Fig. 1: Gene targets and promoters for combinatorial engineering of tryptophan metabolism in S. cerevisiae.

a Gene–gene interaction network built with Cytoscape, showing that pentose phosphate pathway and glycolysis are both in the core of metabolism in close proximity to many genes. Nodes are all 909 genes in yeast metabolism⁶⁷, sharing connections based on the number of shared metabolites by the corresponding reactions that the genes are related to: the thicker the edge, the higher the number of shared metabolites. Currency metabolites such as water, protons, ATP, etc. are removed from the analysis. The prefuse force directed layout is used for displaying the network. Genes are highlighted with a yellow border if they are selected targets by the mechanistic modeling approach, and in orange and dark blue if they belong to the pentose phosphate pathway or glycolysis, respectively. b Simplified map of metabolism showing the selected gene targets from glycolysis (dark blue) and pentose phosphate pathway (orange) based on a combination of mechanistic genome-scale modeling and literature studies for optimizing tryptophan production. Black dashed lines indicate multistep reactions. Dashed green line indicates allosteric activation. G6P glucose 6-phosphate, F6P fructose 6-phosphate, FBP fructose 1,6-bisphosphate, GAP glyceraldehyde 3-phosphate, DHAP dihydroxyacetone phosphate, PEP phosphoenolpyruvate, OAA oxaloacetate, 6PG 6-phosphogluconate, E4P erythrose 4-phosphate, S7P sedoheptulose 7-phosphate, DAHP 3-deoxy-7-phosphoheptulonate, Tyr tyrosine, Phe phenylalanine, Trp tryptophan. c Percentage of genes in glycolysis (dark blue) and pentose phosphate pathway (orange) that were predicted by the mechanistic modeling to increase tryptophan production compared to the percentage of genes predicted as targets from the whole metabolism. ***P-value < 0.05, two-sided Fisher’s exact testing with n = 54 and 24 for the glycolysis and pentose phosphate pathway, respectively. d Relative messenger RNA (mRNA) abundance, calculated for each gene as the proportion of mRNA reads obtained for any given promoter relative to the total sum of mRNA reads from each bin of six promoters. Absolute abundances for the 30 promoters were measured in S. cerevisiae CEN.PK113-7D in the mid-log phase³². The promoters are grouped according to intended combinatorial gene associations. Source data underlying Fig. 1d are provided as a Source data file.