The ErTo model: A dynamical model of optimal protein allocation in E. coli
Summary
In order to adapt to its environment, E. coli regulates large groups of proteins
in cohort using a surprisingly small number of regulators. Despite this, the
regulation of protein allocation in E. coli often results in optimal growth rates.
Previous studies have illuminated how E. coli distributes its resources between
the various groups of resources, and what the resultant growth rates are. This
has been done for wildtype E. coli, and for a mutant in which regulation of the
group of catabolic proteins is broken. Most studies of protein allocation in E.
coli have focused on the steady state regime. However, regulation also happens
dynamically, during transitions between steady states. A recent study was able
to successfully describe the dynamics of protein sectors and the growth rate
under variation of the nutrient source. We derive a model of protein allocation
which can potentially describe steady-state and dynamical behaviour of groups
of protein and the growth rate, both in wildtype E. coli and the non-regulating
mutant. The central assumption is that E. coli maximises its growth rate. Our
model is able to capture steady state behaviour well, but fails in the dynam-
ical regime. We reveal the paradoxical role of product inhibition of catabolic
proteins, which within our framework is both required to predict steady state be-
haviour, but prevents accurate prediction of the dynamics of protein allocation.
In the future our framework could shed light on the link between production
inhibition and regulation in E. coli.