Synthetic oscillator in a single operon that simulates the natural oscillations.

Referring to the expression oscillators, the Elowitz oscillator is the first and the only typically successful one so far, in which three operons express three different transcriptional repressors, lacI, lambda C1 and tetR, respectively. The three transcriptional repressors in the Elowitz oscillators inhibit one another to generate oscillations. However, this is a relatively complex system, and protein accumulation has been observed at the single-cell scale during the oscillating cycles. While the natural oscillations usually works in pulses including a stage when the signal is reset to zero. For example, in the process of the active potential, the cardiac cycles and the muscle contraction, the neural/electric signal is triggered at the state of "zero", and then amplified until a feedback inhibiting mechanism is reinforced to blocked the amplification. At last, as the inhibition dominates, the signal falls to the state of "zero", which can be thought as the "reset". To understand and simulate the natural oscillations, we propose a method to allow the oscillator being reset to "zero" after each cycle and find that it is an still simpler method to generate oscillations. A fast-degrading DNA polymerase and a fast-degrading transcriptional repressor are engaged in this system. This oscillation works in four stages: (1)Triggering: the RNA polymerase gene is expressed by constructive promoters. (2)Amplication: the RNA transcripts the gene coding itself. (3) Inhibiting: the RNA transcripts a transcriptional repressor, which has longer degrading half-life than the RNA polymerase, that blocks the transcription of the RNA polymerase gene. (4) Resetting: the transcription of the RNA polymerase is blocked and until the transcriptional repressor degrades to a concentration below a specific level.

Fast-degrading T7 RNA polymerase.

Fast-degrading transcriptional repressors are available, such as the lacI, lambda C1 and tetR, because those protein are not conservative in their C-terminus and ready to be fused with a degrading marker. While the fast-degrading RNA polymerase is the key in this project. Most RNA polymerases consist of multiple subunits, except for T odd number RNA polymerase, SP6 RNA polymerase and so on. Those RNA polymerases are very conservative at their C-terminus and can not be engineered to fuse a C-terminus degrading marker. Fortunately their N-terminus are not that conservative and can be engineered to get some N-terminus fusions. Some degrading marker of E. coli can be identified on the N-terminus, such as the degrading marker recognized by Lon and other heat shock proteases. UmuD degrades quickly in E. coli and its N-terminal 30 amino residues were reported to work as a N-terminal degrading marker. Therefore, we try to construct a fast

Model and simulation

Strains

Plasmids

Reagents

Extract the PCR product and insert the product into pEASY-B cloning

PCR clone the T7 RNA polymerase gene from a previously construct vector

Die Hu, Tian Fang,

Extract the PCR product and insert the product into pEASY-B cloning

Die Hu, Tian Fang,

Die Hu, Tian Fang,

Die Hu, Tian Fang,

All the clones have the same mutations. The template may contains

Die Hu, Tian Fang,

Die Hu, Tian Fang,

Die Hu, Tian Fang,

Die Hu, Tian Fang,

Extract the PCR product and insert the product into pEASY-B cloning

Die Hu, Tian Fang,

Die Hu, Tian Fang,

Chun Li, Qin Zhou,

Chun Li, Qin Zhou,

Chun Li, Qin Zhou,

Extract the PCR product and insert the product into pEASY-B cloning

Chun Li, Qin Zhou,

Chun Li, Qin Zhou,

Chun Li, Qin Zhou,

Dry Experiment

Wet Experiment