Low-Burden Biological Feedback Controllers for Near-Perfect Adaptation

Abstract

The robustness and reliability of synthetic biological systems can be substantially improved by the introduction of feedback control architectures that parallel those employed in traditional engineering disciplines. One common control goal is adaptation (or disturbance rejection), which refers to a system's ability to maintain a constant output despite variation in some of its constituent processes (as frequently occurs in noisy cellular environments) or external perturbations. In this paper we propose and analyse a control architecture that employs Integrase and Excisionase proteins to invert regions of DNA, and an mRNA-mRNA annihilation reaction. Combined, these components approximate the functionality of a switching controller (as employed in classical control engineering) with three distinct operational modes. We demonstrate that this system is capable of near-perfect adaptation to variation in rates of both transcription and translation, and can also operate without excessive consumption of cellular resources. The system's steady state behaviour is analysed, and limits on its operating range are derived. Deterministic simulations of its dynamics are presented, and are then extended to the stochastic case which treats biochemical reactions as discrete events.

Computational characterization of recombinase circuits for periodic behaviors

“…An improved version of the programmable switch uses tyrosine recombinases FimE and HbiF [28], which are the only special cases of tyrosine recombinases that allow reversible DNA rearrangement. Other dynamical circuit designs based on recombinases include a negative feedback controller to track a reference [29,30], some theoretical designs of toggle switches that incorporate multiple copies of the circuit [22], and a single-input counting circuit [23]. The oscillatory behavior of a recombinase-based circuit has also been analyzed deterministically [24].…”

Computational characterization of recombinase circuits for periodic behaviors

“…Other dynamical circuit designs based on recombinases include a negative feedback controller to track a ref. 23 , 24 , some theoretical designs of toggle switches that incorporate multiple copies of the circuit, 17 and a single-input counting circuit. 18 The oscillatory behavior of a recombinase-based circuit has also been analyzed deterministically.…”

Experimental tools to reduce the burden of bacterial synthetic biology

“…Strategies to ease burden and its impact have focused on rewiring the native cellular machinery [10], the design of orthogonal systems for controlled allocation of cellular resources between endogenous and exogenous genes [11][12][13], identification of low-burden designs [14], adoption of biocontrollers to balance cellular fitness and exogenous expression [15][16][17] as well as less complex systems where gene expression resources are separated from the native cellular context [18][19][20]. While also a plethora of computational approaches is now available for host-aware bacterial engineering [21][22][23][24][25][26], in this review we aim at providing a schematic overview of some more recent experimental strategies adopted to reduce burden in bacteria, describing their advantages and limitations. From these examples it will become clear that we have improved in our ability to take burden into account at the design stage, even if we are still facing uncertainties in controlling the response of engineered cells.…”