Fig. 4: Amino acid metabolism is altered in a INH^R-katG mutant.

a Genes within the amino-acid class with increased vulnerability in INH^R-katG. Bubble plot represents day 14 data. The x-axis quantifies the proportion of genes with increased vulnerability per subclass. The y-axis shows the names and total number of genes per subclass. Dot size indicates the mean ratio of gRNAs (per gene) more depleted in INH^R-katG. Dot colour denotes ATc concentrations used. Pro: Proline and 4-hydroxyproline. Lys-Thr-Met-Cys: Lysine, threonine, methionine, and cysteine. Branched-chain: Branched-chain amino acids. Glu-Asp-NH₄: Glutamine, glutamate, aspartate, asparagine, ammonia assimilation. Aromatics: Aromatic amino acid metabolism. His: histidine metabolism. b Significantly depleted metabolites are labelled with asterisks (p < 0.05 determined by two-sided t-test, n = 5 biological replicates). Schematics of (c) pathways linking aspartate metabolism with the TCA cycle and nucleotide metabolism and (d) aromatic amino acid metabolism. Bolded metabolites highlight those that were detected. Blue, red and black denotes metabolites that are increased, decreased or no-change in INH^R-katG. Bolded genes highlight those that are more vulnerable. e–g DS-parent and INH^R-katG expressing gRNAs targeting (e) metC, (f) lysA and (g) aroK in ATc dose-response assays (mean ± extrema of two biological replicates, n = 3 independent experiments). The (gx) denotes the gRNA name. h Viability plots of DS-parent and INH^R-katG expressing gRNA targeting aroK (mean ± extrema of two biological replicates, n ≥ 3). Inoc denotes the starting CFU/ml and no-cpd denotes the detected CFU/ml in the absence of ATc. Dashed line represents the minimum detection limit. i Growth kinetics of M. tuberculosis DS-parent and INH^R-katG expressing a gRNA targeting aroK (mean ± SD of three biological replicates, n = 2 independent experiments). j Intracellular survival of DS-parent and INH^R-katG cells expressing an aroK gRNA within THP-1 macrophages (mean ± SD of three biological replicates, n = 2 independent experiments). k DS-parent pre-depleted for metA, aroK and lysA for 5 days was exposed to ascorbic acid. No-cpd is the absence of compound but with 300 ng/ml of ATc. Data is the reduction in viable colonies on day 10, relative to the starting inoculum. Non-targeting gRNA is a negative control. l The DS-parent or INH^R-katG were grown in 7H12 media with 1 mM ascorbic acid and the stated amino acids. Data is expressed as the reduction in viable colonies at each time point relative to the starting inoculum. Source data are provided as a Source Data file.