Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale

Metabolic flux analysis (MFA) is
considered to be the gold standard
for determining the intracellular flux distribution of biological
systems. The majority of work using MFA has been limited to core models
of metabolism due to challenges in implementing genome-scale MFA and
the undesirable trade-off between increased scope and decreased precision
in flux estimations. This work presents a tunable workflow for expanding
the scope of MFA to the genome-scale without trade-offs in flux precision.
The genome-scale MFA model presented here, iDM2014, accounts for 537
net reactions, which includes the core pathways of traditional MFA
models and also covers the additional pathways of purine, pyrimidine,
isoprenoid, methionine, riboflavin, coenzyme A, and folate, as well
as other biosynthetic pathways. When evaluating the iDM2014 using
a set of measured intracellular intermediate and cofactor mass isotopomer
distributions (MIDs), it was found that
a total of 232 net fluxes of central and peripheral metabolism could
be resolved in the E. coli network. The increase
in scope was shown to cover the full biosynthetic route to an expanded
set of bioproduction pathways, which should facilitate applications
such as the design of more complex bioprocessing strains and aid in
identifying new antimicrobials. Importantly, it was found that there
was no loss in precision of core fluxes when compared to a traditional
core model, and additionally there was an overall increase in precision
when considering all observable reactions.