Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM
Figure 10
Mechanistic insight into three experimentally validated synthetic lethal auxotrophs and their nutrient rescue.
(A) The nitrogen assimilation pathway contains two alternate routes that convert α-ketoglutarate into the essential metabolite L-glutamine (red). (A1) The en(am)-2 mutant is viable, because α-ketoglutarate can be aminated to L-glutamate via am. (A2) The am mutant is viable, because α-ketoglutarate and L-glutamine can be converted to 2 L-glutamate via en(am)-2. (A3) The double mutant am:en(am)-2 is lethal when ammonium is the nitrogen source because both routes to L-glutamine are blocked, but (A4) can be rescued when the media is supplemented with L-glutamate (A4). (B) The only two routes for the synthesis of the essential metabolite L-proline are through arginine degradation and proline biosynthesis. (B1) The pro-3 mutant is blocked in proline biosynthesis, but can obtain L-proline through arginine degradation. (B2) The ota mutant is blocked in arginine degradation, but can obtain L-proline through proline biosynthesis. (B3) The double mutant pro-3:ota is blocked in both routes, but can be rescued when the nutrient media is supplemented with L-proline (B4). (C) There are only two biosynthetic routes to the essential metabolite uridine-5′-phosphate. (C1) The pyr-1 mutant can still obtain uridine-5′-phosphate from extracellular uracil, and the uc-5 mutant can obtain uridine-5′-phosphate from (S)-dihydroorotate (C2), but the pyr-1:uc-5 double mutant is blocked in both routes (C3). However, it can be rescued when the nutrient media is supplemented with uridine through its conversion to uridine-5′-phosphate in the pyrimidine salvage pathways (C4). Side compounds not shown.