Impact of RNase E and RNase J on Global mRNA Metabolism in the Cyanobacterium Synechocystis PCC6803.

mRNA levels result from an equilibrium between transcription and degradation. Ribonucleases (RNases) facilitate the turnover of mRNA, which is an important way of controlling gene expression, allowing the cells to adjust transcript levels to a changing environment. In contrast to the heterotrophic model bacteriaEscherichia coliandBacillus subtilis, RNA decay has not been studied in detail in cyanobacteria.Synechocystissp. PCC6803 encodes orthologs of bothE. coliandB. subtilisRNases, including RNase E and RNase J, respectively. We show thatin vitro SyRNases E and J have an endonucleolytic cleavage specificity that is very similar between them and also compared to orthologous enzymes fromE. coli, B. subtilis, andChlamydomonas.Moreover,SyRNase J displays a robust 5 '-exoribonuclease activity similar toB. subtilisRNase J1, but unlike the evolutionarily related RNase J in chloroplasts. Both nucleases are essential and gene deletions could not be fully segregated inSynechocystis. We generated partially disrupted strains ofSyRNase E and J that were stable enough to allow for their growth and characterization. A transcriptome analysis of these strains partially depleted for RNases E and J, respectively, allowed to observe effects on specific transcripts. RNase E altered the expression of a larger number of chromosomal genes and antisense RNAs compared to RNase J, which rather affects endogenous plasmid encoded transcripts. Our results provide the first description of the main transcriptomic changes induced by the partial depletion of two essential ribonucleases in cyanobacteria.