A-to-I mRNA editing in Escherichia coli is regulated by nutrients availability, culture growth phase, and tRNA-Arg2 expression
Adenosine-to-inosine (A-to-I) mRNA editing changes genetic information at the RNA level, potentially affecting protein sequence and function. While A-to-I mRNA editing has been investigated for decades in eukaryotes, the factors regulating its occurrence in bacteria are poorly understood.Here, we revealed the A-to-I mRNA editing landscape of E. coli in nutrient-rich (LB) and minimal (M9) media across different growth phases. Our analysis increased the known TadA-dependent A-to-I edited mRNAs to 27, including 12 novel mRNAs/sites reported here. Comparing editing levels between growth phases and growth media revealed that editing levels significantly increased at the stationary phase in rich but not in minimal media. Differential gene expression analysis indicated no connection between edited mRNAs expression and editing levels. However, tRNA-Arg2 expression was significantly downregulated at the stationary phase. Because TadA edits both tRNA-Arg2 and mRNAs in bacteria, we examined whether tRNA-Arg2 expression affects mRNA editing levels. Indeed, overexpressing tRNA-Arg2 decreased global mRNA editing levels, supporting that competition between TadA substrates (tRNA-Arg2 and mRNAs) also affects bacterial mRNA editing levels. Finally, we show that the TadA mutant with deficient editing activity displayed defective growth in LB, but not in M9, suggesting that under nutrient-rich conditions, tRNA-Arg2 editing or mRNA editing (or both) are essential for optimal growth.Our work reveals regulatory principles governing A-to-I mRNA editing occurrence in bacteria and lays the foundation for studying its function.