Fig. 1

Identification of TRAP clients and compensatory proteins by TRAP depletion in HeLa cells. a Cartoon of clipped 80S ribosome together with Sec61-complex (blue color code in subsequent panels and figures), TRAP-complex (green color code in subsequent panels and figures), and OST²⁷. Without clipping, eL38 and helix 51 would be partially hidden. b The experimental strategy was as follows: siRNA-mediated gene silencing using two different siRNAs for each target and one non-targeting (control) siRNA, respectively with six/nine replicates for each siRNA in two/three independent experiments; label-free quantitative proteomic analysis; and differential protein abundance analysis to identify negatively affected proteins (i.e., clients) and positively affected proteins (i.e. compensatory mechanisms). c, e Knock-down efficiencies in experiment 1 were evaluated by western blot. Results are presented as % of residual protein levels (normalized to ß-actin) relative to control, which was set to 100%. Blot results for other experiments are shown in Supplementary Fig. 1a, d. d, f Differentially affected proteins were characterized by the mean difference of their intensities plotted against the respective permutation false discovery rate-adjusted p-values in volcano plots (n = 2 in the case of Sec61 depletion, n = 3 in the case of TRAP depletion). The results for a single siRNA are shown in each case (SEC61A1-UTR siRNA, TRAPB siRNA). Additional plots are shown in Supplementary Fig. 1c, f. Subunits of the Sec61- and TRAP-complexes and of the SRP receptor are indicated