RNA-sequencing reveals novel in vivo cleavage sites of RNase III in Escherichia coli

Ribonucleases (RNases) not only facilitate the degradation of transcripts, but have also been shown to play significant roles in regulating gene expression.  A medley of RNases orchestrate efficient messenger RNA (mRNA) turnover. There is a high level of diversity in the number and type of RNases among bacterial species, yet RNA decay has been primarily studied in the model bacteria Escherichia coli and Bacillus subtilis. These divergent bacterial strains contain a distinct subset of RNases that share many characteristics despite a high level of divergence at the sequence and structural levels. However, after decades of study, only a few known in vivo target sites have been identified for a majority of these enzymes. We used RNA-sequencing to identity in vivo cleavage sites of RNase III in E. coli. The novel cleavage sites that we have uncovered suggest that RNase III plays a significant role in regulating central metabolism. This work provides the framework to expand these studies to non-model organisms that possess unique arrays of RNases. With increased knowledge of how these enzymes function we can advance current models of mRNA decay as well as build tools to control gene expression. We have developed one such tool to increase the half-life of transcripts in an organism where we know little about RNA decay, cyanobacterium Synechococcus sp. PCC 7002. By exploiting the specificities of ribonucleases we can build an expansive toolset to fine-tune gene expression on the level of RNA stability.