Schematic model of substrate recognition and degradation by the Clp protease system. Substrate recognition can be mediated by the ClpF/ClpS adaptors, the DNAJ/Hsp70 pathway, or an alternative system whose components are unknown. These 3 pathways likely deliver substrates to the Clp-associated Hsp100 chaperones (ClpC1, ClpC2 and ClpD) for protein unfolding before degradation by the proteolytic core of the complex (ClpPRT, composed by ClpP, ClpR and ClpT subunits).