Identification of a 350-kDa ClpP Protease Complex with 10 Different Clp Isoforms in Chloroplasts of Arabidopsis thaliana*

A 350-kDa ClpP protease complex with 10 different subunits was identified in chloroplast of Arabidopsis thaliana, using Blue-Native gel electrophoresis, fol-lowed by matrix-assisted laser desorption ionization time-of-flight and nano-electrospray tandem mass spec-trometry. The complex was copurified with the thyla-koid membranes, and all identified Clp subunits show chloroplast targeting signals, supporting that this com-plex is indeed localized in the chloroplast. The complex contains chloroplast-encoded pClpP and six nuclear-en-coded proteins nCpP1–6, as well as two unassigned Clp homologues (nClpP7, nClpP8). An additional Clp pro-tein was identified in this complex; it does not belong to any of the known Clp genes families and is here assigned ClpS1. Expression and accumulation of several of thes