Logic Subsystem
The logic subsystem of a synthetic cell is responsible for processing sensed information and deciding on appropriate actions. This includes both instantaneous input–output computations (combinational logic) and time-dependent behaviors that depend on the history of inputs (memory and state). In synthetic cells, both functions are implemented using the same underlying molecular machinery — chemical reaction networks (CRNs), transcription factors, and DNA-modifying enzymes — rather than the digital circuits used in electronic systems.
Computation
Most modern engineered control systems rely on digital computation, but biological control systems operate closer to analog computation. Chemical reaction networks provide a natural substrate for implementing dynamical behaviors: molecular concentrations play the role of state variables, reaction rates play the role of gains, and the network topology determines the input–output relationship of the circuit. A key advantage of the CRN formalism is that it connects directly to control theory, allowing standard feedback control objectives — reference tracking, disturbance rejection, robustness — to be mapped onto circuit designs and analyzed using established tools.
In addition to analog feedback computation, biological circuits can implement discrete event systems. Recombinase-based circuits are particularly well suited to this role: serine and tyrosine recombinases catalyze irreversible DNA inversions or excisions in response to specific inputs, producing permanent changes in gene expression state that are stable without continued energy input.
Recombinase-based state machines (Roquet et al., 2016)
Roquet and colleagues demonstrated synthetic recombinase-based state machines in living cells that record the order and combination of input signals as distinct DNA configurations, implementing a finite state machine with multiple stable states[1].
Memory and state
Memory in a synthetic cell control system means the ability to store information about past events and use it to influence future behavior. This is essential for implementing hybrid and event-driven behaviors, where the appropriate response depends not just on the current input but on the history of inputs.
Rewritable digital memory (Bonnet et al., 2012)
Bonnet and colleagues showed that recombinases can be composed to create rewritable digital memory elements, enabling discrete, reversible transitions between well-defined genetic states in response to inputs[2]. This established the basic principle that DNA configuration can serve as a stable, readable memory medium in biological systems.
Temporal logic gate (Hsiao et al., 2016)
Hsiao and colleagues demonstrated a population-based temporal logic gate that uses recombinase-mediated DNA rearrangements to encode the order and timing of chemical events[3]. The system distinguishes between signals that arrive in different orders, producing different outputs depending on which input was seen first — a function not achievable with combinational logic alone.
Continuous event logging
More recent approaches extend DNA-based memory to continuous event logging. Shur and Murray introduced an architecture that records multiple chemical stimuli into a growing genomic array by combining serine integrases with CRISPR-dCas9-mediated site selection[4]. The MEMOIR system uses CRISPR-mediated mutagenesis to stochastically encode cellular history into distributed genomic barcodes readable in situ[5].
Logic in the control architecture
The logic subsystem occupies the central processing layer of the synthetic cell control architecture, sitting between the Sensing Subsystem (inputs) and the Mechanical Actuation Subsystem or gene expression outputs (actions). Key design considerations include:
- Analog vs. discrete: CRN-based circuits implement graded, continuous responses well-suited to feedback regulation; recombinase-based circuits implement sharp, irreversible transitions well-suited to state machines and memory. Many applications will require both.
- Resource load: logic circuits consume transcriptional and translational capacity from the shared Cytoplasm Subsystem. Complex circuits with many genes impose significant burden and must be designed with resource competition in mind.
- Composability: circuits designed independently must be combined without unexpected interactions. Orthogonal transcription factors, insulated promoters, and contract-based design frameworks are tools for achieving this.
- Robustness: biological logic circuits operate in a noisy, variable environment. Feedback is a primary tool for achieving robustness to molecular noise and load disturbances.
References
- ↑ N. Roquet, A. P. Soleimany, A. C. Ferris, S. Aaronson, and T. K. Lu, Synthetic recombinase-based state machines in living cells. Science 353(6297):aad8559, 2016.
- ↑ J. Bonnet, P. Subsoontorn, and D. Endy, Rewritable digital data storage in live cells via engineered control of recombination directionality. Proceedings of the National Academy of Sciences 109(23):8884–8889, 2012.
- ↑ V. Hsiao, Y. Hori, P. W. K. Rothemund, and R. M. Murray, A population-based temporal logic gate for timing and recording chemical events. Molecular Systems Biology 12(5):869, 2016. DOI: 10.15252/msb.20156663
- ↑ A. S. Shur and R. M. Murray, Proof of concept continuous event logging in living cells. bioRxiv, 2021. DOI: 10.1101/225151
- ↑ K. L. Frieda et al., Synthetic recording and in situ readout of lineage information in single cells. Nature 541:107–111, 2017.