The cryo-EM structure of the chloroplast ClpP complex reveals an interaction with the co-chaperonin complex that inhibits ClpP proteolytic activity

Abstract

Protein homeostasis in plastids is strategically regulated by the protein quality control system involving multiple chaperones and proteases, among them the Clp protease. We determined the structure of the chloroplast ClpP complex from Chlamydomonas reinhardtiiby cryo-EM. ClpP contains two heptameric catalytic rings without any symmetry. The top ring contains one ClpR6, three ClpP4 and three ClpP5 subunits while the bottom ring is composed of three ClpP1C subunits and one each of the ClpR1-4 subunits. ClpR3, ClpR4 and ClpT4 subunits connect the two rings and stabilize the complex. The chloroplast Cpn11/20/23 co-chaperonin, a co-factor of Cpn60, forms a cap on the top of ClpP by protruding mobile loops into hydrophobic clefts at the surface of the top ring. The co-chaperonin repressed ClpP proteolytic activity in vitro. By regulating Cpn60 chaperone and ClpP protease activity, the co-chaperonin may play a role in coordinating protein folding and degradation in the chloroplast.

Proteomics, phylogenetics, and coexpression analyses indicate novel interactions in the plastid CLP chaperone-protease system

“…We previously observed and highlighted a strong enrichment of CPN20 in protein interactome analysis of CLPT1,2 ( 43 ). Interesting, a recent cryo-EM structure of the affinity-purified chloroplast CLPPR protease complex from the green algae Chlamydomonas reinhardtii showed that a heterotetramer of CPN11, CPN20, and CPN23 associated with one of the axial sides of the CLP core complex to form a stable 550-kDa complex ( 48 ). It was suggested that this cochaperone complex could play a role in coordinating protein folding and degradation in the Chlamydomonas chloroplast.…”

“…Several of these proteins are direct components of the CLP chaperone-protease system (CLPF, CLPT1, CLPT2, CLPD). The >10-fold enrichment of cochaperone pair CPN10 and CPN20 is highly intriguing given the recent identification in the Chlamydomonas CLP core structure through cryo-EM ( 48 ); perhaps the CPN10/20 proteins also directly interact with the CLP protease core complex to regulate access to the catalytic chamber.…”