RNase Z from Deinococcus radiodurans couples tRNA processing with stress-responsive mRNA and sRNA turnover

RNase Z is a conserved metallo-dependent endoribonuclease that catalyzes the 3'-end processing of precursor tRNAs. Although its canonical role in tRNA maturation is well established, its involvement in RNA turnover during stress responses remains poorly understood in many bacteria. In this study, we characterized the biochemical properties and regulatory functions of RNase Z from Deinococcus radiodurans (DrRNase Z). The rnz gene was cloned, overexpressed in Escherichia coli, and the recombinant enzyme was purified to homogeneity. ICP-MS analysis revealed that DrRNase Z coordinates two Zn²⁺ ions per monomer and exhibits Zn²⁺-dependent phosphodiesterase activity. Kinetic analysis demonstrated catalytic parameters comparable to other RNase Z homologues. Using in vitro-transcribed substrates, DrRNase Z efficiently processed precursor tRNA^Arg by endonucleolytic removal of extra nucleotides downstream of the 3'-CCA sequence, while mature tRNA remained resistant to cleavage. Interestingly, rnz transcript levels decreased significantly following γ-irradiation or oxidative stress. In vitro assays further showed that DrRNase Z cleaves the oxidative stress-inducible katA mRNA and the stress-responsive small RNA IGR_1612, which enhances cellular growth under oxidative stress when ectopically expressed. These findings indicate that DrRNase Z not only participates in tRNA maturation but also contributes to the turnover of stress-induced mRNAs and sRNAs, thereby helping restore RNA homeostasis in D. radiodurans following stress exposure.