Photosynthetic Control of Arabidopsis Leaf Cytoplasmic Translation Initiation by Protein Phosphorylation

<div><p>Photosynthetic CO₂ assimilation is the carbon source for plant anabolism, including amino acid production and protein synthesis. The biosynthesis of leaf proteins is known for decades to correlate with photosynthetic activity but the mechanisms controlling this effect are not documented. The cornerstone of the regulation of protein synthesis is believed to be translation initiation, which involves multiple phosphorylation events in Eukaryotes. We took advantage of phosphoproteomic methods applied to <i>Arabidopsis thaliana</i> rosettes harvested under controlled photosynthetic gas-exchange conditions to characterize the phosphorylation pattern of ribosomal proteins (RPs) and eukaryotic initiation factors (eIFs). The analyses detected 14 and 11 new RP and eIF phosphorylation sites, respectively, revealed significant CO₂-dependent and/or light/dark phosphorylation patterns and showed concerted changes in 13 eIF phosphorylation sites and 9 ribosomal phosphorylation sites. In addition to the well-recognized role of the ribosomal small subunit protein RPS6, our data indicate the involvement of eIF3, eIF4A, eIF4B, eIF4G and eIF5 phosphorylation in controlling translation initiation when photosynthesis varies. The response of protein biosynthesis to the photosynthetic input thus appears to be the result of a complex regulation network involving both stimulating (e.g. RPS6, eIF4B phosphorylation) and inhibiting (e.g. eIF4G phosphorylation) molecular events.</p></div

Eukaryotic ribosomal protein and initiation factor phosphopeptides identified by nanoLC-MS/MS.

<p>a- Phosphopeptides sequences are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070692#pone.0070692.s002" target="_blank">Table S2</a>.</p><p>b- A phosphorylation site is considered as new when absent from refs. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070692#pone.0070692-Turkina1" target="_blank">[8]</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070692#pone.0070692-Muench1" target="_blank">[11]</a> and PhosPhAt 4.0 database(<a href="http://phosphat.mpimp-golm.mpg.de/" target="_blank">http://phosphat.mpimp-golm.mpg.de/</a>).</p><p>c- Phosphorylation patterns are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070692#pone-0070692-g003" target="_blank">Figures 3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070692#pone-0070692-g004" target="_blank">4</a>.</p><p>d- By ‘punctually’, we mean occasional detection of phosphorylation, with no clear pattern.</p

Photosynthetic parameters.

<p>leaf net photosynthesis (<b>A</b>), leaf-to-air water vapour drawdown (<b>B</b>), leaf glucose content (<b>C</b>) and Gly-to-Ser ratio (<b>D</b>), under the different photosynthetic contexts used (LC, NC and HC: 100, 380 and 1000 µmol mol⁻¹ CO₂; D: darkness).</p

X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification

X!TandemPipeline is a software designed to perform protein inference and to manage redundancy in the results of phosphosite identification by database search. It provides the minimal list of proteins or phosphosites that are present in a set of samples using grouping algorithms based on the principle of parsimony. Regarding proteins, a two-level classification is performed, where groups gather proteins sharing at least one peptide and subgroups gather proteins that are not distinguishable according to the identified peptides. Regarding phosphosites, an innovative approach based on the concept of phosphoisland is used to gather overlapping phosphopeptides. The graphical interface of X!TandemPipeline allows the users to launch X!tandem identification, to inspect spectra and to manually validate their assignment to peptides, to launch the grouping program, and to visualize elementary data as well as grouping and redundancy information. Identification results obtained from other search engines can also be processed. X!TandemPipeline results can be exported as ready-to-use tabulated files or as XML files that can be directly used by the PROTICdb database or by the MassChroQ quantification software. X!TandemPipeline runs fast, is easy to use, and can process hundreds of samples simultaneously. It is freely available under the GNU General Public License v3.0 at http://pappso.inra.fr/bioinfo/xtandempipeline/

Phosphorylation pattern of ribosomal proteins.

<p><b>A</b>, Heat map representation of the phosphorylation level of significant phosphopeptides (phosphorylated peptides that showed statistically significant changes with conditions). A hierarchical clustering analysis is shown on the left. All significant phosphopeptides had a very similar pattern, except for RPL13D, which was minimally phosphorylated under ordinary conditions (NC). Unavailable data (non-detected peptides) are indicated with a grey cell. <b>B</b> and <b>C</b>, Detailed phosphorylation pattern of RPS6A/B and RPS14A. LC, NC, HC and D: low, normal and high CO₂ and darkness.</p

Tentative summary of protein phosphorylation events involved in translation initiation during photosynthesis, with activating (black) and repressing (grey) effects.

<p>Phosphorylated proteins are indicated with the symbol <b>P</b>. Those associated with phosphopeptides detected in the present study are indicated with a star, with the phosphorylation level that either correlates (black star), anti-correlates (grey star) or stays constant (white star) with photosynthesis. This figure is simplified and does not mention all molecular actors (such as eIF4G and eIF2Bδ).</p

Phosphorylation pattern of initiation factors eIFs.

<p><b>A</b>, Heat map representation of the phosphorylation level of significant phosphopeptides. A hierarchical clustering analysis is shown on the left so as to separate photosynthesis or light-stimulated (top) and -inhibited (bottom) phosphorylation events. Unavailable data (non-detected peptides) are indicated with a grey cell. <b>B</b> and <b>C</b>, Detailed phosphorylation pattern of eIF4B2 and eIF4G. LC, NC, HC and D: low, normal and high CO₂ and darkness.</p

Identification of Ser 229 and Ser 231 in RPS6A/B (A) and Ser 178 and Ser 530 in eIF4G (B) by mass spectrometric sequencing of two phosphorylated peptides.

<p>Spectra of methylated and phosphorylated peptides show b (N-terminal) and y (C-terminal) fragment-ions as displayed in the sequence (top of each spectrum). Lower case p indicates the phosphate group. Phosphorylation is localized according to the pattern of the fragment-ions containing phosphate and fragment-ions with phosphate loss. Ions showing a neutral loss of H₃PO₄ and 2×H₃PO₄ are labelled with “-1P” and “-2P” respectively. Fragment from neutral losses are coloured in pink, and fragment ions are coloured in green. Parental ion fragments are, as shown in insets: DRRpSEpSLAK (<i>m/z</i> 643.31177, <i>z</i> = 2), DRRpSESLAK (<i>m/z</i> 402.55502, <i>z</i> = 3), LGpSPKDR (<i>m/z</i> 458.75925, <i>z</i> = 2) and TTpSAPPNMDDQK (<i>m/z</i> 724.83307, <i>z</i> = 2). They were identified in 6, 20, 1 and 76 spectra, respectively.</p