The DnaJK chaperone of Bacillus subtilis post-transcriptionally regulates gene expression through the YlxR(RnpM)/RNase P complex

To survive in harsh natural environments, translation and mRNA metabolism must be tightly and coordinately controlled, as saving biological costs increases fitness. However, the roles of protein chaperones in this control system are unclear. This study proposes the novel aspect of the link between translation and mRNA metabolism, that is, the co-translational DnaJK chaperone activity is involved in changes in mRNA metabolism by RNase P. We found that the expression of proBA, which encodes proline biosynthetic enzymes, is regulated by ylxR(rnpM) through the proBA promoter. YlxR(RnpM), which is associated with RNase P, was also involved in the posttranscriptional regulation of proBA. To clarify this posttranscriptional regulation, we screened transposon (Tn)-inserted mutants for cells with low proB::lacZ expression and identified the DnaJK chaperone as a regulator of proB. To explore the possibility that the complex of YlxR(RnpM) and RNase P might work with DnaJK, we performed an epistatic analysis using the lacZ fusions, which revealed that the regulation of proB by DnaJK/YlxR(RnpM)/RNase P, that is, co-translational chaperone activity, controlled mRNA metabolism. RNA sequencing analysis of cells deficient in the RNA component of RNase P (rnpB) revealed that 261 genes were upregulated in the rnpB::Tn strain. Among them, we identified yoyD/yodF, besA, and epeXE, which were also under the control of DnaJK/YlxR(RnpM)/RNase P regulatory cascade. Finally, we performed yeast two-hybrid analysis using DnaK as bait and identified two genes, spoIVCA and nupG, whose expression was post-transcriptionally regulated by DnaJK but independent of YlxR(RnpM). These results suggest a broader role for posttranscriptional gene regulation by DnaJK.