Figure 3

Gene-expression signatures at the protein level. (a) The graph shows the pattern of relative changes (fold change) in protein levels with a shift in growth rate (μ) from 0.1 to 0.2/h (doubling time, T_d = 6.9 to 3.5 h) under conditions of carbon limitation (663 proteins in total). ORFs were sorted by biological process [42]. i, Methionine biosynthesis; ii, protein biosynthesis; iii, ubiquitin-dependent protein catabolism. Red, upregulated protein expression; green, downregulated. Selected groups of proteins whose levels are consistently upregulated or downregulated with growth independently of culture condition are labeled in the appropriate color. (b) Box-plot of relative changes in protein expression from growth rate 0.1 to 0.2/h of proteins of representative biological processes (>10 proteins identified per process). 1, Cell wall organization and biogenesis; 2, endoplasmic reticulum (ER) to Golgi transport; 3, ergosterol biosynthesis; 4, glycolysis; 5, methionine biosynthesis and methionine metabolism; 6, protein biosynthesis; 7, protein folding; 8, purine nucleotide, purine base and pyrimidine base biosynthesis; 9, regulation of transcription; 10, ubiquitin-dependent protein catabolism. Open and solid dots indicate presence of outliers that lie more than 3 or 1.5 times the interquartile range, respectively.