transcriptome of RNase E and RNase J mutants of Synechocystis

mRNA levels result from an equilibrium between transcription and degradation. Ribonucleases (RNases) facilitate the rapid 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 bacteria Escherichia coli and Bacillus subtilis, RNA decay has not been studied in detail in cyanobacteria. Synechocystis sp. PCC6803 encodes orthologs of both E. coli and B. subtilis RNases, including RNase E and RNase J, respectively. We show that in vitro Sy RNases E and J have an endonucleolytic cleavage specificity that is very similar between them and also compared to orthologous enzymes from E. coli, B. subtilis and Chlamydomonas. Moreover, Sy RNase J displays a robust 5-exoribonuclease activity similar to B. subtilis RNase J1, but unlike the evolutionarily related RNase J in chloroplasts. Both nucleases are essential and their genes cannot be deleted to homozygosis in Synechocystis. We generated heteroplasmic disrupted strains of Sy RNase 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, with RNase E affecting the expression of a larger number of chromosomal genes and antisense RNAs compared to RNase J, which rather affects 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.