Transcriptome-Wide Analyses of 5′-Ends in RNase J Mutants of a Gram-Positive Pathogen Reveal a Role in RNA Maturation, Regulation and Degradation

Abstract

The long RNA (ribonucleic acid) chains are key intermediates in the transfer of information from the genes on chromosomes to the production of protein. An RNA copy (mRNA) is transcribed from the gene, and this copy is then translated into protein by a complex molecular machine called the ribosome. The amount of mRNA copies of a given gene is therefore important for how much of the corresponding protein can be generated. This “pool” of mRNA depends on how many copies are made per second, but also on how many copies disappear due to degradation. In this study, we examine mutants of the bacterial pathogen Staphylococcus aureus, which have lost one or both of their RNase J genes (ribonuclease J). These mutants grow relatively fine under standard laboratory conditions, but will stop growing if they are stressed by alternative food sources or temperatures equivalent to a high fever (42°C). We show that the RNase J enzymes are major players in the degradation of RNA by removing one link at a time in the RNA-chains, thus influencing the pool of mRNAs in the cell. Furthermore, certain RNAs are processed to stable and active forms by RNase J, instead of being degraded