RNA polyadenylation and cellular ATP levels regulate the stability of RNAs in Escherichia coli

To investigate the extent of the effect of poly(A) polymerase (PAP I)-mediated polyadenylation on RNA stability, we performed the first genome-wide study of RNA stability in the absence of PAP I activity. Inactivation of the pcnB gene coding for PAP I led to a global stabilization of E. coli RNAs, with 1403 stabilized transcripts and only 4 destabilized. Stabilized RNAs were involved in essential cellular functions such as DNA replication and repair, translation, RNA degradation, central carbon metabolism but also in stress responses. Because PAP I is an ATP-consuming enzyme we wondered whether the RNA stabilization observed after inactivation of PAP I could also be related to changes in intracellular ATP levels. We demonstrated for the first time in E. coli, that lowering intracellular ATP levels below 1 µM/OD stabilizes RNAs. Although the ATP level was reduced by 20 % in the pcnB mutant on glucose, the ATP level was still too high to have any role in the observed RNA stabilization. However, in experiments where the ATP level was artificially strongly decreased, inactivation of PAP I by substrate availability was implicated in the stabilization mechanism of certain RNAs. This study clearly demonstrates that PAP I is at the crossroads of the regulation of RNA stability by energy status in E. coli cells. Overall design: We reported RNA-seq data for transriptome and genome-wide RNA half-life determination (stabilome experiments) performed in two strains: the wild-type E. coli MG1655 strain (named MG) and its mutant deleted of the pcnB gene coding for the poly(A) polymerase (PAP I) (named PCNB). Transcriptome experiments were carried out in biological triplicates for MG (3 RNA-seq) and PC (3 RNA-seq) corresponding to the time T0 of the stabilome experiments. For each strain, the stabilome experiment is based on 3 kinetics (K1, K2 and K3) of 4 RNA-seq performed over the time after rifampicin addition.