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.

构成转移 RNA 的核苷的化学修饰是多种多样的。然而，在极少数生物体中系统地绘制了修饰的结构、位置和程度。在这里，我们描述了一种方法，在该方法中，通过高通量转移 RNA 测序 (tRNA-seq) 数据中的逆转录衍生特征快速预测修饰位点，并通过 RNA 质谱法识别 tRNA 修饰。比较 tRNA-seq 能够预测大肠杆菌中不存在的几种霍乱弧菌修饰，还揭示了各种环境条件对霍乱弧菌tRNA 修饰的影响。通过 RNA 质谱分析，我们发现其中两个V. cholerae特异性逆转录特征反映了新修饰（乙酰化 acp ³ U (acacp ³ U)）的存在，而其他结果来自 C-to-Ψ RNA 编辑，这是一个以前没有描述过的过程。这些发现证明了这种方法可用于快速监测 tRNA 修饰谱和 tRNA 修饰的环境控制。