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.