Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) fromThermoplasma acidophilum, a thermo-acidophilic archaeon

et al. 2015

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Archaeosine (G+), which is found only at position 15 in many archaeal tRNA, is formed by two steps, the replacement of the guanine base with preQ0 by archaeosine tRNA-guanine transglycosylase (ArcTGT) and the subsequent modification of preQ0 to G+ by archaeosine synthase. However, tRNALeu from Thermoplasma acidophilum, a thermo-acidophilic archaeon, exceptionally has two G+13 and G+15 modifications. In this study, we focused on the biosynthesis mechanism of G+13 and G+15 modifications in this tRNALeu. Purified ArcTGT from Pyrococcus horikoshii, for which the tRNA recognition mechanism and structure were previously characterized, exchanged only the G15 base in a tRNALeu transcript with 14C-guanine. In contrast, T. acidophilum cell extract exchanged both G13 and G15 bases. Because T. acidophilum ArcTGT could not be expressed as a soluble protein in Escherichia coli, we employed an expression system using another thermophilic archaeon, Thermococcus kodakarensis. The arcTGT gene in T. kodakarensis was disrupted, complemented with the T. acidophilum arcTGT gene, and tRNALeu variants were expressed. Mass spectrometry analysis of purified tRNALeu variants revealed the modifications of G+13 and G+15 in the wild-type tRNALeu. Thus, T. acidophilum ArcTGT has a multisite specificity and is responsible for the formation of both G+13 and G+15 modifications.

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Transfer RNA Methyltransferases from Thermoplasma acidophilum, a Thermoacidophilic Archaeon

Cited by 15 publications

References 65 publications

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

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

Next‐Generation Sequencing‐Based RiboMethSeq Protocol for Analysis of tRNA 2′‐O‐Methylation

Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) fromThermoplasma acidophilum, a thermo-acidophilic archaeon

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