Selective RNA Processing and Stabilization are Multi‐Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli

Abstract Selective RNA processing and stabilization (SRPS) facilitates the differential expression of multiple genes in polycistronic operons. However, how the coordinated actions of SRPS‐related enzymes affect stoichiometric regulation remains unclear. In the present study, the first genome‐wide targetome analysis is reported of these enzymes in Escherichia coli, at a single‐nucleotide resolution. A strictly linear relationship is observed between the RNA pyrophosphohydrolase processing ratio and scores assigned to the first three nucleotides of the primary transcript. Stem‐loops associated with PNPase targetomes exhibit a folding free energy that is negatively correlated with the termination ratio of PNPase at the 3′ end. More than one‐tenth of the RNase E processing sites in the 5′‐untranslated regions（UTR） form different stem‐loops that affect ribosome‐binding and translation efficiency. The effectiveness of the SRPS elements is validated using a dual‐fluorescence reporter system. The findings highlight a multi‐layer and quantitative regulatory method for optimizing the stoichiometric expression of genes in bacteria and promoting the application of SRPS in synthetic biology.