E. coli Automatic Directed Evolution Machine project

iGEM 2009 USTC team project

http://2009.igem.org/Team:USTC/Project

Evolution is more powerful than the God, as Charles Darwin told us 150 years ago. This year, our team is trying to manage the power of evolution, the power of creating everything from biomolecules to ecosystems, by engineering an E. coli Automatic Directed Evolution Machine (E.ADEM).

The ultimate goal is to make E.ADEM a universal framework for evolutionary approaches in synthetic biology. Anything we want in synthetic biology can be automatically created, from promoters, RBS, regulators, receptors, binding partners, aptamers, enzymes and ribozymes, to sensors, logic devices, reporters, metabolic pathways, entire genomes, and even solutions of mathematic problems.

To each evolution object you want it to evolve, a scoring function can be designed to output PoPS as the fitness score to your demand. After that, you can ligate the scoring function device into the E.ADEM plasmid, transform E. coli, culture the cells and wait for them to evolve automatically and robustly, and get what you want at last.

E.ADEM is designed by implementing evolutionary algorithm back into biology. The output of the scoring function is connected to the core of E.ADEM, a self-adaptive controller that can adjust variation rate and selection pressure, base on the fitness score, the population size and the average fitness score calculated by a quorum sensing device. To carry out individual functions, 3 more modules are also designed: a variation function to change the evolution object by mutation or recombination, a selection function to control the survival or death of the cell, and a reporter module to report the score to the user.

We performed comprehensive measurement using constitutive promoter family stimulus signals and modeling of each components. A prototype machine with the self-adaptive controller is built. Modular design and PoPS device boundary standard will ensure the extensibility and universality of the machine.