Originally published In Press as doi:10.1074/jbc.M309212200 on October 30, 2003

J. Biol. Chem., Vol. 279, Issue 6, 4768-4781, February 6, 2004

Clp Protease Complexes from Photosynthetic and Non-photosynthetic Plastids and Mitochondria of Plants, Their Predicted Three-dimensional Structures, and Functional Implications^*

Jean-Benoît Peltier¶, Daniel R. Ripoll||, Giulia Friso, Andrea Rudella, Yang Cai, Jimmy Ytterberg, Lisa Giacomelli, Jaroslaw Pillardy||, and Klaas J. van Wijk**

From the Department of Plant Biology and the ^||Computational Biology Service Unit, Cornell Theory Center, Cornell University, Ithaca, New York 14853

Tetradecameric Clp protease core complexes in non-photosynthetic plastids of roots, flower petals, and in chloroplasts of leaves of Arabidopsis thaliana were purified based on native mass and isoelectric point and identified by mass spectrometry. The stoichiometry between the subunits was determined. The protease complex consisted of one to three copies of five different serine-type protease Clp proteins (ClpP1,3-6) and four non-proteolytic ClpR proteins (ClpR1-4). Three-dimensional homology modeling showed that the ClpP/R proteins fit well together in a tetradecameric complex and also indicated unique contributions for each protein. Lateral exit gates for proteolysis products are proposed. In addition, ClpS1,2, unique to land plants, tightly interacted with this core complex, with one copy of each per complex. The three-dimensional modeling show that they do fit well on the axial sites of the ClpPR cores. In contrast to plastids, plant mitochondria contained a single 320-kDa homo-tetradecameric ClpP2 complex, without association of ClpR or ClpS proteins. It is surprising that the Clp core composition appears identical in all three plastid types, despite the remarkable differences in plastid proteome composition. This suggests that regulation of plastid proteolysis by the Clp machinery is not through differential regulation of ClpP/R/S gene expression, but rather through substrate recognition mechanisms and regulated interaction of chaperone-like molecules (ClpS1,2 and others) to the ClpP/R core.

Received for publication, August 19, 2003 , and in revised form, October 30, 2003.

The atomic coordinates and structure factors (codes 1R8Z, 1R8V, 1R90, 1R91, 1R92, 1R93, 1R96, 1R97, 1R98, 1R99, 1R9a, 1R9B) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains Tables 1-4.

Both authors contributed equally to this work.

^¶ To whom correspondence may be addressed. Tel.: 607-255-6471; Fax: 607-255-5407; E-mail: jp269@cornell.edu.

^** To whom correspondence may be addressed. Tel.: 607-255-3664; Fax: 607-255-5407; E-mail: kv35@Cornell.edu.