title: Memory and Combinatorial Logic Based on DNA Inversions: Dynamics and Evolutionary Stability.
abstract: Genetic memory can be implemented using enzymes that catalyze DNA inversions, where each orientation corresponds to a "bit". Here, we use two DNA invertases (FimE and HbiF) that reorient DNA irreversibly between two states with opposite directionality. First, we construct memory that is set by FimE and reset by HbiF. Next, we build a NOT gate where the input promoter drives FimE and in the absence of signal the reverse state is maintained by the constitutive expression of HbiF. The gate requires ∼3 h to turn on and off. The evolutionary stabilities of these circuits are measured by passaging cells while cycling function. The memory switch is stable over 400 h (17 days, 14 state changes); however, the gate breaks after 54 h (>2 days) due to continuous invertase expression. Genome sequencing reveals that the circuit remains intact, but the host strain evolves to reduce invertase expression. This work highlights the need to evaluate the evolutionary robustness and failure modes of circuit designs, especially as more complex multigate circuits are implemented.
authors.affiliation: Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.
authors.forename: Jesus
authors.initials: J
authors.lastname: Fernandez-Rodriguez
authors.affiliation: Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.
authors.forename: Lei
authors.initials: L
authors.lastname: Yang
authors.affiliation: Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Gorochowski
authors.affiliation: Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.|Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States.
authors.forename: D Benjamin
authors.initials: DB
authors.lastname: Gordon
authors.affiliation: Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.|Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Voigt
mesh_terms: D039301:Computers, Molecular; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D008128:Logic; D045522:Recombinases / Q000737:chemistry*; D057345:Sequence Inversion
chemical_list: D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C512599:HbiF protein, E coli; D045522:Recombinases; C081955:fimE protein, E coli; D004247:DNA
keywords: design automation; genetic circuit; genetic compiler; synthetic biology; systems biology