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

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© 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/.

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Fig. 5 — Characterization of trhP-mediated tRNA hydroxylation. a A shikimate pathway and related metabolism. Chemical structures of metabolites and the responsible genes (italicized) at each step are shown. Two or three genes at each step indicate a redundant pathway [e.g., prephenate is redundantly synthesized from chorismate mediated by pheA(CM) and tyrA]. Black or gray arrows represent pathways indispensable or dispensable for trhP-mediated ho⁵U34 formation, respectively (Supplementary Fig. 9). White arrows represent pathways not examined in this study. b Genetic complementation of ho⁵U34 formation. Mass-spectrometric shotgun analysis of total tRNAs obtained from the E. coli ΔpheA/ΔtyrA/ΔcmoA/ΔtrhO strain transformed with a control plasmid (left panels) or pMW-pheA(CM) (right panels). XICs show multiply charged negative ions of anticodon-containing fragments of tRNA^Val1 with U34 (upper panels) and ho⁵U34 (lower panels). Sequence, m/z value, and charge state of each fragment are shown on the right. c Metabolic complementation of ho⁵U34 formation. Mass-spectrometric shotgun analysis of total tRNAs obtained from the E. coli ΔpheA/ΔtyrA/ΔcmoA/ΔtrhO strain cultured in the absence (left panels) or presence (right panels) of 1 mM prephenate. XICs show multiply charged negative ions of anticodon-containing fragments of tRNA^Val1 with U34 (upper panels) and ho⁵U34 (lower panels). Sequence, m/z value, and charge state of each fragment are shown on the right. d Domain organization of E. coli TrhP, which contains Peptidase_U32 (PF01136) and Peptidase_U32_C (PF16325) domains. Six residues in the Peptidase_U32 domain that are essential for TrhP-mediated hydroxylation are indicated. e Mutation study of trhP. Mass-spectrometric shotgun analysis of total tRNA in the E. coli ∆trhP strain transformed with plasmid-encoded trhP WT or mutants, as indicated. XICs show multiply charged negative ions of the anticodon-containing fragments of tRNA^Val1 with U34 (black lines) and cmo⁵U34 (red lines) in total tRNAs. Sequence, m/z value, and charge state of each fragment are shown on the right