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

RNA 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 as Synechocystis sp. PCC 6803 ( Synechocystis ), encode RNase E and RNase J homologs. Here, we constructed a Synechocystis strain 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 gene lsiR ; trxA, apcE and atpI mRNAs, encoding proteins related to energy metabolism; as well as sbtB and rbcLXS encoding proteins relevant for carbon fixation. Cyanobacterial 5’ sensing is important for the maturation of rRNA and several tRNAs, including tRNA Glu UUC . 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 major Synechocystis plasmids pSYSA and pSYSM. The results provide a first step towards understanding the relative importance of different target mechanisms of RNase E outside Escherichia coli .