Synthetic devices based on transcriptional logic. (a) A modular AND gate. Two input promoters control the expression of the SupD tRNA suppressor and a T7 polymerase with two TAG stop codons, denoted by asterisks. Activation of both input promoters allows SupD to suppress the early stop codons by inserting serine, and the functional T7 protein activates expression of the reporter (Anderson et al. 2007). (b) A genetic toggle switch. Bistability is achieved via two mutually repressing genes. Addition of inducer molecules allows switching between stable states (Gardner et al. 2000). (c) A cellular memory device. Galactose induces expression of an RFP-tagged transcriptional activator that triggers expression of a YFP-tagged reporter. The YFP-tagged protein then activates itself, maintaining YFP expression (Ajo-Franklin et al. 2007).

RNA-based logic gates. (a) Modular ribozymes consist of ‘actuators’ (red) that contain the HHRz ribozyme; ‘transmitters’ that transmit conformational changes to the actuator; and ‘sensors’, the RNA aptamers that bind ligands. An arrow next to the actuator denotes that the ribozyme is active in the absence of ligand. A crossed out arrow denotes that the ribozyme is inactive in the absence of ligand. Multiple sensor domains can be added to either end of the actuator. An example AND gate and NAND gate are shown, multiple actuators can also be incorporated in series on a single mRNA (Win & Smolke 2008). (b) Evaluation of complex logic in an RNAi-based device. Input A represses transcription of the ‘A’ siRNA and activates transcription of the ‘NOT A’ siRNA. Inputs C, B and E repress transcription of their respective siRNAs. Each siRNA downregulates the expression of its target mRNA if expressed (Rinaudo et al. 2007).

A synthetic GEF re-routes PKA signalling to activate the CDC42 pathway. The Dbl homology–pleckstrin homology domain (DH–PH) from a GEF involved in CDC42 signalling is combined with a PDZ domain and a PKA target peptide. The PDZ domain is normally bound to the target peptide, inactivating the DH–PH. Forskolin activates PKA that phosphorylates the target peptide. Phosphorylation of the target allows the DH–PH to activate CDC42 signalling (Yeh et al. 2007).

Engineered pathway for artemisinic acid production in S. cerevisiae. Blue arrows indicate enzymes indirectly upregulated by expression of upc2-1. Green arrows indicate enzymes that were directly upregulated. The red repression arrow indicates that ERG9 was placed under the control of a methionine-repressed promoter, reducing flux to squalene synthesis. Green boxes indicate the exogenous enzymes ADS and CYP71AV1 and the redox partner protein CPR (Ro et al. 2006). CoA, coenzyme A; HMG-CoA, 3-hydroxy-3-methyl-glutaryl-CoA; IPP, isopentenylpyrophosphate; GPP, geranyl pyrophosphate.

The DEBS1 PKS that catalyses the first steps in synthesizing 6-deoxyerythronolide B. Blue domains comprise the loading module, containing an acyl transferase (AT) and an acyl carrier protein (ACP). Two extender modules, in green and orange, each contain a ketosynthase (KS), an AT, a ketoreductase (KR) and an ACP (Menzella et al. 2005).