Fig. 3: Differential proteome analysis of lysine producers and consumers reveals extensive diauxie-like heterogeneity in young colonies.

a, The lysine biosynthesis pathway is upregulated in producer cells, but their overall proteome profile is not explained by lysine producer/consumer status. The y axis shows protein abundance ratios in producer versus consumer cells within colonies supplemented with 200 µM lysine, determined from the ratio of lysine heavy versus light peptides by DILAC (Supplementary Dataset 3 (DS3); n = 6 biological replicates). The x axis shows abundance ratios from a separate experiment comparing colonies grown on unlabelled medium with and without 400 µM lysine supplement (Supplementary Dataset 4 (DS4); n = 5 biological replicates). While the lysine biosynthesis pathway is concordantly affected, the overall correlation is low, indicating that lysine availability alone is not the main driver of producer/consumer proteome differences. b, Producer/consumer proteome profiles correlate with proteomes from top and bottom layers of colonies. In an independent experiment (x axis, Supplementary Dataset 5 (DS5); n = 7 biological replicates), colonies were grown on unlabelled and non-supplemented medium; the top layer of cells was then removed using a cell scraper and both top and bottom layers analysed separately. c, Differences in producer/consumer proteomes (Supplementary Dataset 3) mapped to metabolic pathways using iPATH⁸⁰ indicate strong and concordant changes in expression of key metabolic pathways. The colour of edges indicates the direction (red, up; blue, down) and edge width reflects the magnitude of change. d, Changes in expression of proteins of key metabolic pathways between producers and consumers (Supplementary Dataset 3). Following convention, box-plot elements are defined as follows: centre line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; points, outliers. e, Producer/consumer protein ratio profiles (Supplementary Dataset 3, y axis) correlate with changes in gene expression associated with the diauxic shift observed in liquid cultures³⁸. a,b,e, Pearson correlation coefficient is shown. f, Pathway map illustrating changes in expression of the ethanol degradation pathway and glyoxlyate cycle in three datasets (left to right): producer/consumer protein ratios obtained with DILAC (Supplementary Dataset 3), top and bottom layer in non-supplemented, unlabelled medium (Supplementary Dataset 5) and proteome changes from postdiauxic versus early exponential growth³⁸.