Multiple host proteins are targeted for proteasomal degradation early during HCMV infection
To build a comprehensive mechanistic picture of host protein degradation early during HCMV infection, data from experimental samples described inFigure 1A (that included the 2 µM bortezomib condition) was analysed in detail. Overall, 7192 host proteins were quantified, 145 of which were down-regulated by HCMV >1.5-fold (with p<0.01) compared to mock infection. MG132 and bortezomib ‘rescue ratios’ were calculated for each protein, obtained by comparing protein abundance during HCMV infection +/- inhibitor with protein abundance during mock infection +/- inhibitor (Figure 2A ).
For simplicity and consistency with our previous study (Nightingale et al., 2018), a rescue ratio of >1.5-fold with p<0.01 was set as a threshold to identify proteins rescued by either MG132, bortezomib or both (Figures 2A, Table S1 ). Using these criteria, 64/145 (44%) proteins were considered to be rescued by either inhibitor, with 34/64 proteins rescued by both drugs. Notably, this group contained the known HCMV restriction factors Sp100, MORC3, DAXX and HLTF in addition to cell cycle regulating protein ANAPC1, all of which have been reported to be degraded by ourselves and others (Figure 2B) (Tran et al., 2010;Chen et al., 2011;Kim et al., 2011;Tavalai et al., 2011;Schreiner and Wodrich, 2013;Sloan et al., 2016;Nightingale et al., 2018).
Data from all proteomic experiments in this study are shown inTable S2 . Here, the worksheet “Plotter” is interactive, enabling generation of graphs of protein expression of any of the proteins quantified.