Switches

In electronics, one of the most basic elements for storing memory is the reset–set (RS) latch based on logical NOR gates^*. This device is bistable in that it possesses two stable states that can be toggled with the delivery of specified inputs. Upon removal of the input, the circuit retains memory of its current state indefinitely. These forms of memory and state switching have important functions in biology, such as in the differentiation of cells from an initially undifferentiated state. One means by which cellular systems can achieve bistability is through genetic mutual repression. The natural P_R–P_RM genetic switch from bacteriophage λ, which uses this network architecture to govern the lysis–lysogeny decision, consists of two promoters that are each repressed by the gene product of the other (that is, by the Cro and CI repressor proteins). The genetic toggle switch (Gardner et al., 2000) constructed by our research group is a synthetically engineered version of this co-repressed gene regulation scheme. In one version of the genetic toggle, the P_L promoter from λ phage was used to drive transcription of lacI, the product of which represses a second promoter, Ptrc2 (a lac promoter variant). Conversely, Ptrc2 drives expression of a gene (cI-ts) encoding the temperature-sensitive (ts) λ CI repressor protein, which inhibits the P_L promoter. The activity of the circuit is monitored through the expression of a GFP promoter.

The system can be toggled in one direction with the exogenous addition of the chemical inducer isopropyl-β-d-thiogalactopyranoside(IPTG) or in the other direction with a transient increase in temperature. Importantly, upon removal of these exogenous signals, the system retains its current state, creating a cellular form of memory.

Oscillators

Timing mechanisms, much like memory, are fundamental to many electronic and biological systems. Electronic timekeeping can be achieved with basic oscillator circuits — such as the LC circuit (inductor L and capacitor C) — which act as resonators for producing periodic electronic signals. Biological timekeeping, which is widespread among living organisms (Dunlap, 1999), is achieved with circadian clocks and similar oscillator circuits, such as the one responsible for synchronizing the crucial processes of photosynthesis and nitrogen fixation in cyanobacteria. The circadian clock of cyanobacteria is based on, among other regulatory mechanisms, intertwined positive and negative feedback loops on the clock genes kaiA, kaiB and kaiC. Elowitz and Leibler constructed a synthetic genetic oscillator based not on clock genes but on standard transcriptional repressors (the repressilator) (Elowitz and Leibler, 2000). Here, a cyclic negative feedback loop composed of three promoter–gene pairs, in which the ‘first’ promoter in the cascade drives expression of the ‘second’ promoter’s repressor, and so on, was used to drive oscillatory output in gene expression.

*

NOR gate – A digital logic gate that implements logical NOR, or the negation of the OR operator. It produces a HIGH output (1) only if both inputs to the gate are LOW (0).