Fig. 5: Characterization of QCAP degrons.
From: Conserved degronome features governing quality control associated proteolysis
a Comparison of mean amino acid distribution between TMDs in the yeast proteome with high degron probability (P ≥ 0.85; White color; n = 1204) to those with lower probability (P < 0.85; Gray color; n = 107). Data are presented as mean values + /- low and high confidence intervals. Statistical tests were (a) Chi-square (p = 0.018; DF = 19) that was followed by (b) Two sided Mann Whitney U test (***: p < 0.001). Amino acid residues serine, methionine and asparagine did not show significant differences between the two groups. b Pie chart of the classification and relative proportions of protein secondary structure versus that of QCDPred-predicted degrons within the entire yeast proteome, based on the AlphaFold Protein Structure Database. c Plot of the percentile of α helix structures versus QCDPred assigned non-TMD degron probabilities, divided into four equal bins. d Flow cytometry histograms of the normalized yeG/yeC ratio in cells expressing P1 peptide emerged from the yeast protein Cob1 and two randomly scrambled variants SC1 and SC2. Stability scale: Median value of the yeG/yeC ratio in empty vector (EV) control was set as one. All other histograms were distributed accordingly. e Plot of QCDPred calculated degron centers within the entire yeast proteome, as a function of protein length. ρ: Spearman’s correlation coefficient. p < 0.0001. f Gene ontology (GO) process annotations of the fold change of top twelve significant pathways (p < 0.05) enriched or devoid of degrons, compared to a reference yeast proteome (strain S288C). g Violin plot displaying changes in the PSI of 2175 degrons (PSI ≤ 1.7) upon knocking out ORFs of the tested QCAP E3 enzymes. ∆PSI values between degrons in pdr5∆ strain and E3∆ strains were calculated. The red line marks two standard errors from the mean for each strain. Degrons above this threshold were considered stabilized by the knockout. The Percentile of stabilized degrons is indicated for each tested QCAP E3. h Venn diagram displaying overlapping functions of the tested QCAP E3 enzymes. Sequences of the top 10% ∆PSI values for each knockout strain (218 peptides) were compared. Source data for panels a, d and e are provided as a Source Data file.
