Fig. 4

Architecture-dependent turnover of the proteasome subunits. a Upper panel: proteasome subunits are shown color-coded as gradient from red (short half-life) to blue (long half-life). For each cell type, half-lives were averaged over biological replicates, except for rare cases where only one half-life value was available, and converted to a color gradient as explained in the Methods. The median, minimum, and maximum half-lives are indicated together with the color bars. Subunits with undetermined half-lives are colored green. Lower panel: distributions of the reproducibly measured half-lives of the regulatory and the non-exchangeable core subunits of the proteasome in the different cell types. Differences in the distributions of log₁₀ half-lives were assessed by Wilcoxon-rank test (significance levels were encoded as *** p < 0.001, ** p < 0.01, * p < 0.05). Center line in box plots is the median, the bounds of the boxes are the 75 and 25% percentiles i.e., the interquartile range (IQR) and the whiskers correspond to the highest or lowest respective value or if the lowest or highest value is an outlier (greater than 1.5 * IQR from the bounds of the boxes) it is exactly 1.5 * IQR b Heatmap showing the comparison for each pair of proteasome subunits by calculating the root mean square error between their four log₁₀ transformed half-lives in the four different human cell types. Hierarchical clustering leads to separation of the regulatory subunits from the non-exchangeable core subunits. The 19S proteasome subunits PSMD4 and the recently discovered ADRM1 form a distinct cluster