Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation

Bioreporters
are living cells that generate an easily measurable
signal in the presence of a chemical compound. They acquire their
functionality from synthetic gene circuits, the configuration of which
defines the response signal and signal-to-noise ratio. Bioreporters
based on the Escherichia coli ArsR system have raised
significant interest for quantifying arsenic pollution, but they need
to be carefully optimized to accurately work in the required low concentration
range (1–10 μg arsenite L–1). To better
understand the general functioning of ArsR-based genetic circuits,
we developed a comprehensive mechanistic model that was empirically
tested and validated in E. coli carrying different
circuit configurations. The model accounts for the different elements
in the circuits (proteins, DNA, chemical species), and their detailed
affinities and interactions, and predicts the (fluorescent) output
from the bioreporter cell as a function of arsenite concentration.
The model was parametrized using existing ArsR biochemical data, and
then complemented by parameter estimations from the accompanying experimental
data using a scatter search algorithm. Model predictions and experimental
data were largely coherent for feedback and uncoupled circuit configurations,
different ArsR alleles, promoter strengths, and presence or absence
of arsenic efflux in the bioreporters. Interestingly, the model predicted
a particular useful circuit variant having steeper response at low
arsenite concentrations, which was experimentally confirmed and may
be useful as arsenic bioreporter in the field. From the extensive
validation we expect the mechanistic model to further be a useful
framework for detailed modeling of other synthetic circuits.