1. The Chloroplast Kinase Network: New Insights from Large-Scale Phosphoproteome Profiling 
Baginsky Sacha , Gruissem Wilhelm  
Molecular Plant 
Volume 2, Issue 6, Pages (November 2009)
DOI: /mp/ssp058
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

2. Figure 1
Protein Phosphorylation and the Responsible Kinase Activities in Chloroplasts.
The model network reflects current knowledge about chloroplast protein kinases and their regulatory functions.
(A) CKII phoshorylates ATPB (Kanekatsu et al., 1998), components of nucleoids (e.g. MFP1) and the transcription machinery (Ogrzewalla et al., 2002; Jeong et al., 2004), as well as the p54 endonuclease and RNA-binding proteins in a light-dependent manner (Kanekatsu et al., 1993; Lisitsky and Schuster, 1995; Liere and Link, 1997; Kleffmann et al., 2007). Phosphorylation-site prediction also suggested one CKII phosphorylation site in the state transition kinase STN7 (Reiland et al., 2009).
(B) STN7 phosphorylates subunits of the light-harvesting complexes, which regulate the mobility of the antenna and the distribution of light energy between the two photosystems (Rochaix, 2007).
(C) STN8, a homolog of STN7, phosphorylates core subunits of photosystem II as well as a soluble calcium-sensitive protein (CaS) (Rochaix, 2007; Vainonen et al., 2008).
(D) The chloroplast sensor kinase (CSK) is involved in the regulation of gene expression for photosynthetic genes. Its activity is dependent on reducing reagents, which has led to the hypothesis that CSK is regulated by redox signals originating at the thylakoid membrane (Puthiyaveetil et al., 2008).
(E) Three thylakoid-associated kinases (TAKs) were identified and TAK I was shown to phosphorylate subunits of the light-harvesting complexes as well as CP43 (Snyders and Kohorn, 2001).
(F) A presently unknown kinase X was introduced into the model network based on evidence for additional chloroplast kinases that remain to be isolated. Furthermore, two presently uncharacterized kinases were found to localize to plastids (Schliebner et al., 2008). CKII activity was decreased after in vitro phosphorylation by PKA, suggesting that CKII activity may be controlled by another unknown chloroplast kinase (Baginsky et al., 1999). The question marks (?) suggest cross-talk with currently unknown network components.
Molecular Plant 2009 2, DOI: ( /mp/ssp058)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

3. Figure 2
Identification of Plastid Proteins in Three Large-Scale Arabidopsis Phosphoproteome Analyses.
In order to compare and integrate the data from three large-scale phosphoproteome analyses, we assembled a chloroplast proteome reference table from two previously published lists (Yu et al., 2008; Reiland et al., 2009) and accepted only those proteins as chloroplast protein that are present in both. With this list of 1156 proteins, we searched in large-scale phosphoproteomics data for chloroplast proteins to illustrate the distribution and overlap of phosphoprotein identification in the different studies (Sugiyama et al., 2008; Lohrig et al., 2009; Reiland et al., 2009).
Molecular Plant 2009 2, DOI: ( /mp/ssp058)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

4. Figure 3 Phosphorylation Sites in Enzymes of the Calvin Cycle.
Phosphorylation sites in Calvin cycle enzymes are presented as WebLogo sequences ( We included five amino acids N- and C-terminal of the phosphorylation site in the plot. In cases in which one enzyme was found phosphorylated at several sites, we included all information in the alignment to illustrate possible recurrence of motifs.
Molecular Plant 2009 2, DOI: ( /mp/ssp058)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

5. Figure 4 Phosphorylation Sites in Enzymes of the Tetrapyrrole Pathway.
Phosphorylation sites in enzymes of the tetrapyrrole pathway are presented as WebLogo sequences ( We included five amino acids N- and C-terminal of the phosphorylation site in the plot. The phosphorylated amino acid is presented in a box. We addressed the question of how conserved the phosphorylation sites are by aligning the phosphorylation site (+/– 10 amino acids) for up to 100 plant homologs of the indicated enzyme (right panel) with WebLogo ( For this purpose, we used the BLink option provided on the NCBI homepage (
Molecular Plant 2009 2, DOI: ( /mp/ssp058)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions