Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs

Wurm, Jan Philip; Griese, M; Bahr, U.; Held, Martin; Heckel, Alexander; Karas, Michael; Soppa, Jörg; Wöhnert, Jens

doi:10.1261/rna.028498.111

Cited by 21 publications

(20 citation statements)

References 42 publications

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“…As no pseudouridine-specific mapping was performed (63,64), the localization of this modification to positions 54 and 55 of specific tRNAs is expected but not verified here. The DUF358 SPOUT-methyltransferase MJ1640 (renamed TrmY) acts in concert with Pus10 to catalyze the biosynthesis of m 1 ⌿ at position 54 (65)(66)(67). Data consistent with m 1 ⌿(54) were obtained from tRNA GAC Val .…”

Section: Discussionmentioning

confidence: 89%

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

Jora

Solivio

et al. 2019

J Bacteriol

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tRNAs play a critical role in mRNA decoding, and posttranscriptional modifications within tRNAs drive decoding efficiency and accuracy. The types and positions of tRNA modifications in model bacteria have been extensively studied, and tRNA modifications in a few eukaryotic organisms have also been characterized and localized to particular tRNA sequences. However, far less is known regarding tRNA modifications in archaea. While the identities of modifications have been determined for multiple archaeal organisms, Haloferax volcanii is the only organism for which modifications have been extensively localized to specific tRNA sequences. To improve our understanding of archaeal tRNA modification patterns and codondecoding strategies, we have used liquid chromatography and tandem mass spectrometry to characterize and then map posttranscriptional modifications on 34 of the 35 unique tRNA sequences of Methanocaldococcus jannaschii. A new posttranscriptionally modified nucleoside, 5-cyanomethyl-2-thiouridine (cnm 5 s 2 U), was discovered and localized to position 34. Moreover, data consistent with wyosine pathway modifications were obtained beyond the canonical tRNA Phe as is typical for eukaryotes. The high-quality mapping of tRNA anticodon loops enriches our understanding of archaeal tRNA modification profiles and decoding strategies. IMPORTANCE While many posttranscriptional modifications in M. jannaschii tRNAs are also found in bacteria and eukaryotes, several that are unique to archaea were identified. By RNA modification mapping, the modification profiles of M. jannaschii tRNA anticodon loops were characterized, allowing a comparative analysis with H. volcanii modification profiles as well as a general comparison with bacterial and eukaryotic decoding strategies. This general comparison reveals that M. jannaschii, like H. volcanii, follows codon-decoding strategies similar to those used by bacteria, although position 37 appears to be modified to a greater extent than seen in H. volcanii.

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Section: Discussionmentioning

confidence: 89%

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

Jora

Solivio

et al. 2019

J Bacteriol

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“…Recently, two groups independently identified new SPOUT tRNA methyltransferases (Mja 1640 from Methanocaldococcus jannaschii and Hvo 1989 from Haloferax volcanii) producing the m 1 ⌿54 modification in archaeal tRNA (43,44). These proteins, which share homology with the catalytic domain of 18 S rRNA methyltransferase (Nep1), which gives rise to m 1 acp 3 ⌿ (52, 53), are mainly formed by the catalytic domain (42)(43)(44). This observation is in line with our current findings that a small part(s) of the catalytic domain discriminates the substrate RNA.…”

Section: Discussionmentioning

confidence: 99%

The Catalytic Domain of Topological Knot tRNA Methyltransferase (TrmH) Discriminates between Substrate tRNA and Nonsubstrate tRNA via an Induced-fit Process

Ochi

Makabe

Yamagami

et al. 2013

Journal of Biological Chemistry

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Background: Topologically knotted tRNA methyltransferases specifically recognize substrate tRNA. Results: Site-directed mutagenesis studies, chimeric protein analysis, and pre-steady state kinetics clarify the tRNA recognition sites of TrmH. Conclusion:The N-and C-terminal regions function in the initial binding process, and substrate tRNA is discriminated by the catalytic domain in an induced-fit process. Significance: Study of how proteins recognize RNA is crucial for understanding RNA maturation processes.

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“…These studies established the structural foundation of SPOUT enzymes (Anantharaman et al, 2002 ; Tkaczuk et al, 2007 ), which can be identified on the basis of the topological-knot structure. To date, several tRNA methyltransferases have been identified as members of the SPOUT superfamily on the basis of crystal structures (Kuratani et al, 2008 ; Chen and Yuan, 2010 ; Chatterjee et al, 2012 ; Wurm et al, 2012 ; Shao et al, 2013 ) or structures predicted from amino acid sequences and conserved motifs (Renalier et al, 2005 ; Purta et al, 2006 ; Tkaczuk et al, 2007 ; Kempenaers et al, 2010 , and Figure 4B ). Furthermore, the SPOUT superfamily is expanding beyond the SpoU and TrmD families: novel enzymes such as an archaeal Trm10 homolog (Kempenaers et al, 2010 ) and TrmY (Chen and Yuan, 2010 ; Chatterjee et al, 2012 ; Wurm et al, 2012 ) have been identified.…”

Section: Structures Of Trna Methyltransferasesmentioning

confidence: 99%

Methylated nucleosides in tRNA and tRNA methyltransferases

2014

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To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon-anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.

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Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs

Cited by 21 publications

References 42 publications

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

The Catalytic Domain of Topological Knot tRNA Methyltransferase (TrmH) Discriminates between Substrate tRNA and Nonsubstrate tRNA via an Induced-fit Process

Methylated nucleosides in tRNA and tRNA methyltransferases

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