Wybutosine biosynthesis: Structural and mechanistic overview

Perche-Letuvée, Phanélie; Molle, Thibaut; Forouhar, F.; Mulliez, Etienne; Atta, Mohamed

doi:10.4161/15476286.2014.992271

Cited by 42 publications

(32 citation statements)

References 49 publications

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“…Four modifications, cnm 5 U, cnm 5 s 2 U, agmatidine, and mimG, have only been discovered in archaea to date. Our analyses revealed the presence of imG and imG-14, which are believed to be within the wybutosine pathway and have previously been found in eukaryotes (20,36).…”

Section: Discussionsupporting

confidence: 70%

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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: Discussionsupporting

confidence: 70%

“…T1, RNase T1; A, RNase A; MC1, RNase MC1; Cus, cusativin; U2, RNase U2. Anticodon positions34,35,36, and 37 are identified by boldface. The M. jannaschii tRNAs are italicized.…”

mentioning

confidence: 99%

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

Jora

Solivio

et al. 2019

J Bacteriol

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“…The key step involved in the formation of the tricyclic imG-14 core is catalyzed by TYW1, which converts m 1 G to imG-14 by adding two carbons that are derived from pyruvate, creating the imidazoline ring 10 . Additional species-specific modifications tailor the core wyosine base to form the known wyosine derivatives 4,6,11,12 .…”

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confidence: 99%

Mechanistic Studies of the Radical S-Adenosyl-l-methionine Enzyme 4-Demethylwyosine Synthase Reveal the Site of Hydrogen Atom Abstraction

Young

Bandarian

2015

Biochemistry

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TYW1 catalyzes the formation of 4-demethylwyosine via the condensation of N-methylguanosine (m1G) with carbons 2 and 3 of pyruvate. In this study labeled transfer ribonucleic acid (tRNA) and pyruvate were utilized to determine the site of hydrogen atom abstraction and regiochemistry of the pyruvate addition. tRNA containing a 2H labeled m1G methyl group was used to identify the methyl group of m1G as the site of hydrogen atom abstraction by S-adenosyl-L-methionine. [2-13C1,3,3,3-2H3]-Pyruvate was used to demonstrate retention of all the pyruvate protons indicating that C2 of pyruvate forms the bridging carbon of the imidazoline ring and C3 the methyl.

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“…Although 1-methylguanosine (m 1 G) is not reported in tRNA Phe GAA, we found around 0.3 m 1 G per tRNA. This observation can be explained by the fact that m 1 G is a precursor during the biosynthesis of wybutosine (yW), a hypermodified nucleoside reported at position 37 of tRNA Phe GAA 34,35 . Due to the unavailability of a synthetic standard, yW could not be quantified in this study.…”

Section: Absolute Quantification Of Human Trna Phe Modificationsmentioning

confidence: 99%

Cell culture NAIL-MS allows insight into human RNA modification dynamicsin vivo

Heiss

Hagelskamp

Kellner

2020

Preprint

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In the last years, studies about the dynamics of RNA modifications are among the most controversially discussed. As the main reason, we have identified the unavailability of a technique which allows to follow the temporal dynamics of RNA transcripts in human cell culture.Here, we present a NAIL-MS (nucleic acid isotope labeling coupled mass spectrometry) scheme for efficient stable isotope labeling in both RNA and DNA (>95% within 7 days) in common human cell lines and growth media. Validation experiments reveal that the labeling procedure itself does neither interfere with the isotope dilution MS quantification nor with RNA modification density. We design pulse chase NAIL-MS experiments and apply the new tool to study the temporal placement of modified nucleosides in e.g. tRNA Phe and 18S rRNA. In existing RNAs, we observe a constant loss of modified nucleosides over time which is masked by a post-transcriptional methylation mechanism and thus not detectable without NAIL-MS. During alkylation stress, NAIL-MS reveals an adaptation of tRNA modifications in new transcripts but not existing transcripts.Overall, we present a fast and reliable stable isotope labeling strategy which allows a more detailed study of RNA modification dynamics in human cell culture. With cell culture NAIL-MS it is finally possible to study the speed of both modification and demethylation reactions inside human cells. Thus it will be possible to study the impact of external stimuli and stress on human RNA modification kinetics and processing of mature RNA.

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Wybutosine biosynthesis: Structural and mechanistic overview

Cited by 42 publications

References 49 publications

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

Mechanistic Studies of the Radical S-Adenosyl-l-methionine Enzyme 4-Demethylwyosine Synthase Reveal the Site of Hydrogen Atom Abstraction

Cell culture NAIL-MS allows insight into human RNA modification dynamicsin vivo

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