Mathematical Modeling: Bridging the Gap between Concept and Realization in Synthetic Biology

Figure 3

Conceptual design and biological implementation of the oscillatory circuit metabolator in Fung et al. [6]. (a) Conceptual design. The metabolator consists of two interconverting metabolite pools M₁ and M₂; their interconversions are catalyzed by the enzymes E₁ and E₂. Dashed lines indicate positive (arrow) and negative (blunt bar) regulation by M₂ at the transcriptional or translational level; the accumulation of M₂ represses E₁ and induces E₂. The circuit functions as follows. Influx into the circuit (from upstream processes) increases the concentration of M₁, which is converted to M₂ by E₁. Initially the concentration of M₁ is high and M₂ is low. However, M₂ gradually accumulates causing E₁ to be repressed and E₂ to be induced, eventually causing a net conversion of M₂ to M₁, which then starts a new cycle. (b) Biological implementation. The design of the metabolator was implemented using the acetate pathway in E. coli. The M₁ pool is acetyl-CoA; the M₂ pool consists of AcP, OAc^-, and HOAc. Pta and Acs correspond to enzymes E₁ and E₂. Pta converts Acetyl-CoA to AcP, and AcP is further converted to OAc^- by Ack. The protonated form of OAc^- (HOAc) is permeable across the cell membrane. AcP is used as a signaling molecule and functions as follows. When AcP builds up, it will activate promoter glnAp2 through phosphorylation. The promoter glnAp2 controls the expression of Acs and lac repressor (LacI), and LacI in turn represses the expression of Pta. Ack: acetate kinase; AcP: acetyl phosphate; Acs: acetyl-CoA synthetase; HOAc: protonated form of acetate; LacI: lac repressor; OAc^-: acetate; Pta: phosphate acetyltransferase (adapted from Fung et al. [6]).