Fig. 4: 2D-TPP identifies ribosomal proteins and ribosome biogenesis factors as differently affected by TET in the two strains.
a Comparison of the number of significantly affected proteins in abundance (blue shades), thermal stability (green shades), and solubility (orange/brown shades) for E. coli K-12 (left side) and E. coli ED1a (right side). Timepoint T1 represents untreated cells grown for 30 min, timepoints T2 and T4 represent TET-treated cells grown for 30 min and 3 h, respectively. The scores are calculated relative to the control condition T0 (untreated cells, 0 min LB). Timepoint T3 (3 h, untreated control) is shown in Supplemental Fig. 2C since the data were not comparable as cells shifted to stationary phase only in this set-up. b Scatter plot of abundance (upper panel) and stability values (lower panel) for TTP hits overlapping in both strains for T2 (30 min TET), comparing K-12 scores (x-axis) against ED1a scores (y-axis). A two-sided t-test was applied based on the effect size distribution resulting from the respective K-12 vs. ED1a scores. P values were adjusted using the Benjamini-Hochberg method. Each dot represents a protein; if it is highlighted with a black contour, it indicates that there is a significant difference between K-12 and ED1a scores (Padj < 0.05, confidence interval 0.95). Exact p values for each protein can be found in Supplementary Data 1. The color scheme is explained in the legend below the figure panel. c Gene ontology (GO) enrichment plot of TPP results for different cellular compartments, with compartments ordered according to their physical location on the outer membrane – cytosol axis. The enrichment for each GO-term in the significant protein set (global & local FDR < 0.05) in each respective condition (30 min LB, 30 min TET, 3 h TET) is calculated using the Fisher Exact Test (two-sided), relative to the insignificant portion of proteins in each condition (displayed as color gradient for p from highest (yellow) to lowest (blue) significance). If the GO-term is enriched in at least one condition (P < 0.01) and has at least 10 significant protein components significantly affected in the dataset, it is shown on the y-axis of the bubble plot. The bubble size indicates the odds enrichment, whereas the bubble color reflects the P value (-log10 scale).
