Landscape and dynamics of TadA-dependent RNA editing in Escherichia coli reveal a role in nutrient-rich growth

Adenosine-to-inosine A-to-I mRNA editing alters genetic information post-transcriptionally and can impact protein sequence and function, yet its regulation in bacteria remains unclear. Here, we profiled A-to-I editing in Escherichia coli across nutrient-rich LB and minimal M9 media and different growth phases. Our analysis expanded the repertoire of TadA-dependent A-to-I edited mRNAs to 27, including 12 novel sites, and revealed that editing levels were dynamic and markedly increased at stationary phase in LB but not in M9. Editing levels were independent of mRNA expression yet correlated with tRNA-Arg2 downregulation, and overexpressing tRNA-Arg2 reduced mRNA editing, demonstrating substrate competition for TadA, the sole bacterial tRNA adenosine deaminase. Mutants with TadA-deficient editing or reduced tRNA-Arg2 expression displayed similar LB-specific growth defects. Moreover, tRNA-Arg2 expression, tRNA-Arg2-dependent codon usage, and tRNA-Arg2 editing were all elevated in LB compared to M9. These findings establish regulatory principles for bacterial RNA editing, implicate tRNA editing in nutrient-responsive fitness, and provide a framework to explore the physiological roles of mRNA editing

腺苷脱氨肌苷（A-to-I）mRNA编辑可在转录后改变遗传信息，并对蛋白质序列与功能产生影响，但其在细菌中的调控机制仍有待阐明。
本研究针对大肠杆菌，在营养丰富的LB培养基与基本M9培养基中，以及不同生长阶段下的A-to-I编辑事件开展了全景分析。
我们的分析将依赖TadA的A-to-I编辑mRNA靶标库拓展至27个，其中包含12个全新编辑位点；同时揭示编辑水平呈动态变化特征：在LB培养基中，编辑水平于稳定期显著升高，而在M9培养基中未观察到此现象。
编辑水平与mRNA的表达量无显著关联，但与tRNA-Arg2的表达下调呈显著相关；过表达tRNA-Arg2可降低mRNA编辑水平，这证明了作为细菌唯一tRNA腺苷脱氨酶的TadA存在底物竞争现象。
TadA编辑缺陷型突变株，或tRNA-Arg2表达水平降低的突变株，均表现出类似的LB培养基特异性生长缺陷。此外，相较于M9培养基，LB培养基中tRNA-Arg2的表达水平、tRNA-Arg2依赖的密码子使用偏好，以及tRNA-Arg2的编辑水平均显著升高。
本研究确立了细菌RNA编辑的调控规律，阐明了tRNA编辑在营养响应适应性中的作用，并为探究mRNA编辑的生理功能提供了研究框架。