Unique features of magic spot metabolism in Clostridioides difficile

The magic spot alarmones (pp)pGpp, previously implicated in Clostridioides difficile antibiotic survival, are synthesized by CdRSH and CdRelQ. These enzymes are transcriptionally activated by diverse environmental stresses, but both exclusively synthesize pGpp rather than ppGpp as has previously been reported. While direct synthesis of pGpp from a GMP substrate and (p)ppGpp hydrolysis into pGpp by NUDIX hydrolases have previously been reported, there is no precedent for a bacterium synthesizing pGpp exclusively. Hydrolysis of the 5-prime phosphate or pyrophosphate from GDP or GTP substrates is necessary for activity by the clostridial enzymes, neither of which can utilize GMP as a substrate. Both enzymes are remarkably insensitive to the size of their metal ion cofactor, tolerating a broad array of metals that do not allow activity in (pp)pGpp synthetases from other organisms. It is clear that while C. difficile utilizes magic spot signaling, its mechanisms of alarmone synthesis are not directly homologous to those in more completely characterized organisms.