Synthetic biological circuit

In studies of diauxic growth of E. coli on two-sugar media, Jacques Monod and Francois Jacob discovered that E.coli preferentially consumes the more easily processed glucose before switching to lactose metabolism.

IPTG, a molecule similar to lactose, but with a sulfur bond that is not hydrolyzable so that E. coli does not digest it, is used to activate or "induce" the production of the new protein.

One, by Tim Gardner, Charles Cantor, and Jim Collins working at Boston University, demonstrated a "bistable" switch in E. coli.

[3] The second, by Michael Elowitz and Stanislas Leibler, showed that three repressor genes could be connected to form a negative feedback loop termed the Repressilator that produces self-sustaining oscillations of protein levels in E.

[5] There has been significant interest in encouraging education and outreach as well: the International Genetically Engineered Machines Competition[6] manages the creation and standardization of BioBrick parts as a means to allow undergraduate and high school students to design their own synthetic biological circuits.

[8] However, methods involving direct genetic introduction are not inherently effective without invoking the basic principles of synthetic cellular circuits.

This is a biological circuit where a simple repressor or promoter is introduced to facilitate creation of the product, or inhibition of a competing pathway.

However, with the limited understanding of cellular networks and natural circuitry, implementation of more robust schemes with more precise control and feedback is hindered.

Development in understanding cellular circuitry can lead to exciting new modifications, such as cells which can respond to environmental stimuli.

For example, cells could be developed that signal toxic surroundings and react by activating pathways used to degrade the perceived toxin.

[21] At the moment, circuit design is improving at a slow pace because of insufficient organization of known multiple gene interactions and mathematical models.

The lac operon is a natural biological circuit on which many synthetic circuits are based. Top: Repressed, Bottom: Active.
1 : RNA polymerase, 2 : Repressor, 3 : Promoter, 4 : Operator, 5 : Lactose, 6 : lacZ , 7 : lacY , 8 : lacA .
A ribosome is a biological machine .
The logical AND gate . [ 15 ] [ 16 ] If Signal A AND Signal B are present, then the desired gene product will result. All promoters shown are inducible, activated by the displayed gene product. Each signal activates expression of a separate gene (shown in light blue). The expressed proteins then can either form a complete complex in cytosol , that is capable of activating expression of the output (shown), or can act separately to induce expression, such as separately removing an inhibiting protein and inducing activation of the uninhibited promoter.
The logical OR gate . [ 15 ] [ 16 ] If Signal A OR Signal B are present, then the desired gene product will result. All promoters shown are inducible. Either signal is capable of activating the expression of the output gene product, and only the action of a single promoter is required for gene expression. Post-transcriptional regulation mechanisms can prevent the presence of both inputs producing a compounded high output, such as implementing a low binding affinity ribosome binding site .
The logical Negated AND gate . [ 15 ] [ 16 ] If Signal A AND Signal B are present, then the desired gene product will NOT result. All promoters shown are inducible. The activating promoter for the output gene is constitutive, and thus not shown. The constitutive promoter for the output gene keeps it "on" and is only deactivated when (similar to the AND gate) a complex as a result of two input signal gene products blocks the expression of the output gene.
Computational design and evaluation of DNA circuits to achieve optimal performance