Supplementary Figure 1. Effect of the double knockout of histidase (HISD) and citrate synthase (CSm) on the optimal flux distribution for virus production under minimal media conditions with uptake fluxes set to -1000 mmol∙gDW-1∙h-1. (A)Distribution of the producing (‘in’) and consuming (‘out’) fluxes for histidine and its precursors carnosine in the cytosol. Note that carnosine is only used for the production of histidine in the model histidine is only involved in the SARS-CoV-2 biosynthesis and the HISD reactions (as shown in part (B)). For each metabolite, the in and out fluxes have been computed for the unmodified model (left), the model with CSm reaction blocked (center), and the model with HISD reaction blocked (right). The fluxes in the case of both reactions blocked is not shown, as fluxes in this case are all zero. (B) Cartoon representation of the reaction network involving histidine and other metabolites, with reaction fluxes from normal and perturbation conditions colour-mapped onto reaction arrows. The upper panel represents the flux distribution in the normal condition, the center panel represents flux distribution under CSm knockout, and the lower panel represents flux distribution under HISD knockout. Metabolite notations used are: trans-urocanate (urcan), carnosine (carn), β-alanine (β-Ala). Note that when CSm is blocked (middle panel) the flux through the carnosine-to-histidine (the CARNPEPT1tc and NBAHH_ir reactions) increases. This is because the blocking of CSm perturbs proton balances and requires a higher flux through the CARNPEPT1tc reaction, which imports a proton. When HISD reaction is blocked (lower panel), however, the CARNPEPT1tc reaction cannot carry high flux. This is because the only output to histidine is SARS-CoV-2 biomass production, which is limited by other building blocks. Thus, the combined blocking of CSm and HISD reactions (or any other combination of CSm with reactions in the histidine consumption pathway) creates an incompatible situation for proton balancing in the model (i.e. cell).
Supplementary File 1. Results of the flux variability analysis, where flux range for each reaction is calculated while maintaining an optimal biomass flux to SARS-CoV-2 production. Results for simulations with minimal media (flux limits set to -10 or -1000 mmol∙gDW-1∙h-1) or rich media are shown. Reactions are ordered according to metabolic subsystems used in the RECON2.2 model, with associated genes identified in the model curation process included as well.