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Published on April 17, 2009; 10.1104/pp.109.138677

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Received March 13, 2009
Accepted April 14, 2009

Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks

Sonja Reiland , Gaelle Messerli , Katja Baerenfaller , Bertran Gerrits , Anne Endler , Jonas Grossmann , Wilhelm Gruissem *, and Sacha Baginsky

Department of Biology, ETH Zurich, Universitatstrasse 2, 8092 Zurich, Switzerland, and Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland

* Corresponding author; email: wgruissem{at}ethz.ch.

We have characterized the phosphoproteome of Arabidopsis thaliana seedlings using high-accuracy mass spectrometry and report the identification of 1429 phosphoproteins and 3029 unique phosphopeptides. Among these, 174 proteins were chloroplast phosphoproteins. Motif-X analysis of the phosphorylation sites in chloroplast proteins identified four significantly enriched kinase motifs, which include casein kinase II (CKII) and proline-directed kinase motifs, as well as two new motifs at the C-terminus of ribosomal proteins. Using the phosphorylation motifs as a footprint for the activity of a specific kinase class, we connected the phosphoproteins with their putative kinases and constructed a chloroplast CKII phosphorylation network. The network topology suggests that CKII is a central regulator of different chloroplast functions. To provide insights into the dynamic regulation of protein phosphorylation we analyzed the phosphoproteome at the end-of-day and end-of-night. The results revealed only minor changes in chloroplast kinase activities and phosphorylation site utilization. A notable exception was ATPB, which is found phosphorylated at CKII phosphorylation sites preferentially in the dark. We propose that ATP synthase is regulated in cooperation with 14-3-3 proteins by CKII-mediated phosphorylation of ATPB in the dark.




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