The DnaJK chaperone of <i>Bacillus subtilis</i> 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 <i>proBA,</i> which encodes proline biosynthetic enzymes, is regulated by <i>ylxR</i>(<i>rnpM</i>) through the <i>proBA</i> promoter. YlxR(RnpM), which is associated with RNase P, was also involved in the posttranscriptional regulation of <i>proBA</i>. To clarify this posttranscriptional regulation, we screened transposon (Tn)-inserted mutants for cells with low <i>proB::lacZ</i> expression and identified the DnaJK chaperone as a regulator of <i>proB</i>. To explore the possibility that the complex of YlxR(RnpM) and RNase P might work with DnaJK, we performed an epistatic analysis using the <i>lacZ</i> fusions, which revealed that the regulation of <i>proB</i> 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 (<i>rnpB</i>) revealed that 261 genes were upregulated in the <i>rnpB</i>::Tn strain. Among them, we identified <i>yoyD/yodF, besA</i>, and <i>epeXE,</i> 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, <i>spoIVCA</i> and <i>nupG</i>, 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.IMPORTANCE<i>Bacillus subtilis</i> lacking the DnaJK chaperone has not been reported to exhibit a distinct phenotype. However, our study revealed proline-dependent growth in a minimal medium in the <i>dnaJ</i>::Tn strain. Inhibition of <i>spoIVCA</i> expression in this strain was identified as a probable cause of the sporulation deficiency in previous and current studies using a single cell-level analysis. We also observed posttranscriptional regulation of <i>proBA</i> by the DnaJK and YlxR(RnpM)/RNase P complex. LacZ analyses of <i>proB::lacZ</i> in different backgrounds suggested that the above regulation ultimately functions in mRNA metabolism. In DnaJK-deficient cells, the nascent peptide may be misfolded, and if DnaJK chaperone activity is lost, such a signal may be transferred to RNase P. Therefore, <i>proBA</i> mRNA may be degraded in an RNase P-dependent manner if the misfolding of the polypeptide translated from this mRNA is detected. This system is useful for reducing the biological costs of futile mRNA elongation.