Cross-regulation between RNA stability, carbon metabolism and energy level in Escherichia coli: role of RNA polyadenylation.

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English. Background: Bacteria must adapt to changing environments using complex regulatory networks. Post-transcriptional regulations, particularly RNA degradation allow rapid metabolic adjustments by regulating protein synthesis. In E. coli, the machinery of RNA degradation involved RNases, RNA chaperones and poly(A) polymerase I (PAP I). PAP I promotes RNA degradation by polyadenylating their 3’-ends [1]. Interestingly, recent studies on individual metabolic pathways and RNAs have identified cross-regulations between RNA degradation and metabolism [2], raising the possibility of a more general regulatory network linking the two processes. In this work, we first aimed to assess the genome-wide role of RNA degradation, and more specifically the role of RNA polyadenylation in the regulation of E. coli metabolism. We also addressed the question of a possible influence of cellular energy level on RNA stability.Methods: We performed genome-wide analyses of RNA concentrations and half-lives by RNA-seq along with metabolome quantifications by mass spectrometry during exponential growth on glucose in three E. coli strains: the wild type strain, a strain deficient in PAP I activity and a strain overexpressing PAP I. We also artificially reduced the intracellular ATP level of E. coli cells using an uncoupling agent and measured the effect on RNA stability by RT-qPCR.Results: Upon inactivation and overexpression of PAP I, we observed strong rearrangements of the central carbon metabolism. More particularly, PAP I targets the metabolisms of acetate, UDP-sugars and nucleotides, and the pentose phosphate pathways. In the absence of RNA polyadenylation, we observed a global RNA stabilization with 1403 transcripts significantly stabilized and only 4 destabilized. This is the first report of a genome-wide destabilizing effect of RNA polyadenylation in E. coli. Stabilized RNAs were involved in essential cellular functions such as DNA replication and repair, translation, RNA degradation, envelope biogenesis, central carbon metabolism and stress responses. When we explored the link between RNA stability and cellular ATP level, we found a stabilization at a selection of RNAs at low ATP levels. For some of these RNAs, PAP I activity contributed to stabilization.Conclusion: These results provide the first evidence of global metabolic regulation by PAP I in E. coli. This finding coupled with the global RNA stabilization observed in the absence of PAP I, led us to conclude that E. coli cells can use the polyadenylation-mediated RNA degradation pathway to regulate their metabolic activity. These results also provide the first evidence of RNA stabilization at low ATP levels, suggesting that RNA stability is regulated by energy level. Altogether, this study highlights a clear interaction between the RNA degradation process, and carbon and energy metabolism in E. coli.[1]E. Hajnsdorf et V. R. Kaberdin, « RNA polyadenylation and its consequences in prokaryotes », Philos. Trans. R. Soc. Lond., B, Biol. Sci., vol. 373, no 1762, 05 2018, doi: 10.1098/rstb.2018.0166.[2]C. Roux et al., « The essential role of mRNA degradation in understanding and engineering E. coli metabolism », Biotechnol Adv, Jan-Feb 2022;54:107805.doi: 10.1016/j.biotechadv.2021.107805.