Extended Data Fig. 5: Differential protein abundance by functional groups.
From: Interspecies interactions drive bacterial proteome reorganization and emergent metabolism
(a) Number of up- (red) and down-regulated (blue) proteins annotated to the phosphotransferase system (PTS) in each protein species in the presence of each partner species. The PTS system is absent in Bacteroides. (b) Number of up- (red) and down-regulated (blue) proteins annotated to the ATP-binding cassette transporters (ABC) in each protein species in the presence of each partner species. L. saccharolytica has an extraordinarily high number of (regulated) ABC transporters. (c) Regulation of PTS system components in C. difficile. Asterisks indicate significant interactions. (d) Regulation of polysaccharide utilising loci (PULs) in B. thetaiotaomicron. The colour scale reflects the abundance change of the most strongly changed protein annotated to that PUL. The fractions of proteins which are significantly up-/down-regulated are indicated in the heatmap. Only reliably measured (in at least 6 co-culture conditions) and strongly regulated (sum(abs(log2(fold-change))) > 4) PULs are shown. PUL annotation was obtained from (Ryan et al. 2024)118 which integrated data from refs. 119,120,121,122,123,124,125,126,127. (e) Number of proteins annotated to ‘Arginine biosynthesis’ which are up-/down-regulated in the presence of C. aerofaciens.
