Fig. 2

Predicting the effect of genetic deletion and nutrient changes on bulk acetylation using FBA. a The bar chart depicts the impact of reducing (purple bars) or increasing (orange bars) the level of metabolites in the culture media on acetylation flux (mmol/h per gram dry weight). b The plot shows the effect of gene deletions on bulk acetylation. The impact of gene deletion on the biomass production was used as a counter-screen to identify those genes that specifically impact protein acetylation. Gene deletions that exhibit at least 50% of the wild-type biomass production rate are shown. The top 20 genes that preferentially affect acetylation over growth are highlighted as red markers and displayed in the table. c Our model correctly predicted the impact of removing amino acids, pyruvate, glucose, acetate, fatty acids, vitamins, and minerals from the media on acetylation. The plus/minus sign indicates the presence or absence of specific nutrients in the media. Conditions predicted to have less than 5% of the wild-type acetylation flux by the model were assumed to be not supporting acetylation. Conditions experimentally observed to support (+) or not support (−) acetylation are also denoted by a plus or minus sign. The condition with incorrect prediction is shown in red. This incorrect prediction was resolved by accounting for trace nutrients in serum (Additional file 1: Figure S1)