Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications
Name
nihms-1687866.pdf
Description
Accepted version
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5.38 MB
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Unknown
Checksum (MD5)
a35c7ead23a031cd0d5d2b78d02d1445
Author(s)
Kimura, Satoshi
Dedon, Peter C
Waldor, Matthew K
Date Issued
June 2020
Journal
Nature Chemical Biology
Publisher
Springer Science and Business Media LLC
Version
Author's final manuscript
Abstract
© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. 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. [Figure not available: see fulltext.].
MIT Department
Howard Hughes Medical Institute
Massachusetts Institute of Technology. Department of Biological Engineering
Singapore-MIT Alliance in Research and Technology (SMART)
Terms of Use
Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1038/S41589-020-0558-1
