Journal Article

Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications

Dedon, Peter C., Kimura, Satoshi, Waldor, Matthew K.

2020

Overview

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 acp 3 U (acacp 3 U)), 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. A combination of tRNA sequencing and mass spectrometry was developed to profile tRNA modification enabling identification of a new modification acacp 3 U and the presence of cytosine-to-pseudouracil RNA editing in Vibrio cholerae .

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/45/2783 / 631/92/500 / 631/92/610 / Acetylation / Acetyltransferases - genetics / Acetyltransferases - metabolism / Animals / Bacteria / Biochemical Engineering / Biochemistry / Bioorganic Chemistry / Cell Biology / Chemistry / Chemistry and Materials Science / Chemistry/Food Science / Cholera - microbiology / Cytidine - genetics / Cytosine / E coli / Editing / Environmental conditions / Environmental control / Escherichia coli - genetics / Gene sequencing / High-Throughput Nucleotide Sequencing - methods / Mass spectrometry / Mass Spectrometry - methods / Mass spectroscopy / Rabbits / Reverse transcription / RNA Editing / RNA modification / RNA, Transfer - chemistry / RNA, Transfer - genetics / RNA, Transfer - metabolism / RNA, Transfer, Tyr - genetics / RNA, Transfer, Tyr - metabolism / Scientific imaging / Signatures / Spectroscopy / Surveying / Transfer RNA / tRNA / tRNA Ala / Vibrio cholerae / Vibrio cholerae - genetics / Vibrio cholerae - pathogenicity / Waterborne diseases