Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2019 Jun 28;10:2858. doi: 10.1038/s41467-019-10750-8

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Fig. 2 — Identification of trhP responsible for tRNA hydroxylation. a Mass-spectrometric shotgun analysis of total tRNAs in E. coli strains. Extracted ion chromatograms (XICs) show multiply charged negative ions of the anticodon-containing fragments of tRNA^Val1 with U34 (upper panels) and cmo⁵U34 (lower) in total tRNAs from wild-type (left), ∆yegQ (center), and ∆yegQ/∆yhbU/∆yhbV/∆rlhA strains (right). Sequence, m/z value, and charge state of each fragment are shown on the right. Asterisks indicate nonspecific peaks with the same m/z values. b Mass-spectrometric analysis of the wobble modification in E. coli tRNA^Ala1 isolated from WT (left panels) and ∆yegQ (right) strains. XICs show anticodon-containing fragments of tRNA^Ala1 with U34 (top panels), cmo⁵U34 (middle panels), and mcmo⁵U34 (bottom panels). The cleavage sites of RNase T₁ are shown in Fig. 1a. It is assumed that cmo⁵U detected in this tRNA was generated by artificial hydrolysis of mcmo⁵U during tRNA isolation¹³. The black arrowhead indicates a small peak corresponding to the U34-containing fragment detected in the WT. c Modification frequencies of cmo⁵U derivatives at the wobble position of six tRNA species isolated from WT and ∆yegQ strains. Relative compositions of each modification were calculated from the peak area ratio of mass chromatograms of RNase T₁ digest fragments containing mcmo⁵Um (red), mcmo⁵U (green), cmo⁵U (blue), or U (gray) at the wobble position (Supplementary Fig. 2)¹³. Source data are provided as a Source Data file. d Gene organization of a B. subtilis operon containing yrrM, yrrN, and yrrO. Genomic positions in B. subtilis are indicated. The new name for each gene is shown in parenthesis. e Mass-spectrometric shotgun analysis of total tRNAs in B. subtilis strains. XICs are shown of doubly charged negative ions of the anticodon-containing fragments of tRNA^Val1a,b with U34 (top panels), ho⁵U34 (middle panels), and mo⁵U34 (bottom panels) in total tRNA from wild-type (leftmost panels), ∆yrrN (left panels), ∆yrrO (middle panels), ∆yrrN/∆yrrO (right panels), and ∆yrrM (rightmost panels) strains