Quantitative proteome analysis and comparison between wildtype and <i>tic56-3</i>.

(A) To compare the abundance of proteins in wildtype and the tic56-3 mutant, we calculated the total abundance of every identified protein from the sum of its abundance in the individual gel slices. These data were normalized and transformed into ppm values [20]. We then calculated average Log2 ratios for every protein from its abundance in wildtype and tic56-3 mutant plastids and calculated a p-value from a two-sided t-test from the four replicates (two-sided paired t-test). Proteins with a significantly changed abundance in tic56-3 compared to wildtype are labeled in color (above the line indicating a p-value of 0.05). (B) Comparison of TOC and TIC protein abundances in wildtype and the tic56-3 mutant illustrates the specificity of the 1-MDa TIC complex downregulation. Tic20-I (see inset from an immunoblotting experiment), Grp23, Tic56, Tic214 and Tic100 have a significantly decreased abundance in the tic56-3 mutant, while all other translocon components, i.e. Tic110, Tic55, Toc159, Toc75, Toc33 and Toc34 are unaffected. The error bars illustrate the standard deviation from four replicates. (C) All identified protein were classified into MapMan bins [33]. The ppm values for every identified protein in every bin were summed up to give rise to the total amount of ppm in every bin. We display here the data for the bin cytochrome b6/f complex, proteins involved in cyclic electron flow (CET) and the 1-MDa TIC complex including Grp23. (D) Same as in C except that the abundance of proteins for the photosynthetic complexes, the Calvin cycle and the ribosome are displayed. Significance (p<0.05) was calculated from a two-sided pairwise t-test and is illustrated with a “*”.