Insights into the global effect on Staphylococcus aureus growth arrest by induction of the endoribonuclease MazF toxin

A crucial bacterial strategy to avoid killing by antibiotics is to enter a growth arrested state, yet the molecular mechanisms behind this process remain elusive. The conditional overexpression of MazF, the endoribonuclease toxin of the MazEF toxin-antitoxin system in Staphylococcus aureus, is one approach to induce bacterial growth arrest, but its targets remain largely unknown. We used overexpression of MazF and high-throughput sequence analysis following the exact mapping of non-phosphorylated transcriptome ends (nEMOTE) technique to reveal in vivo toxin cleavage sites on a global scale. We obtained a catalogue of MazF cleavage sites and unearthed an extended MazF cleavage specificity that goes beyond the previously reported one. We correlated transcript cleavage and abundance in a global transcriptomic profiling during mazF overexpression. We observed that MazF affects RNA molecules involved in ribosome biogenesis, cell wall synthesis, cell division and RNA turover and thus deliver a plausible explanation for how mazF overexpression induces stasis. We hypothesize that autoregulation of MazF occurs by directly modulating the MazEF operon, such as the rsbUVW genes that regulate the alternative SigB, including an observed cleavage site on the MazF mRNA that would ultimately play a role in entry and exit from bacterial stasis. Overall design: mazF is a toxin with an endoribonuceolitic activity. To study mazF in S. aureus, we build the strain dmazEF where the toxin (mazF) and its antitoxin (mazE) are deleted. We introduced into it a plasmid (pF) with mazF under the control of anhydrotetracycline inducible promoter. At OD 0.4, and after 10 minutes induction of mazF, the RNA is extracted and prepared folowing two protocols: RNA-seq and nEMOTE-seq. While RNA-seq allow to obtain a global picture of the expressed RNA fragments in the cell, nEMOTE-seq focus specifically on mono-phosphorylated 5'-ends. As the endoribonucleic activity of mazF is expected to create new monoposphorylated 5'-ends when an RNA is cleaved, nEMOTE-seq is used to find cleavage sites of mazF by looking at 5'-ends specifically appearing when mazF is expressed.