Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins (original) (raw)
Figure 3
High-Confidence Physical Interactions and Putative Multiprotein Complexes
(A) Benchmarking of the experimentally derived PI network in E. coli against positive and negative gold standards by receiver operating characteristic (ROC)-curve analysis; cumulative area-under-the-curve (AUC) is shown as an overall performance measure.
(B) Overlap of PI identified in this study with previous proteomic reports [1,4] and low-throughput PI obtained from DIP, BIND, and IntAct.
(C and D) Putatively interacting proteins have highly correlated gene expression patterns (C) and similar phylogenetic profiles (D) based on mutual information as for low-throughput curated PI and in contrast to control protein pairs derived from different subcellular compartments.
(E) Graphical schematic of putative stable, soluble multiprotein complexes, drawn using the GenePRO Cytoscape plugin [104] (see Table S7 for listing). Each node represents a complex, whose size reflects the number of contained proteins; edge widths reflect the number of interactions between subunits of different complexes.
(F) Multiprotein complexes implicated in the bacterial translation apparatus; orphan and annotated genes mentioned in the main text are highlighted in bold.
(G) Reduced rate of total protein synthesis in a strain lacking ybcJ relative to wild-type cells (WT).
(H) Perturbed ribosome profiles in an yfgB deletion strain.
(I) Elevated rates of frame-shifting and stop-codon readthrough in yfgB and ybcJ deletion strains relative to wild-type (WT). β-gal activity is only produced after the corresponding translational defect has occurred; error bars indicate standard deviation.