Network Analysis
We converted the metabolic model to a metabolite-metabolite graph of
primary carbon metabolism using the method of Ranganathan and Maranas
(2010). A full list of the nodes and edges is available on Zenodo (DOI:
10.5281/zenodo.3366934). We then used the networkx (version 1.10)
package in Python (Version 3.6.9) in order to iteratively identify
pathways with fewer than 20 nodes connecting Rubisco and fumarate node.
We checked the 17 identified pathways against the flux sampling
solutions of the Col-0 models and identified two pathways which carried
a flux substantial enough to account for fumarate accumulation in the
model. All other pathways had at least one reaction for which the
sampling solutions were either zero or close to zero. For fluxes to be
considered close to zero, we used a cut-off of 0.4, which is 3 times
lower than the carbon flux to fumarate (i.e. not substantial enough to
explain our observed accumulation of fumarate in wild-type Col-0
plants).