Fig. 5: In-depth analysis of Golgi protein behaviour caused by starvation and Bafilomycin A1 treatment.

Source data are provided as a Source Data file. a Some Golgi proteins cycle to the plasma membrane and back, via endosomes (red). BafA treatment compromises the retrieval pathway, trapping Golgi proteins in endosomes; non-cycling Golgi proteins (green) remain unaffected. Created with BioRender.com. b Correlation matrix of delta profiles and clustering of integral membrane and lumenal Golgi proteins. Gene name colours: red = primary hits from MR outlier analysis, blue = lumenal proteins. Boxes highlight the three sets of proteins shown in panels (c) (cycling), (d) (static) and Fig. S6A (also static). c, d Protein trajectories starting at untreated positions (pin head) overlaid with contour density plots of relevant organellar marker proteins. These are calculated from the PCA coordinates of the non-treated condition also shown in Fig. 4a. Please note that axes are scaled by PC variance, for faithful visualization of translocations in PCA space. c Anterograde cycling Golgi proteins (Cluster 1) shift towards the endosome/lysosome. d Static Golgi proteins (Cluster 2) stay within the core density of the Golgi apparatus. e The relative shift towards an average endosomal profile stratifies phenotype strength. The plot shows Cluster 1 proteins identified in (b), in order of observed shift magnitude. The vertical line indicates the cut-off below which the shift was considered negligible. Proteins indicated with an asterisk were selected for further validation by imaging (Figs. 6, 7). Categorization into complete, partial and small shifts was based on the increase in correlation with the average endosomal profile, relative to endosomal shifts observed in the whole proteome (Supplementary Fig. 6B).