Degradation of Nonribosomal Peptide Synthetase Megasynthetases SrfAA and SrfAB by Acyldepsipeptide‐Activated ClpP in <i>Bacillus Subtilis</i>

Protein degradation is a tightly controlled biological process and is essential for maintaining bacterial proteostasis. ClpPs are a highly conserved family of serine proteases that interact with ATPases and play key roles in diverse cellular activities, including heat-shock response, expression of virulence factors, and protein turnover and homeostasis. Owing to their vital roles, drugs targeting ClpP-ATPases have attracted interest in treating bacterial infections. The mode of action of the antibiotic acyldepsipeptide (ADEP) is uncontrolled proteolysis by an ATPase-independent ClpP-ADEP complex. The cell division protein FtsZ is the only bacterial protein confirmed to be hydrolyzed by the ClpP-ADEP complex in recombinant enzyme systems and cells. Here, the ClpP-ADEP complex that causes degradation of the secondary metabolite nonribosomal peptide synthetases (NRPSs) SrfAA and SrfAB in Bacillus subtilis is reported. Using in vivo and in vitro studies coupled with activity-based protein profiling of NRPSs, the ClpP-ADEP complex that degrades SrfAA and SrfAB is demonstrated. Furthermore, the ClpP-ADEP complex is reconstructed in cell lysates, confirming that SrfAA and SrfAB are sensitive to degradation by the ClpP-ADEP complex. These findings demonstrate that SrfAA and SrfAB are protein substrates for the ClpP-ADEP complex, providing novel insights into the ClpP degradation machinery.