Fig. 3: The prototroph proteome responds to the presence of auxotrophs.
a, Schematic representation of auxotrophic SeMeCos strains where prototrophy is restored genomically, and in which the indicated plasmids are marked with CFP. Prototrophic and auxotrophic populations were sorted according to CFP expression. b, Proteomic analysis of sorted auxotrophic versus prototrophic cells in SeMeCos; n = 16 independent sorting experiments (n = 4 independent experiments for each of the auxotrophic SeMeCos strains), with differentially expressed proteins (DEP) illustrated as volcano plots. c, Top left: proteomic analysis of auxotrophs relative to cogrowing prototrophs in SeMeCos. Top right: summary of differentially expressed proteins and metabolic enzymes participating in amino acid biosynthesis; n = 16, whereby four bioreplicates of each of the four auxotrophic populations are compared to each other. Comparisons were made exclusively between proteins significantly differentially expressed in b where P < 0.05. Bottom: differential expression (log2 FC) of metabolic enzymes in auxotrophs relative to prototrophs in SeMeCos, mapped to the yeast metabolic network using iPATH3 (ref. 83); n = 4. d, Top left: proteomic analysis of prototrophic cells isolated from SeMeCos relative to prototrophs grown on their own. Top right: summary of differentially expressed proteins and metabolic enzymes in amino acid biosynthesis; n = 16, whereby four bioreplicates of each of the four prototrophic populations in SeMeCos and in WT communities were compared with each other. Comparisons were made exclusively between proteins significantly differentially expressed in b where P < 0.05. Bottom: differential protein expression (log2 FC) of enzymes in prototrophic cells cogrowing with auxotrophs (in SeMeCos) and metabolic enzyme expression relative to prototrophic cells cogrowing in WT communities mapped to the yeast metabolic network using iPATH3 (ref. 83); n = 4. c,d, Boxplots represent median (50% quantile (middle line) and lower and upper quantiles (lower (25% quantile) and upper (75% quantile), respectively) for the number of differentially expressed proteins. A protein is considered DEP when P < 0.05 (moderated t-test, two-sided) and log FC <0 or >0, downregulated or upregulated, respectively. Abs, absolute.
