Fig. 1: Computationally guided predictions for metabolic rewiring in P. putida. | Nature Communications

Fig. 1: Computationally guided predictions for metabolic rewiring in P. putida.

From: Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

Fig. 1

a Modeling and engineering workflow diagram. This approach can potentially be extended to any carbon source, host and/or metabolite. Input specific to this specific host/final product work is marked in green font. b The central metabolism of P. putida engineered to produce indigoidine from either glucose or galactose. Heterologous genes are indicated in purple text. Indigoidine is derived from the TCA intermediate α-ketoglutarate (AKG) via two molecules of glutamine. The genes targeted in P. putida central metabolism for knockdown by dCpf1/CRISPRi are indicated with red X marks. Additional gene targets outside of P. putida central metabolism are indicated in the box on the bottom right. A total of 14 genes were targeted for CRISPR interference excluding mqo-I and cynT, as the latter are essential by genome-wide transposon mutagenesis (RB-TnSeq). Abbreviations include Genome-scale Model (GSM), maximum theoretical yield (MTY), size of reaction cut set (Z), Gene–protein-reaction relationships (GPRs), knockout (KO), biomass yield (YBS), glucose-6-phosphate (G6P), fructose-6-phosphate (F6P), fructose-1,6-biphosphate (FBP), 6-phosphogluconate (6PG), 2-keto-3-deoxy-6-phosphogluconate (KDPG), ribulose-5-phosphate (Ri5P), ribose-5-phosphate (R5P), xylulose-5-phosphate (X5P), sedoheptulose-7-phosphate (S7P), erythrose-4-phosphate (E4P), glyceraldehyde-3-phosphate (G3P), glycerate-3-phosphate (3PG), dihydroxyacetone phosphate (DHAP), phosphoenolpyruvate (PEP) and oxaloacetate (OAA). Refer to Supplementary Fig. 1 and Supplementary Data 1 for more information.

Back to article page