Fig. 2: Inferring the eIF3 assembly process based on cooperative stabilization interactions.

A Model of eIF3 subunit architecture based on dissociation and mass spectrometry analyses. Subunits of modules I, II, and III are colored blue, magenta, and green, respectively. Black arrows denote physical interactions not readily presented in this model. B The eIF3 physical interaction map according to the available literature. Different detection methods (shown at right) are colored differently. C, D Correlation analyses for results generated from IRES- versus 2A-based GPS systems, and N- versus C-terminal GFP-tagged eIF3 subunits. Data points represent fold-changes in protein stability (GFP/RFP ratio). E The eIF3 subunit stability connectivity map, as measured by the IRES-based GPS system. The matrix heatmap represents a log2-fold-change in the value of protein stability (GFP/RFP ratio) for the eIF3 subunit indicated on the left in response to overexpressing the eIF3 subunit indicated on top. F The synthesis-abundance correlation of the eIF3 subunit indicated on top with (red) or without (blue) providing the eIF3 subunit indicated on the plot. G Louvain network modularity analysis of data shown in (E). Arrows represent stabilization interactions. X→Y indicates that X stabilizes Y, whereas X↔Y denotes that X and Y mutually stabilize each other. The thickness of the arrows is proportional to the intensity of protein stabilization. Subunits in the same network cluster are shown in the same color and surrounded by a light gray shadow. H The score distribution for all possible binary eIF3 assembly trees. I Correlation analysis between likelihood scores and the presence of intermediate subcomplexes formed by cooperative stabilization partners (eIF3D-E, G-I, F-M, K-L). The box plots illustrate the 25th and 75th percentiles, and the whiskers extend to 1.5 times of the interquartile range (IQR). Horizontal lines within the box plots represent medians. Outliers are plotted as individual points. The number of points for each box plot from left to right, are 357,194,157,953, 66,973,726,080, 5,272,663,680, 211,003,200, and 3,752,640, respectively. J DAG presentation of the top 1000 ranked binary eIF3 assembly trees. The thickness of lines and the size of circles are proportional to the likelihood. Source data are provided as a source data file.