RNA stability is regulated by both RNA polyadenylation and ATP levels, linking RNA and energy metabolisms in Escherichia coli
The post-transcriptional process of RNA polyadenylation sits at the crossroads of energy metabolism and RNA metabolism. RNA polyadenylation is catalyzed by poly(A) polymerases which use ATP as a substrate to add adenine residues to the 3' end of RNAs, which can alter their stability. In E. coli, RNA polyadenylation mediated by the major poly(A) polymerase (PAP I) was previously shown to facilitate degradation of individual RNAs. In this study, we performed the first ever genome-wide study of RNA stability in the absence of PAP I. Inactivation of the pcnB gene coding for PAP I led to the stabilization of more than a thousand of E. coli RNAs in the form of full-length functional molecules or non-functional fragments, involved in essential cellular functions such as DNA replication and repair, translation, central carbon metabolism, and stress response. The absence of PAP I also altered the energy metabolism, with an almost 20 % reduction in ATP levels. To better understand how RNA and energy metabolisms are interconnected, we investigated the role of ATP levels in regulating RNA stability. When we lowered intracellular ATP levels below 0.5 mM, certain RNAs were stabilized demonstrating the causal link between ATP levels and RNA stability for the first time in E. coli. Above this concentration, changes in ATP levels had no impact on RNA stability. We also demonstrated that some RNAs were stabilized when PAP I was inactivated by low ATP availability. These results clearly demonstrate that PAP I mediates an energy-dependent RNA stabilization which may contribute to cell energy homeostasis under energy-limited conditions. Overall design: We reported RNA-seq data for genome-wide RNA half-life determination (stabilome experiments) performed in E. coli MG1655 cells treated with 0.7 mM or 2 mM 2,4-dinitrophenol (DNP). For each treatment, stabilome experiments are  based on 2 kinetics  of 6 RNA-seq performed over the time (T0, 0.4, 1, 2, 4 and 7 minutes) after rifampicin addition.