Global identification of transfer RNAs by liquid chromatography–mass spectrometry (LC–MS)

Wetzel, Collin; Limbach, Patrick A.

doi:10.1016/j.jprot.2011.09.015

Cited by 20 publications

(13 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Among them, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) Limbach 2007, 2009), liquid chromatography-mass spectrometry (LC-MS) (Castleberry and Limbach 2010;Wetzel and Limbach 2012), and liquid chromatography tandem MS (LC-MS/MS) (Wetzel and Limbach 2012) have been developed. These methods consist of: (i) enzymatic digestion of tRNA by ribonucleases (e.g., RNase T1), which generates unique or Bsignature^digestion products; (ii) detection by MS or by a combination of chromatography and MS.…”

Section: The State Of the Trna Population In The Cellmentioning

confidence: 99%

Protein folding and tRNA biology

2017

View full text Add to dashboard Cite

Polypeptides can fold into tertiary structures while they are synthesized by the ribosome. In addition to the amino acid sequence, protein folding is determined by several factors within the cell. Among others, the folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins, ligands, or the ribosome, as well as by the translocation through membrane pores. Particularly, the translation machinery and the population of tRNA under different physiological or adaptive responses can dramatically affect protein folding. This review summarizes the scientific evidence describing the role of translation kinetics and tRNA populations on protein folding and addresses current efforts to better understand tRNA biology. It is organized into three main parts, which are focused on: (i) protein folding in the cellular context; (ii) tRNA biology and the complexity of the tRNA population; and (iii) available methods and technical challenges in the characterization of tRNA pools. In this manner, this work illustrates the ways by which functional properties of proteins may be modulated by cellular tRNA populations.

show abstract

Section: The State Of the Trna Population In The Cellmentioning

confidence: 99%

Protein folding and tRNA biology

2017

View full text Add to dashboard Cite

show abstract

“…Techniques for qualification and quantification of modified nucleosides in tRNA without the use of derivation methods have been well-documented (Chan et al, 2011;Krog et al, 2011;Wetzel & Limbach, 2012), and can be described in general methodologies shown in Figure 17. Several groups Farmer et al (2005) have adopted this general method to identify modified nucleosides in tRNA for a variety of different organisms-bacteria and fungi (shown in Fig.…”

Section: Modified Nucleoside Within Trna Analysismentioning

confidence: 99%

Mass spectrometry analysis of nucleosides and nucleotides

Dudley

Bond

2013

Mass Spec Rev

View full text Add to dashboard Cite

Mass spectrometry has been widely utilised in the study of nucleobases, nucleosides and nucleotides as components of nucleic acids and as bioactive metabolites in their own right. In this review, the application of mass spectrometry to such analysis is overviewed in relation to various aspects regarding the analytical mass spectrometric and chromatographic techniques applied and also the various applications of such analysis.

show abstract

“…SDPs are RNase digestion products detected by mass spectrometry that are unique to a single RNA (usually tRNA) sequence (29)(30)(31)(32). SDP specificity arises through a combination of oligonucleotide base composition, sequence, and modification status.…”

mentioning

confidence: 99%

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

Jora

Solivio

et al. 2019

J Bacteriol

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Global identification of transfer RNAs by liquid chromatography–mass spectrometry (LC–MS)

Cited by 20 publications

References 50 publications

Protein folding and tRNA biology

Protein folding and tRNA biology

Mass spectrometry analysis of nucleosides and nucleotides

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

Contact Info

Product

Resources

About