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First published online September 15, 2006; 10.1105/tpc.106.044594

The Plant Cell 18:2635-2649 (2006)
© 2006 American Society of Plant Biologists

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Structural and Functional Insights into the Chloroplast ATP-Dependent Clp Protease in Arabidopsis

Lars L.E. Sjögrena, Tara M. Stannea, Bo Zhengb, Sirkka Sutinenc and Adrian K. Clarkea,1

a Department of Plant and Environmental Sciences, Gothenburg University, 405 30 Gothenburg, Sweden
b Umeå Plant Science Center, Umeå University, S-901 87 Umeå, Sweden
c Finnish Forest Research Institute, Joensuu Research Center, Fin-801 01 Joensuu, Finland

1 To whom correspondence should be addressed. E-mail adrian.clarke{at}botany.gu.se; fax 46-31-7732626.

In contrast with the model Escherichia coli Clp protease, the ATP-dependent Clp protease in higher plants has a remarkably diverse proteolytic core consisting of multiple ClpP and ClpR paralogs, presumably arranged within a dual heptameric ring structure. Using antisense lines for the nucleus-encoded ClpP subunit, ClpP6, we show that the Arabidopsis thaliana Clp protease is vital for chloroplast development and function. Repression of ClpP6 produced a proportional decrease in the Clp proteolytic core, causing a chlorotic phenotype in young leaves that lessened upon maturity. Structural analysis of the proteolytic core revealed two distinct subcomplexes that likely correspond to single heptameric rings, one containing the ClpP1 and ClpR1-4 proteins, the other containing ClpP3-6. Proteomic analysis revealed several stromal proteins more abundant in clpP6 antisense lines, suggesting that some are substrates for the Clp protease. A proteolytic assay developed for intact chloroplasts identified potential substrates for the stromal Clp protease in higher plants, most of which were more abundant in young Arabidopsis leaves, consistent with the severity of the chlorotic phenotype observed in the clpP6 antisense lines. The identified substrates all function in more general housekeeping roles such as plastid protein synthesis, folding, and quality control, rather than in metabolic activities such as photosynthesis.




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