Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications.

Nature Chemical Biology
Satoshi KimuraMatthew K Waldor

Abstract

Chemical modifications of the nucleosides that comprise transfer RNAs are diverse. However, the structure, location and extent of modifications have been systematically charted in very few organisms. Here, we describe an approach in which rapid prediction of modified sites through reverse transcription-derived signatures in high-throughput transfer RNA-sequencing (tRNA-seq) data is coupled with identification of tRNA modifications through RNA mass spectrometry. Comparative tRNA-seq enabled prediction of several Vibrio cholerae modifications that are absent from Escherichia coli and also revealed the effects of various environmental conditions on V. cholerae tRNA modification. Through RNA mass spectrometric analyses, we showed that two of the V. cholerae-specific reverse transcription signatures reflected the presence of a new modification (acetylated acp3U (acacp3U)), while the other results from C-to-Ψ RNA editing, a process not described before. These findings demonstrate the utility of this approach for rapid surveillance of tRNA modification profiles and environmental control of tRNA modification.

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Citations

Jan 18, 2021·Briefings in Functional Genomics·Satoshi Kimura
Feb 24, 2021·Critical Reviews in Biochemistry and Molecular Biology·Yasemin YoluçStefanie Kellner
Mar 5, 2021·Nature Reviews. Molecular Cell Biology·Tsutomu Suzuki
Jul 15, 2020·Current Opinion in Microbiology·Satoshi KimuraMatthew K Waldor
Jul 29, 2020·Trends in Microbiology·Valérie de Crécy-Lagard, Marshall Jaroch
Apr 3, 2021·Frontiers in Molecular Biosciences·Ricardo EhrlichMónica Marín
Aug 28, 2021·International Journal of Molecular Sciences·Adamantia KouvelaVassiliki Stamatopoulou
Oct 14, 2021·Proceedings of the National Academy of Sciences of the United States of America·Roni RakYitzhak Pilpel

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Methods Mentioned

BETA
chemical treatments
tRNA-seq
acetylation
acetylate
PCR

Software Mentioned

BLAST
ChemCalc Molecular Formula Finder
samtools mpileup
Graphpad Prism
Bowtie 46
R
Mpileup
bedtools genomecov

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