Functional flexibility in bacterial hub proteins is driven by proteome expansion

Protein-protein interaction networks play a key role in the living cells, with hub proteins (hubs) acting as central nodes in the transmission of biological signals. The features enabling hubs to interact with other proteins in bacteria remain unexplored. We present the first cross-phylum analysis of bacterial hubs using AlphaFold and IUPred. Hubs exhibit higher levels of intrinsic disorder compared to whole proteomes. In contrast to the highly structured proteomes of obligate pathogens, proteomes of free-living bacterial species are more disordered. We show that proteome size is a stronger predictor of disorder accumulation than GC content. Analyses of conserved orthologous hubs show that protein cores are conserved in sequence, 3D structure and length, accumulating disorder in terminal regions in bacteria with large proteomes. Analysis of the Escherichia coli interactome shows that 63% of proteins with disorder (> 30 AA) have more than 10 known interaction partners, compared to 19% of fully structured proteins, emphasizing the functional importance of disorder in bacteria. Our results indicate that intrinsic disorder in bacterial proteins is associated with proteome complexity and cannot be explained by GC content alone. Disorder expansion in complex bacteria may contribute to interaction plasticity in different environments similar to those in eukaryotes.