The role of the 5’ sensing function of ribonuclease E in cyanobacteria

Abstract

AbstractRNA degradation is crucial for many processes in pro- and eukaryotic organisms. In bacteria, the preference of the central ribonucleases RNase E, RNase J and RNase Y towards 5’-monophosphorylated RNAs is considered important for RNA degradation. For RNase E, the underlying mechanism is termed 5’ sensing. Cyanobacteria, such asSynechocystissp. PCC 6803 (Synechocystis), encode RNase E and RNase J homologs. Here, we constructed aSynechocystisstrain lacking the 5’ sensing function of RNase E and mapped on a transcriptome-wide level 292 5’-sensing-dependent cleavage sites. These included so far unknown targets such as the 5’ untranslated region of the response regulator genelsiR;trxA, apcEandatpImRNAs, encoding proteins related to energy metabolism; as well assbtBandrbcLXSencoding proteins relevant for carbon fixation. Cyanobacterial 5’ sensing is important for the maturation of rRNA and several tRNAs, including tRNAGluUUC. This tRNA activates glutamate for tetrapyrrole biosynthesis in plant chloroplasts and most prokaryotes. We found that increased RNase activities leads to a higher copy number of the majorSynechocystisplasmids pSYSA and pSYSM. The results provide a first step towards understanding the relative importance of different target mechanisms of RNase E outsideEscherichia coli.