ClpP1P2 peptidase activity promotes biofilm formation in Pseudomonas aeruginosa

Caseinolytic proteases (Clp) are central to bacterial proteolysis and control cellular physiology and stress responses. They are composed of a double‐ring compartmentalized peptidase (ClpP) and a AAA+ unfoldase (ClpX or ClpA/ClpC). Unlike many bacteria, the opportunistic pathogen Pseudomonas aeruginosa contains two ClpP homologs: ClpP1 and ClpP2. The specific functions of these homologs, however, are largely elusive. Here, we report that the active form of PaClpP2 is a part of a heteromeric PaClpP17P27 tetradecamer that is required for proper biofilm development. PaClpP114 and PaClpP17P27 complexes exhibit distinct peptide cleavage specificities and interact differentially with P. aeruginosa ClpX and ClpA. Crystal structures reveal that PaClpP2 has non‐canonical features in its N‐ and C‐terminal regions that explain its poor interaction with unfoldases. However, experiments in vivo indicate that the PaClpP2 peptidase active site uniquely contributes to biofilm development. These data strongly suggest that the specificity of different classes of ClpP peptidase subunits contributes to the biological outcome of proteolysis. This specialized role of PaClpP2 highlights it as an attractive target for developing antimicrobial agents that interfere specifically with late‐stage P. aeruginosa development. The Pseudomonas aeruginosa quorum‐sensing‐controlled peptidase ClpP2 forms an active heterocomplex with ClpP1. PaClpP17P27 peptidase activity is distinct from PaClpP114 and contributes to biofilm architecture in vivo.