Effect of tRNA maturase depletion on the levels and stabilities of ribosome assembly cofactor mRNAs in Bacillus subtilis

The impact of translation on mRNA stability can be varied, ranging from a protective effect of ribosomes that shield mRNA from ribonucleases (RNases), to preferentially exposing sites of RNase cleavage. These effects can change depending on whether ribosomes are actively moving along the mRNA or whether they are stalled at particular sequences, structures or awaiting charged tRNAs. We recently observed that depleting B. subtilis cells of its tRNA maturation enzymes RNase P or RNase Z, led to altered mRNA levels of a number of assembly factors involved in the biogenesis of the 30S ribosomal subunit. Here, we extend this study to other assembly factor mRNAs and identify multiple transcriptional and translational layers of regulation of the rimM operon mRNA that occur in response to the depletion of functional tRNAs. ImportanceThe passage of ribosomes across individual mRNAs during translation can have different effects on their degradation, ranging from a protective effect by shielding from ribonucleases, to in some cases, making the mRNA more vulnerable to RNase action. We recently showed that some mRNAs coding for proteins involved in ribosome assembly were highly sensitive to the availability of functional tRNA. Using strains depleted for the major tRNA processing enzymes RNase P and RNase Z, we expanded this observation to a wider set of mRNAs, including some unrelated to ribosome biogenesis. We characterize the impact of tRNA maturase depletion on the rimM operon mRNA and show it is highly complex, with multiple levels of transcriptional and post-transcriptional effects coming into play.